PDB Short entry for 3K0B HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 24-SEP-09 3K0B TITLE CRYSTAL STRUCTURE OF A PREDICTED N6-ADENINE-SPECIFIC DNA METHYLASE TITLE 2 FROM LISTERIA MONOCYTOGENES STR. 4B F2365 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PREDICTED N6-ADENINE-SPECIFIC DNA METHYLASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LISTERIA MONOCYTOGENES STR. 4B; SOURCE 3 ORGANISM_TAXID: 265669; SOURCE 4 STRAIN: F2365; SOURCE 5 GENE: LMOF2365_1916; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21MAGIC KEYWDS METHYLASE,PF01170, PUTATIVE RNA METHYLASE, PSI,MCSG, STRUCTURAL KEYWDS 2 GENOMICS, PROTEIN STRUCTURE INITIATIVE, MIDWEST CENTER FOR KEYWDS 3 STRUCTURAL GENOMICS, METHYLTRANSFERASE, TRANSFERASE, UNKNOWN KEYWDS 4 FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR B.NOCEK,X.XU,H.CUI,A.SAVCHENKO,A.EDWARDS,A.JOACHIMIAK,MIDWEST CENTER AUTHOR 2 FOR STRUCTURAL GENOMICS (MCSG) REVDAT 2 13-JUL-11 3K0B 1 VERSN REVDAT 1 13-OCT-09 3K0B 0 JRNL AUTH B.NOCEK,X.XU,H.CUI,J.NG,A.SAVCHENKO,A.EDWARDS,A.JOACHIMIAK JRNL TITL CRYSTAL STRUCTURE OF A PREDICTED N6-ADENINE-SPECIFIC DNA JRNL TITL 2 METHYLASE FROM LISTERIA MONOCYTOGENES STR. 4B F2365 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 59033 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3160 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4159 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.05 REMARK 3 BIN R VALUE (WORKING SET) : 0.2880 REMARK 3 BIN FREE R VALUE SET COUNT : 231 REMARK 3 BIN FREE R VALUE : 0.2960 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2998 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 520 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 29.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.69 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.24000 REMARK 3 B22 (A**2) : -0.89000 REMARK 3 B33 (A**2) : 0.86000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.92000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.071 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.074 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.047 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.778 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3080 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2109 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4176 ; 1.625 ; 1.966 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5125 ; 0.984 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 380 ; 5.859 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 140 ;36.363 ;23.929 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 520 ;12.684 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;17.737 