PDB Short entry for 3HPE HEADER TRANSPORT PROTEIN 04-JUN-09 3HPE TITLE CRYSTAL STRUCTURE OF YCEI (HP1286) FROM HELICOBACTER PYLORI COMPND MOL_ID: 1; COMPND 2 MOLECULE: CONSERVED HYPOTHETICAL SECRETED PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 18-181; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 3 ORGANISM_TAXID: 210; SOURCE 4 STRAIN: CCUG17874; SOURCE 5 GENE: HP1286; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET151-HP1286 KEYWDS HP1286, HELICOBACTER PYLORI, ERUCAMIDE, FATTY-ACID BINDING, TRANSPORT KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.SISINNI,L.CENDRON,G.ZANOTTI REVDAT 5 06-SEP-23 3HPE 1 REMARK SEQADV HETSYN REVDAT 4 01-NOV-17 3HPE 1 REMARK REVDAT 3 13-JUL-11 3HPE 1 VERSN REVDAT 2 28-APR-10 3HPE 1 JRNL REVDAT 1 14-APR-10 3HPE 0 JRNL AUTH L.SISINNI,L.CENDRON,G.FAVARO,G.ZANOTTI JRNL TITL HELICOBACTER PYLORI ACIDIC STRESS RESPONSE FACTOR HP1286 IS JRNL TITL 2 A YCEI HOMOLOG WITH NEW BINDING SPECIFICITY. JRNL REF FEBS J. V. 277 1896 2010 JRNL REFN ISSN 1742-464X JRNL PMID 20236316 JRNL DOI 10.1111/J.1742-4658.2010.07612.X REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH N.HANDA,T.TERADA,Y.DOI-KATAYAMA,H.HIROTA,J.R.TAME,S.Y.PARK, REMARK 1 AUTH 2 S.KURAMITSU,M.SHIROUZU,S.YOKOYAMA REMARK 1 TITL CRYSTAL STRUCTURE OF A NOVEL POLYISOPRENOID-BINDING PROTEIN REMARK 1 TITL 2 FROM THERMUS THERMOPHILUS HB8. REMARK 1 REF PROTEIN SCI. V. 14 1004 2005 REMARK 1 REFN ISSN 0961-8368 REMARK 1 PMID 15741337 REMARK 1 DOI 10.1110/PS.041183305 REMARK 1 REFERENCE 2 REMARK 1 AUTH A.V.TOMS,A.L.HAAS,J.H.PARK,T.P.BEGLEY,S.E.EALICK REMARK 1 TITL STRUCTURAL CHARACTERIZATION OF THE REGULATORY PROTEINS TENA REMARK 1 TITL 2 AND TENI FROM BACILLUS SUBTILIS AND IDENTIFICATION OF TENA REMARK 1 TITL 3 AS A THIAMINASE II. REMARK 1 REF BIOCHEMISTRY V. 44 2319 2005 REMARK 1 REFN ISSN 0006-2960 REMARK 1 PMID 15709744 REMARK 1 DOI 10.1021/BI0478648 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0072 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 19367 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) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1519 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1284 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.78 REMARK 3 BIN R VALUE (WORKING SET) : 0.2300 REMARK 3 BIN FREE R VALUE SET COUNT : 103 REMARK 3 BIN FREE R VALUE : 0.2780 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2632 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 79 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 33.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 7.54 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.35000 REMARK 3 B22 (A**2) : -1.27000 REMARK 3 B33 (A**2) : -1.88000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.06000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.293 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.233 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.183 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.711 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.935 