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 459 ; 0.104 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3421 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 636 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1890 ; 1.026 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 771 ; 0.318 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3038 ; 1.779 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1190 ; 2.961 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1137 ; 4.638 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 15 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A -10 A 5 REMARK 3 ORIGIN FOR THE GROUP (A): -5.5743 35.6811 37.2008 REMARK 3 T TENSOR REMARK 3 T11: 0.2039 T22: 0.1272 REMARK 3 T33: 0.0992 T12: 0.0234 REMARK 3 T13: -0.0378 T23: -0.0701 REMARK 3 L TENSOR REMARK 3 L11: 0.6009 L22: 0.0044 REMARK 3 L33: 2.4012 L12: 0.0504 REMARK 3 L13: -1.2004 L23: -0.1006 REMARK 3 S TENSOR REMARK 3 S11: 0.0726 S12: 0.0922 S13: 0.0529 REMARK 3 S21: 0.0061 S22: 0.0256 S23: 0.0008 REMARK 3 S31: -0.0919 S32: -0.1822 S33: -0.0982 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 6 A 29 REMARK 3 ORIGIN FOR THE GROUP (A): -1.6176 22.4228 23.6040 REMARK 3 T TENSOR REMARK 3 T11: 0.1006 T22: 0.0704 REMARK 3 T33: 0.0798 T12: -0.0160 REMARK 3 T13: 0.0029 T23: 0.0110 REMARK 3 L TENSOR REMARK 3 L11: 1.9455 L22: 0.8872 REMARK 3 L33: 1.4749 L12: -0.4819 REMARK 3 L13: -0.5463 L23: -0.0630 REMARK 3 S TENSOR REMARK 3 S11: -0.0917 S12: -0.0082 S13: -0.2414 REMARK 3 S21: 0.0510 S22: 0.0885 S23: 0.1502 REMARK 3 S31: 0.0962 S32: -0.0127 S33: 0.0032 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 30 A 41 REMARK 3 ORIGIN FOR THE GROUP (A): -8.2770 25.2796 23.2330 REMARK 3 T TENSOR REMARK 3 T11: 0.0932 T22: 0.0854 REMARK 3 T33: 0.0984 T12: -0.0232 REMARK 3 T13: 0.0091 T23: 0.0186 REMARK 3 L TENSOR REMARK 3 L11: 4.9146 L22: 4.8996 REMARK 3 L33: 1.7814 L12: 0.3556 REMARK 3 L13: -0.9622 L23: 2.0485 REMARK 3 S TENSOR REMARK 3 S11: -0.1475 S12: 0.1021 S13: -0.2934 REMARK 3 S21: 0.1621 S22: 0.0378 S23: 0.0974 REMARK 3 S31: 0.1658 S32: -0.2325 S33: 0.1098 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 42 A 66 REMARK 3 ORIGIN FOR THE GROUP (A): -2.9315 31.4421 22.0751 REMARK 3 T TENSOR REMARK 3 T11: 0.0859 T22: 0.0882 REMARK 3 T33: 0.0609 T12: -0.0057 REMARK 3 T13: 0.0000 T23: 0.0060 REMARK 3 L TENSOR REMARK 3 L11: 1.4818 L22: 0.5032 REMARK 3 L33: 0.2922 L12: -0.4571 REMARK 3 L13: 0.0847 L23: -0.1366 REMARK 3 S TENSOR REMARK 3 S11: -0.0155 S12: 0.0086 S13: 0.0321 REMARK 3 S21: 0.0394 S22: 0.0438 S23: -0.0248 REMARK 3 S31: 0.0901 S32: -0.0394 S33: -0.0284 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 67 A 126 REMARK 3 ORIGIN FOR THE GROUP (A): -17.9524 41.9544 12.9045 REMARK 3 T TENSOR REMARK 3 T11: 0.0620 T22: 0.0766 REMARK 3 T33: 0.0494 T12: -0.0175 REMARK 3 T13: 0.0014 T23: -0.0128 REMARK 3 L TENSOR REMARK 3 L11: 1.9937 L22: 1.5659 REMARK 3 L33: 1.8521 L12: 0.5413 REMARK 3 L13: -0.0395 L23: -0.3226 REMARK 3 S TENSOR REMARK 3 S11: -0.0670 S12: -0.0740 S13: 0.0725 REMARK 3 S21: -0.0906 S22: -0.0022 S23: 0.0721 REMARK 3 S31: 0.1243 S32: -0.1691 S33: 0.0692 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 127 A 154 REMARK 3 ORIGIN FOR THE GROUP (A): -11.8698 41.6562 14.2899 REMARK 3 T TENSOR REMARK 3 T11: 0.0891 T22: 0.0676 REMARK 3 T33: 0.0560 T12: -0.0144 REMARK 3 T13: -0.0012 T23: 0.0116 REMARK 3 L TENSOR REMARK 3 L11: 2.0771 L22: 0.8015 REMARK 3 L33: 1.4799 L12: 0.4516 REMARK 3 L13: -0.2154 L23: 0.1871 REMARK 3 S TENSOR REMARK 3 S11: -0.0724 S12: -0.0817 S13: 0.0076 REMARK 3 S21: -0.0983 S22: -0.0349 S23: -0.1161 REMARK 3 S31: 0.1559 S32: -0.0189 S33: 0.1073 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 155 A 171 REMARK 3 ORIGIN FOR THE GROUP (A): 9.4170 31.3639 11.9371 REMARK 3 T TENSOR REMARK 3 T11: 0.1333 T22: 0.0834 REMARK 3 T33: 0.1064 T12: 0.0115 REMARK 3 T13: 0.0258 T23: 0.0163 REMARK 3 L TENSOR REMARK 3 L11: 2.8993 L22: 1.9422 REMARK 3 L33: 0.4578 L12: -1.7957 REMARK 3 L13: -0.3344 L23: -0.2355 REMARK 3 S TENSOR REMARK 3 S11: 0.1610 S12: 0.2032 S13: 0.1122 REMARK 3 S21: -0.3159 S22: -0.1505 S23: -0.1727 REMARK 3 S31: 0.0486 S32: -0.0450 S33: -0.0104 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 172 A 191 REMARK 3 ORIGIN FOR THE GROUP (A): 11.5724 16.9958 17.0822 REMARK 3 T TENSOR REMARK 3 T11: 0.0868 T22: 0.0506 REMARK 3 T33: 0.0735 T12: -0.0110 REMARK 3 T13: 0.0066 T23: -0.0059 REMARK 3 L TENSOR REMARK 3 L11: 2.4325 L22: 1.6959 REMARK 3 L33: 1.4762 L12: -1.1306 REMARK 3 L13: 0.0015 L23: -0.2032 REMARK 3 S TENSOR REMARK 3 S11: -0.0727 S12: 0.0041 S13: -0.1663 REMARK 3 S21: -0.0404 S22: 0.0659 S23: 0.0465 REMARK 3 S31: 0.0368 S32: -0.0818 S33: 0.0068 REMARK 3 REMARK 3 TLS GROUP : 9 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 192 A 228 REMARK 3 ORIGIN FOR THE GROUP (A): 13.8736 25.8969 18.5010 REMARK 3 T TENSOR REMARK 3 T11: 0.0859 T22: 0.0796 REMARK 3 T33: 0.0779 T12: -0.0014 REMARK 3 T13: -0.0097 T23: -0.0051 REMARK 3 L TENSOR REMARK 3 L11: 0.9115 L22: 1.1131 REMARK 3 L33: 0.1769 L12: -0.7705 REMARK 3 L13: -0.3484 L23: 0.3371 REMARK 3 S TENSOR REMARK 3 S11: -0.0313 S12: -0.0566 S13: 0.0901 REMARK 3 S21: 0.0162 S22: 0.0576 S23: -0.1531 REMARK 3 S31: 0.0054 S32: 0.0087 S33: -0.0263 REMARK 3 REMARK 3 TLS GROUP : 10 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 229 