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.894 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2732 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3650 ; 1.921 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 326 ; 6.658 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 124 ;40.696 ;25.323 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 518 ;18.491 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;25.502 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 388 ; 0.129 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2012 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 1630 ; 0.665 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2636 ; 1.217 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1102 ; 2.368 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1014 ; 3.801 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 0 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 656 ; .16 ; .50 REMARK 3 LOOSE POSITIONAL 1 A (A): 660 ; .28 ; 5.00 REMARK 3 MEDIUM THERMAL 1 A (A**2): 656 ; 2.59 ; 2.00 REMARK 3 LOOSE THERMAL 1 A (A**2): 660 ; 2.97 ; 10.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 16 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 18 A 39 REMARK 3 ORIGIN FOR THE GROUP (A): 7.3473 -4.5739 28.0847 REMARK 3 T TENSOR REMARK 3 T11: .0650 T22: .2420 REMARK 3 T33: .2277 T12: -.0357 REMARK 3 T13: .0170 T23: -.0073 REMARK 3 L TENSOR REMARK 3 L11: .7872 L22: 6.2495 REMARK 3 L33: 3.2039 L12: -1.8750 REMARK 3 L13: -.8022 L23: 1.1195 REMARK 3 S TENSOR REMARK 3 S11: .1097 S12: -.0733 S13: .0562 REMARK 3 S21: -.3180 S22: .0763 S23: .0675 REMARK 3 S31: -.2412 S32: .2372 S33: -.1860 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 40 A 69 REMARK 3 ORIGIN FOR THE GROUP (A): 5.4396 -14.3629 31.2895 REMARK 3 T TENSOR REMARK 3 T11: .0510 T22: .1961 REMARK 3 T33: .1735 T12: .0199 REMARK 3 T13: .0199 T23: .0135 REMARK 3 L TENSOR REMARK 3 L11: 2.9181 L22: 8.7141 REMARK 3 L33: 2.8706 L12: 2.0026 REMARK 3 L13: -.7570 L23: 1.7208 REMARK 3 S TENSOR REMARK 3 S11: -.2187 S12: -.0610 S13: -.1921 REMARK 3 S21: -.0619 S22: .2277 S23: .0110 REMARK 3 S31: .3281 S32: .1863 S33: -.0090 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 70 A 101 REMARK 3 ORIGIN FOR THE GROUP (A): 13.0759 .8987 40.0973 REMARK 3 T TENSOR REMARK 3 T11: .1180 T22: .2432 REMARK 3 T33: .1415 T12: -.0157 REMARK 3 T13: -.0488 T23: -.0957 REMARK 3 L TENSOR REMARK 3 L11: 6.1315 L22: 3.3617 REMARK 3 L33: 6.0988 L12: 2.7867 REMARK 3 L13: .3834 L23: .1976 REMARK 3 S TENSOR REMARK 3 S11: .0391 S12: -.4196 S13: .1726 REMARK 3 S21: .3433 S22: .0982 S23: -.3795 REMARK 3 S31: -.6144 S32: .6867 S33: -.1373 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 102 A 125 REMARK 3 ORIGIN FOR THE GROUP (A): -3.9134 -10.9888 37.7639 REMARK 3 T TENSOR REMARK 3 T11: .0382 T22: .2589 REMARK 3 T33: .2486 T12: .0099 REMARK 3 T13: .0025 T23: .0479 REMARK 3 L TENSOR REMARK 3 L11: 3.8353 L22: 5.1959 REMARK 3 L33: 7.8158 L12: 2.4669 REMARK 3 L13: 2.4013 L23: 4.9297 REMARK 3 S TENSOR REMARK 3 S11: -.1908 S12: -.1910 S13: .1679 REMARK 3 S21: -.1314 S22: -.0754 S23: .4639 REMARK 3 S31: .0750 S32: -.5079 S33: .2661 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 126 A 141 REMARK 3 ORIGIN FOR THE GROUP (A): 6.6830 -21.4414 18.2083 REMARK 3 T TENSOR REMARK 3 T11: .3291 T22: .0473 REMARK 3 T33: .1742 T12: .0168 REMARK 3 T13: -.0917 T23: .0054 REMARK 3 L TENSOR REMARK 3 L11: 5.6033 L22: 5.1746 REMARK 3 L33: 13.0122 L12: -.6630 REMARK 3 L13: -5.1720 L23: 3.0261 REMARK 3 S TENSOR REMARK 3 S11: -.2794 S12: .2997 S13: -.2670 REMARK 3 S21: -.9425 S22: -.0647 S23: .0159 REMARK 3 S31: .2518 S32: .1421 S33: .3441 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 142 A 152 REMARK 3 ORIGIN FOR THE GROUP (A): 1.2782 -9.9071 27.3825 REMARK 3 T TENSOR REMARK 3 T11: .0405 T22: .2089 REMARK 3 T33: .2762 T12: -.0534 REMARK 3 T13: -.0264 T23: .0200 REMARK 3 L TENSOR REMARK 3 L11: 8.2970 L22: 27.3421 REMARK 3 L33: 27.2687 L12: -14.7991 REMARK 3 L13: -13.7360 L23: 25.5522 REMARK 3 S TENSOR REMARK 3 S11: .1839 S12: .1533 S13: -.2240 REMARK 3 S21: -.3376 S22: -.3787 S23: .5959 REMARK 3 S31: -.3982 S32: -.5067 S33: .1948 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 153 A 171 REMARK 3 ORIGIN FOR THE GROUP (A): 1.4382 7.6073 39.7471 REMARK 3 T TENSOR REMARK 3 T11: .1166 T22: .0735 REMARK 3 T33: .1221 T12: .0142 REMARK 3 T13: .0876 T23: -.0124 REMARK 3 L TENSOR REMARK 3 L11: 3.0311 L22: 8.7964 REMARK 3 L33: 6.6445 L12: -2.2524 REMARK 3 L13: -4.4140 L23: 2.0542 REMARK 3 S TENSOR REMARK 3 S11: .2472 S12: .1158 S13: .1850 REMARK 3 S21: .0725 S22: .1246 S23: .1517 REMARK 3 S31: -.4773 S32: -.2082 S33: -.3717 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 181 REMARK 3 ORIGIN FOR THE GROUP (A): 6.4126 -12.3991 25.9728 REMARK 3 T TENSOR REMARK 3 T11: .0494 T22: .2245 REMARK 3 T33: .2218 T12: -.0489 REMARK 3 T13: -.0557 T23: .0137 REMARK 3 L TENSOR REMARK 3 L11: 7.9532 L22: 25.5776 REMARK 3 L33: 7.4246 L12: -13.3115 REMARK 3 L13: -6.1336 L23: 11.7546 REMARK 3 S TENSOR REMARK 3 S11: .1355 S12: .0988 S13: .0014 REMARK 3 S21: -.3256 S22: -.0736 S23: .0856 REMARK 3 S31: -.0898 S32: .1846 S33: -.0619 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 : B 18 B 32 REMARK 3 ORIGIN FOR THE GROUP (A): 13.0454 12.9503 20.1489 REMARK 3 T TENSOR REMARK 3 T11: .2493 T22: .1403 REMARK 3 T33: .1734 T12: -.1101 REMARK 3 T13: .1229 T23: -.0735 REMARK 3 L TENSOR REMARK 3 L11: .8665 L22: 9.9672 REMARK 3 L33: 3.3454 L12: -.5671 REMARK 3 L13: -.6659 L23: 2.4944 REMARK 3 S TENSOR REMARK 3 S11: .3457 S12: -.1493 S13: .2264 REMARK 3 S21: .3518 S22: -.2052 S23: -.3134 REMARK 3 S31: -.4847 S32: .0385 S33: -.1405 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 : B 33 B 48 REMARK 3 ORIGIN FOR THE GROUP (A): 11.9975 -5.4449 17.0399 REMARK 3 T TENSOR REMARK 3 T11: .1020 T22: .2156 REMARK 3 T33: .1566 T12: -.0640 REMARK 3 T13: .0318 T23: -.0133 REMARK 3 L TENSOR REMARK 3 L11: 3.6803 L22: 11.1231 REMARK 3 L33: 1.5256 L12: 4.7453 REMARK 3 L13: .5030 L23: 1.0733 REMARK 3 S TENSOR REMARK 3 S11: .1522 S12: -.3070 S13: .1400 REMARK 3 S21: .1952 S22: -.1824 S23: .3115 REMARK 3 S31: .1800 S32: .0665 S33: .0302 