A 248 REMARK 3 ORIGIN FOR THE GROUP (A): 7.8641 38.0242 30.1574 REMARK 3 T TENSOR REMARK 3 T11: 0.1105 T22: 0.0978 REMARK 3 T33: 0.0816 T12: 0.0142 REMARK 3 T13: -0.0276 T23: -0.0382 REMARK 3 L TENSOR REMARK 3 L11: 2.0250 L22: 3.7452 REMARK 3 L33: 1.3078 L12: -2.6902 REMARK 3 L13: -0.3030 L23: 0.5459 REMARK 3 S TENSOR REMARK 3 S11: -0.0313 S12: -0.0539 S13: 0.0446 REMARK 3 S21: 0.1687 S22: 0.1402 S23: -0.1040 REMARK 3 S31: 0.0343 S32: 0.0751 S33: -0.1090 REMARK 3 REMARK 3 TLS GROUP : 11 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 249 A 307 REMARK 3 ORIGIN FOR THE GROUP (A): 24.0222 17.3722 12.7699 REMARK 3 T TENSOR REMARK 3 T11: 0.0626 T22: 0.0551 REMARK 3 T33: 0.0948 T12: -0.0117 REMARK 3 T13: 0.0054 T23: -0.0026 REMARK 3 L TENSOR REMARK 3 L11: 1.3349 L22: 1.2237 REMARK 3 L33: 0.8420 L12: -0.7515 REMARK 3 L13: -0.2762 L23: 0.2416 REMARK 3 S TENSOR REMARK 3 S11: 0.0054 S12: -0.0148 S13: 0.0764 REMARK 3 S21: -0.0505 S22: 0.0669 S23: -0.2000 REMARK 3 S31: 0.0207 S32: 0.0488 S33: -0.0723 REMARK 3 REMARK 3 TLS GROUP : 12 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 308 A 328 REMARK 3 ORIGIN FOR THE GROUP (A): 17.4352 5.7994 -0.8119 REMARK 3 T TENSOR REMARK 3 T11: 0.0567 T22: 0.0818 REMARK 3 T33: 0.1034 T12: -0.0120 REMARK 3 T13: 0.0092 T23: -0.0156 REMARK 3 L TENSOR REMARK 3 L11: 2.1122 L22: 1.5853 REMARK 3 L33: 7.3286 L12: -0.9539 REMARK 3 L13: 3.0346 L23: -0.9032 REMARK 3 S TENSOR REMARK 3 S11: -0.2010 S12: 0.1021 S13: 0.1404 REMARK 3 S21: 0.0444 S22: -0.1018 S23: -0.0107 REMARK 3 S31: -0.1143 S32: 0.0580 S33: 0.3028 REMARK 3 REMARK 3 TLS GROUP : 13 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 329 A 344 REMARK 3 ORIGIN FOR THE GROUP (A): 14.5649 4.4990 9.7010 REMARK 3 T TENSOR REMARK 3 T11: 0.0988 T22: 0.0640 REMARK 3 T33: 0.1015 T12: -0.0103 REMARK 3 T13: 0.0351 T23: -0.0023 REMARK 3 L TENSOR REMARK 3 L11: 0.8622 L22: 1.0919 REMARK 3 L33: 1.7020 L12: -0.3268 REMARK 3 L13: 0.3855 L23: 0.5404 REMARK 3 S TENSOR REMARK 3 S11: -0.0210 S12: 0.0970 S13: -0.0958 REMARK 3 S21: 0.0134 S22: -0.0664 S23: -0.0488 REMARK 3 S31: 0.1570 S32: 0.0024 S33: 0.0873 REMARK 3 REMARK 3 TLS GROUP : 14 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 345 A 354 REMARK 3 ORIGIN FOR THE GROUP (A): 10.5392 -1.0959 8.3171 REMARK 3 T TENSOR REMARK 3 T11: 0.1066 T22: 0.0247 REMARK 3 T33: 0.1136 T12: -0.0230 REMARK 3 T13: 0.0428 T23: -0.0109 REMARK 3 L TENSOR REMARK 3 L11: 5.9537 L22: 0.5241 REMARK 3 L33: 8.2150 L12: -0.1546 REMARK 3 L13: -5.0912 L23: 0.5492 REMARK 3 S TENSOR REMARK 3 S11: -0.1957 S12: 0.0403 S13: -0.1406 REMARK 3 S21: -0.0598 S22: 0.0240 S23: 0.0191 REMARK 3 S31: 0.4568 S32: -0.0080 S33: 0.1717 REMARK 3 REMARK 3 TLS GROUP : 15 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 355 A 372 REMARK 3 ORIGIN FOR THE GROUP (A): 6.0146 6.5278 12.2102 REMARK 3 T TENSOR REMARK 3 T11: 0.0864 T22: 0.0613 REMARK 3 T33: 0.1069 T12: -0.0145 REMARK 3 T13: 0.0268 T23: -0.0109 REMARK 3 L TENSOR REMARK 3 L11: 3.1339 L22: 3.0848 REMARK 3 L33: 3.0904 L12: -0.1054 REMARK 3 L13: -1.0291 L23: -1.2945 REMARK 3 S TENSOR REMARK 3 S11: 0.0503 S12: 0.1212 S13: 0.0068 REMARK 3 S21: -0.0299 S22: 0.0540 S23: 0.1580 REMARK 3 S31: -0.1393 S32: -0.2717 S33: -0.1043 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3K0B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-SEP-09. REMARK 100 THE RCSB ID CODE IS RCSB055384. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-AUG-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9794 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62193 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 32.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.52000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: HKL-3000,SHELX,DM, ARP/WARP,COOT,CCP4,MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE 25 % PEG3350 REMARK 280 0.1 M HEPES, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 62.97450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.07800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 62.97450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.07800 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: LIKELY MONOMER REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ASN A 359A REMARK 465 GLY A 359B REMARK 465 TYR A 359C REMARK 465 LEU A 359D REMARK 465 ARG A 373 REMARK 465 LYS A 374 REMARK 465 PRO A 375 REMARK 465 ARG A 376 REMARK 465 PRO A 377 REMARK 465 LYS A 378 REMARK 465 LYS A 379 REMARK 465 GLU A 380 REMARK 465 ASP A 381 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A -6 CG CD OE1 OE2 REMARK 470 LEU A -4 CG CD1 CD2 REMARK 470 LYS A 2 CG CD CE NZ REMARK 470 ARG A 363 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OH TYR A 306 OE2 GLU A 313 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 248 75.92 -113.42 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 398 DISTANCE = 5.02 ANGSTROMS REMARK 525 HOH A 401 DISTANCE = 5.45 ANGSTROMS REMARK 525 HOH A 505 DISTANCE = 5.76 ANGSTROMS REMARK 525 HOH A 506 DISTANCE = 5.63 ANGSTROMS REMARK 525 HOH A 561 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH A 847 DISTANCE = 5.46 ANGSTROMS REMARK 525 HOH A 880 DISTANCE = 5.10 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 701 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: APC64818 RELATED DB: TARGETDB DBREF 3K0B A 1 381 UNP Q71YC9 Q71YC9_LISMF 1 382 SEQADV 3K0B SER A -10 UNP Q71YC9 EXPRESSION TAG SEQADV 3K0B SER A -9 UNP Q71YC9 EXPRESSION TAG SEQADV 3K0B GLY A -8 UNP Q71YC9 EXPRESSION TAG SEQADV 3K0B ARG A -7 UNP Q71YC9 EXPRESSION TAG SEQADV 3K0B GLU A -6 UNP Q71YC9 EXPRESSION TAG SEQADV 3K0B ASN A -5 UNP Q71YC9 EXPRESSION TAG SEQADV 3K0B LEU A -4 UNP Q71YC9 EXPRESSION TAG SEQADV 3K0B TYR A -3 UNP Q71YC9 EXPRESSION TAG SEQADV 3K0B PHE A -2 UNP Q71YC9 EXPRESSION TAG SEQADV 3K0B GLN A -1 UNP Q71YC9 EXPRESSION TAG SEQADV 3K0B GLY A 0 UNP Q71YC9 EXPRESSION TAG SEQRES 1 A 393 SER SER GLY ARG GLU ASN LEU TYR PHE GLN GLY MSE LYS SEQRES 2 A 393 SER PHE GLN LEU VAL ALA THR ALA ALA SER GLY LEU GLU SEQRES 3 A 393 ALA ILE VAL GLY LYS GLU VAL ALA ARG LEU GLY TYR ASP SEQRES 4 A 393 PRO LYS VAL GLU ASN GLY LYS VAL TYR PHE GLU GLY ASP SEQRES 5 A 393 LEU SER ALA ILE ALA ARG ALA ASN LEU TRP LEU ARG VAL SEQRES 6 A 393 ALA ASP ARG VAL LYS ILE VAL VAL GLY VAL PHE LYS ALA SEQRES 7 A 393 THR THR PHE ASP GLU LEU PHE GLU LYS THR LYS ALA LEU SEQRES 8 A 393 PRO TRP GLU ASP TYR LEU PRO LEU ASP ALA GLN PHE PRO SEQRES 9 A 393 VAL ALA GLY LYS SER VAL LYS SER THR LEU TYR SER VAL SEQRES 10 A 393 PRO ASP CYS GLN ALA ILE VAL LYS LYS ALA ILE VAL ASN SEQRES 11 A 393 ARG VAL SER GLU LYS TYR ARG ARG SER GLY ARG LEU MSE SEQRES 12 A 393 GLU THR GLY ALA LEU PHE LYS LEU GLU VAL SER ILE LEU SEQRES 13 A 393 LYS ASP GLU VAL THR LEU THR ILE ASP THR SER GLY ALA SEQRES 14 A 393 GLY LEU HIS LYS ARG GLY TYR ARG LEU ALA GLN GLY SER SEQRES 15 A 393 ALA PRO ILE LYS GLU THR MSE ALA ALA ALA LEU VAL LEU SEQRES 16 A 393 LEU THR SER TRP HIS PRO ASP ARG PRO PHE TYR ASP PRO SEQRES 17 A 393 VAL CYS GLY SER GLY THR ILE PRO ILE GLU ALA ALA LEU SEQRES 18 A 393 ILE GLY GLN ASN ILE ALA PRO GLY PHE ASN ARG GLU PHE SEQRES 19 A 393 VAL SER GLU THR TRP ASP TRP MSE PRO LYS GLN VAL TRP SEQRES 20 A 393 ALA ASP ALA ARG GLN GLU ALA GLU ASP LEU ALA ASN TYR SEQRES 21 A 393 ASP GLN PRO LEU ASN ILE ILE GLY GLY ASP ILE ASP ALA SEQRES 22 A 393 ARG LEU ILE GLU ILE ALA LYS GLN ASN ALA VAL GLU ALA SEQRES 23 A 393 GLY LEU GLY ASP LEU ILE THR PHE ARG GLN LEU GLN VAL SEQRES 24 A 393 ALA ASP PHE GLN THR GLU ASP GLU TYR GLY VAL VAL VAL SEQRES 25 A 393 ALA ASN PRO PRO TYR GLY GLU ARG LEU GLU ASP GLU GLU SEQRES 26 A 393 ALA VAL ARG GLN LEU TYR ARG GLU MSE GLY ILE VAL TYR SEQRES 27 A 393 LYS ARG MSE PRO THR TRP SER VAL TYR VAL LEU THR SER SEQRES 28 A 393 TYR GLU LEU PHE GLU GLU VAL TYR GLY LYS LYS ALA THR SEQRES 29 A 393 LYS LYS ARG LYS LEU TYR ASN GLY TYR LEU ARG THR ASP SEQRES 30 A 393 LEU TYR GLN TYR TRP GLY PRO ARG LYS PRO ARG PRO LYS SEQRES 31 A 393 LYS GLU ASP MODRES 3K0B MSE A 1 MET SELENOMETHIONINE MODRES 3K0B MSE A 132 MET SELENOMETHIONINE MODRES 3K0B MSE A 178 MET SELENOMETHIONINE