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 : B 49 B 73 REMARK 3 ORIGIN FOR THE GROUP (A): 13.3983 16.7659 13.3727 REMARK 3 T TENSOR REMARK 3 T11: .4961 T22: .1025 REMARK 3 T33: .1840 T12: -.1594 REMARK 3 T13: .1934 T23: -.0560 REMARK 3 L TENSOR REMARK 3 L11: 4.3971 L22: 9.8088 REMARK 3 L33: 3.4882 L12: -3.7836 REMARK 3 L13: .3999 L23: -2.3150 REMARK 3 S TENSOR REMARK 3 S11: .2558 S12: .0022 S13: .6497 REMARK 3 S21: -.2948 S22: .0899 S23: -.4642 REMARK 3 S31: -.8773 S32: .0785 S33: -.3456 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 : B 74 B 95 REMARK 3 ORIGIN FOR THE GROUP (A): 24.2809 -5.4533 14.0769 REMARK 3 T TENSOR REMARK 3 T11: .0406 T22: .3169 REMARK 3 T33: .2342 T12: -.0583 REMARK 3 T13: .0056 T23: -.0360 REMARK 3 L TENSOR REMARK 3 L11: 5.8014 L22: 7.7452 REMARK 3 L33: 13.5889 L12: -.7047 REMARK 3 L13: .8030 L23: -3.2880 REMARK 3 S TENSOR REMARK 3 S11: .1455 S12: -.2706 S13: .0622 REMARK 3 S21: -.3347 S22: -.1301 S23: -.4494 REMARK 3 S31: .0839 S32: .7299 S33: -.0154 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 : B 96 B 122 REMARK 3 ORIGIN FOR THE GROUP (A): 12.5792 10.7696 4.4305 REMARK 3 T TENSOR REMARK 3 T11: .4309 T22: .1684 REMARK 3 T33: .1881 T12: -.1461 REMARK 3 T13: .1070 T23: -.0077 REMARK 3 L TENSOR REMARK 3 L11: 4.4574 L22: 8.0462 REMARK 3 L33: 2.9398 L12: -4.6024 REMARK 3 L13: -1.3904 L23: -1.3741 REMARK 3 S TENSOR REMARK 3 S11: .4711 S12: .2865 S13: .0636 REMARK 3 S21: -.5554 S22: -.1988 S23: .0999 REMARK 3 S31: -.2855 S32: -.1462 S33: -.2723 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 : B 123 B 146 REMARK 3 ORIGIN FOR THE GROUP (A): 5.1130 18.8549 22.0811 REMARK 3 T TENSOR REMARK 3 T11: .4293 T22: .0830 REMARK 3 T33: .2363 T12: -.0483 REMARK 3 T13: .0902 T23: -.0024 REMARK 3 L TENSOR REMARK 3 L11: 1.4953 L22: 5.3958 REMARK 3 L33: 13.7070 L12: .4436 REMARK 3 L13: -.9952 L23: 7.9914 REMARK 3 S TENSOR REMARK 3 S11: .2305 S12: .0282 S13: .1943 REMARK 3 S21: .1310 S22: -.0176 S23: .0083 REMARK 3 S31: -.0570 S32: -.0571 S33: -.2130 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 : B 147 B 164 REMARK 3 ORIGIN FOR THE GROUP (A): 13.7139 -4.4728 5.3557 REMARK 3 T TENSOR REMARK 3 T11: .1117 T22: .1382 REMARK 3 T33: .0942 T12: -.0332 REMARK 3 T13: -.0229 T23: -.0127 REMARK 3 L TENSOR REMARK 3 L11: 4.2539 L22: 15.6660 REMARK 3 L33: 3.0559 L12: -4.7544 REMARK 3 L13: -2.5472 L23: 5.1632 REMARK 3 S TENSOR REMARK 3 S11: .1588 S12: .0793 S13: .0346 REMARK 3 S21: -.4545 S22: -.1289 S23: -.1617 REMARK 3 S31: -.0368 S32: .0358 S33: -.0299 REMARK 3 REMARK 3 TLS GROUP : 16 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 165 B 181 REMARK 3 ORIGIN FOR THE GROUP (A): 10.0225 4.4120 15.4775 REMARK 3 T TENSOR REMARK 3 T11: .1457 T22: .1061 REMARK 3 T33: .0922 T12: -.0189 REMARK 3 T13: .0022 T23: .0149 REMARK 3 L TENSOR REMARK 3 L11: .9278 L22: 27.7866 REMARK 3 L33: 4.6797 L12: -1.4034 REMARK 3 L13: -.3205 L23: 10.8288 REMARK 3 S TENSOR REMARK 3 S11: .1346 S12: -.0467 S13: .1241 REMARK 3 S21: -.0821 S22: -.3622 S23: .3226 REMARK 3 S31: -.2072 S32: -.1788 S33: .2276 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 3HPE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1000053418. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-FEB-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8726 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19367 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.12400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 0.42400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1WUB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL, 2M AMMONIUM SULFATE, PH REMARK 280 8.5, VAPOR DIFFUSION, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 30.65600 REMARK 290 SMTRY3 2 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 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.6 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 19 C - N - CA ANGL. DEV. = 16.2 DEGREES REMARK 500 PRO A 19 C - N - CD ANGL. DEV. = -13.5 DEGREES REMARK 500 LEU B 116 CA - CB - CG ANGL. DEV. = 14.4 DEGREES REMARK 500 ASP B 169 CB - CG - OD2 ANGL. DEV. = 6.9 DEGREES 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 LYS A 37 -33.76 76.32 REMARK 500 THR A 58 -20.72 78.16 REMARK 500 ASN A 74 -76.49 -115.52 REMARK 500 THR A 75 -20.77 65.69 REMARK 500 ASN A 77 113.58 -175.74 REMARK 500 PHE A 89 -98.30 -123.03 REMARK 500 ALA A 131 151.32 176.18 REMARK 500 MET A 137 -72.78 -89.16 REMARK 500 LYS B 37 -37.77 71.68 REMARK 500 THR B 58 -30.80 68.31 REMARK 500 ASN B 74 -85.58 -121.11 REMARK 500 THR B 75 -12.76 70.80 REMARK 500 PHE B 89 -94.35 -130.40 REMARK 500 ASP B 107 52.63 34.63 REMARK 500 ALA B 131 149.38 -170.48 REMARK 500 MET B 137 -70.86 -80.55 REMARK 500 LYS B 139 6.54 58.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ERU A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ERU B 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1WUB RELATED DB: PDB REMARK 900 POLYISOPRENOID-BINDING PROTEIN FROM THERMUS THERMOPHILUS REMARK 900 RELATED ID: 1Y0G RELATED DB: PDB REMARK 900 YCEI PROTEIN FROM ESCHERICHIA COLI DBREF 3HPE A 18 181 UNP Q1CRX8 Q1CRX8_HELPH 18 181 DBREF 3HPE B 18 181 UNP Q1CRX8 Q1CRX8_HELPH 18 181 SEQADV 3HPE LYS A 85 UNP Q1CRX8 ARG 85 VARIANT SEQADV 3HPE VAL A 92 UNP Q1CRX8 ALA 92 VARIANT SEQADV 3HPE VAL A 93 UNP Q1CRX8 MET 93 VARIANT SEQADV 3HPE LYS B 85 UNP Q1CRX8 ARG 85 VARIANT SEQADV 3HPE VAL B 92 UNP Q1CRX8 ALA 92 VARIANT SEQADV 3HPE VAL B 93 UNP Q1CRX8 MET 93 VARIANT SEQRES 1 A 164 LYS PRO TYR THR ILE ASP LYS ALA ASN SER SER VAL TRP SEQRES 2 A 164 PHE GLU VAL LYS HIS PHE LYS PHE ASN GLU THR ARG GLY SEQRES 3 A 164 VAL PHE ASP SER PHE ASP GLY LYS ILE ASP ALA ASP PRO SEQRES 4 A 164 ASN THR LYS ALA LEU ASN VAL PHE GLU GLY LYS ILE ASP SEQRES 5 A 164 ILE LYS SER ILE ASN THR ARG ASN LYS LYS ARG ASP ASP SEQRES 6 A 164 HIS LEU LYS THR ALA GLU PHE PHE ASP VAL VAL LYS TYR SEQRES 7 A 164 PRO LYS GLY SER PHE LYS MET THR LYS TYR GLU ASP GLY SEQRES 8 A 164 LYS ILE HIS GLY ASP LEU THR LEU HIS GLY VAL THR LYS SEQRES 9 A 164 PRO VAL VAL LEU GLU ALA LYS ILE GLN ALA PRO LEU GLN SEQRES 10 A 164 ASN PRO MET ASN LYS LYS GLU PHE MET VAL LEU GLN ALA SEQRES 11 A 164 GLU GLY LYS ILE ASN ARG LYS