MODRES 3K0B MSE A 231 MET SELENOMETHIONINE MODRES 3K0B MSE A 323 MET SELENOMETHIONINE MODRES 3K0B MSE A 330 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 132 8 HET MSE A 178 8 HET MSE A 231 8 HET MSE A 323 8 HET MSE A 330 8 HET EDO A 601 4 HET GOL A 701 6 HETNAM MSE SELENOMETHIONINE HETNAM EDO 1,2-ETHANEDIOL HETNAM GOL GLYCEROL HETSYN EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 MSE 6(C5 H11 N O2 SE) FORMUL 2 EDO C2 H6 O2 FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *520(H2 O) HELIX 1 1 ASN A -5 GLY A 0 5 6 HELIX 2 2 LEU A 14 LEU A 25 1 12 HELIX 3 3 ASP A 41 LEU A 52 1 12 HELIX 4 4 THR A 69 ALA A 79 1 11 HELIX 5 5 PRO A 81 TYR A 85 5 5 HELIX 6 6 SER A 105 TYR A 125 1 21 HELIX 7 7 LYS A 175 THR A 186 1 12 HELIX 8 8 GLY A 202 GLN A 213 1 12 HELIX 9 9 PHE A 223 TRP A 228 5 6 HELIX 10 10 PRO A 232 ALA A 247 1 16 HELIX 11 11 ASP A 261 ALA A 275 1 15 HELIX 12 12 GLN A 287 PHE A 291 5 5 HELIX 13 13 ARG A 309 ARG A 329 1 21 HELIX 14 14 LEU A 343 GLY A 349 1 7 SHEET 1 A 7 LYS A 30 GLU A 32 0 SHEET 2 A 7 LYS A 35 GLY A 40 -1 O LYS A 35 N GLU A 32 SHEET 3 A 7 PHE A 4 THR A 9 -1 N PHE A 4 O GLY A 40 SHEET 4 A 7 VAL A 58 LYS A 66 -1 O VAL A 61 N GLN A 5 SHEET 5 A 7 GLU A 148 ASP A 154 -1 O VAL A 149 N PHE A 65 SHEET 6 A 7 LEU A 140 LEU A 145 -1 N SER A 143 O THR A 150 SHEET 7 A 7 VAL A 94 VAL A 99 1 N ALA A 95 O LEU A 140 SHEET 1 B 7 THR A 282 GLN A 285 0 SHEET 2 B 7 ILE A 255 ASP A 259 1 N ILE A 255 O THR A 282 SHEET 3 B 7 PHE A 194 ASP A 196 1 N ASP A 196 O GLY A 258 SHEET 4 B 7 VAL A 299 ALA A 302 1 O VAL A 299 N TYR A 195 SHEET 5 B 7 SER A 334 THR A 339 1 O SER A 334 N VAL A 300 SHEET 6 B 7 THR A 364 TYR A 369 -1 O TYR A 369 N VAL A 335 SHEET 7 B 7 LYS A 354 LEU A 358 -1 N ARG A 356 O LEU A 366 LINK C GLY A 0 N MSE A 1 1555 1555 1.34 LINK C MSE A 1 N LYS A 2 1555 1555 1.34 LINK C LEU A 131 N MSE A 132 1555 1555 1.33 LINK C MSE A 132 N GLU A 133 1555 1555 1.32 LINK C THR A 177 N MSE A 178 1555 1555 1.33 LINK C MSE A 178 N ALA A 179 1555 1555 1.32 LINK C TRP A 230 N MSE A 231 1555 1555 1.32 LINK C MSE A 231 N PRO A 232 1555 1555 1.33 LINK C GLU A 322 N MSE A 323 1555 1555 1.33 LINK C MSE A 323 N GLY A 324 1555 1555 1.32 LINK C ARG A 329 N MSE A 330 1555 1555 1.34 LINK C MSE A 330 N PRO A 331 1555 1555 1.34 SITE 1 AC1 7 ARG A 57 GLY A 159 HIS A 161 LYS A 162 SITE 2 AC1 7 HOH A 631 HOH A 822 HOH A 837 SITE 1 AC2 7 THR A 9 ASP A 56 ARG A 57 LYS A 59 SITE 2 AC2 7 HOH A 531 HOH A 564 HOH A 848 CRYST1 125.949 46.156 91.376 90.00 131.09 90.00 C 1 2 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.007940 0.000000 0.006924 0.00000 SCALE2 0.000000 0.021666 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014520 0.00000