ASP PHE GLY ILE GLY LYS SEQRES 12 A 164 THR PHE SER ASP ALA VAL VAL GLY ASP GLU VAL LYS ILE SEQRES 13 A 164 GLU LEU LYS LEU GLU ALA TYR ALA SEQRES 1 B 164 LYS PRO TYR THR ILE ASP LYS ALA ASN SER SER VAL TRP SEQRES 2 B 164 PHE GLU VAL LYS HIS PHE LYS PHE ASN GLU THR ARG GLY SEQRES 3 B 164 VAL PHE ASP SER PHE ASP GLY LYS ILE ASP ALA ASP PRO SEQRES 4 B 164 ASN THR LYS ALA LEU ASN VAL PHE GLU GLY LYS ILE ASP SEQRES 5 B 164 ILE LYS SER ILE ASN THR ARG ASN LYS LYS ARG ASP ASP SEQRES 6 B 164 HIS LEU LYS THR ALA GLU PHE PHE ASP VAL VAL LYS TYR SEQRES 7 B 164 PRO LYS GLY SER PHE LYS MET THR LYS TYR GLU ASP GLY SEQRES 8 B 164 LYS ILE HIS GLY ASP LEU THR LEU HIS GLY VAL THR LYS SEQRES 9 B 164 PRO VAL VAL LEU GLU ALA LYS ILE GLN ALA PRO LEU GLN SEQRES 10 B 164 ASN PRO MET ASN LYS LYS GLU PHE MET VAL LEU GLN ALA SEQRES 11 B 164 GLU GLY LYS ILE ASN ARG LYS ASP PHE GLY ILE GLY LYS SEQRES 12 B 164 THR PHE SER ASP ALA VAL VAL GLY ASP GLU VAL LYS ILE SEQRES 13 B 164 GLU LEU LYS LEU GLU ALA TYR ALA HET ERU A 301 24 HET ERU B 301 24 HETNAM ERU (13Z)-DOCOS-13-ENAMIDE HETSYN ERU ERUCAMIDE; ERUCYLAMIDE FORMUL 3 ERU 2(C22 H43 N O) FORMUL 5 HOH *79(H2 O) HELIX 1 1 LYS A 71 ILE A 73 5 3 HELIX 2 2 ASN A 77 THR A 86 1 10 HELIX 3 3 LYS A 154 GLY A 157 5 4 HELIX 4 4 LYS B 71 ILE B 73 5 3 HELIX 5 5 ASN B 77 THR B 86 1 10 HELIX 6 6 LYS B 154 GLY B 157 5 4 SHEET 1 A 4 THR A 21 ILE A 22 0 SHEET 2 A 4 VAL A 167 TYR A 180 -1 O TYR A 180 N THR A 21 SHEET 3 A 4 SER A 28 HIS A 35 -1 N SER A 28 O LYS A 176 SHEET 4 A 4 ASN A 39 VAL A 44 -1 O ASN A 39 N HIS A 35 SHEET 1 B 8 THR A 21 ILE A 22 0 SHEET 2 B 8 VAL A 167 TYR A 180 -1 O TYR A 180 N THR A 21 SHEET 3 B 8 GLU A 141 ASN A 152 -1 N LEU A 145 O LEU A 177 SHEET 4 B 8 VAL A 119 GLN A 134 -1 N GLU A 126 O GLU A 148 SHEET 5 B 8 LYS A 109 LEU A 116 -1 N ILE A 110 O LEU A 125 SHEET 6 B 8 LYS A 97 GLU A 106 -1 N SER A 99 O THR A 115 SHEET 7 B 8 ALA A 60 ASP A 69 -1 N PHE A 64 O MET A 102 SHEET 8 B 8 PHE A 48 ASP A 55 -1 N ASP A 53 O ASN A 62 SHEET 1 C 9 ASN B 39 VAL B 44 0 SHEET 2 C 9 THR B 21 HIS B 35 -1 N HIS B 35 O ASN B 39 SHEET 3 C 9 GLU B 170 TYR B 180 -1 O GLU B 174 N TRP B 30 SHEET 4 C 9 GLU B 141 ASN B 152 -1 N ALA B 147 O LEU B 175 SHEET 5 C 9 VAL B 119 GLN B 134 -1 N GLN B 130 O VAL B 144 SHEET 6 C 9 LYS B 109 LEU B 116 -1 N ILE B 110 O LEU B 125 SHEET 7 C 9 LYS B 97 GLU B 106 -1 N THR B 103 O HIS B 111 SHEET 8 C 9 LEU B 61 ASP B 69 -1 N PHE B 64 O MET B 102 SHEET 9 C 9 PHE B 48 ALA B 54 -1 N ASP B 49 O LYS B 67 CISPEP 1 LYS A 18 PRO A 19 0 7.38 CISPEP 2 ALA A 131 PRO A 132 0 -11.34 CISPEP 3 LYS B 18 PRO B 19 0 4.50 CISPEP 4 ALA B 131 PRO B 132 0 -8.58 SITE 1 AC1 8 VAL A 29 PHE A 31 VAL A 33 GLY A 66 SITE 2 AC1 8 ILE A 68 ARG A 80 PHE A 90 ILE A 173 SITE 1 AC2 10 PHE B 31 VAL B 33 PHE B 45 GLY B 66 SITE 2 AC2 10 ARG B 80 LEU B 84 PHE B 100 LEU B 116 SITE 3 AC2 10 ILE B 173 HOH B 186 CRYST1 30.936 61.312 88.316 90.00 92.88 90.00 P 1 21 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 0.032325 0.000000 0.001624 0.00000 SCALE2 0.000000 0.016310 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011337 0.00000