PDB Short entry for 3F8F HEADER TRANSCRIPTION REGULATOR 12-NOV-08 3F8F TITLE CRYSTAL STRUCTURE OF MULTIDRUG BINDING TRANSCRIPTIONAL REGULATOR LMRR TITLE 2 COMPLEXED WITH DAUNOMYCIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL REGULATOR, PADR-LIKE FAMILY; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: TRANSCRIPTION REGULATOR LMRR; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTOCOCCUS LACTIS SUBSP. CREMORIS; SOURCE 3 ORGANISM_TAXID: 416870; SOURCE 4 STRAIN: MG1363; SOURCE 5 GENE: LMRR; SOURCE 6 EXPRESSION_SYSTEM: LACTOCOCCUS LACTIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 1358; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: NZ9000; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PNSC8048 KEYWDS WINGED HELIX TURN HELIX, TRANSCRIPTION REGULATOR EXPDTA X-RAY DIFFRACTION AUTHOR P.K.MADOORI,H.AGUSTIANDARI,A.J.M.DRIESSEN,A.-M.W.H.THUNNISSEN REVDAT 4 01-NOV-23 3F8F 1 REMARK SEQADV REVDAT 3 09-APR-14 3F8F 1 JRNL REVDAT 2 13-JUL-11 3F8F 1 VERSN REVDAT 1 30-DEC-08 3F8F 0 JRNL AUTH P.K.MADOORI,H.AGUSTIANDARI,A.J.DRIESSEN,A.M.THUNNISSEN JRNL TITL STRUCTURE OF THE TRANSCRIPTIONAL REGULATOR LMRR AND ITS JRNL TITL 2 MECHANISM OF MULTIDRUG RECOGNITION. JRNL REF EMBO J. V. 28 156 2009 JRNL REFN ISSN 0261-4189 JRNL PMID 19096365 JRNL DOI 10.1038/EMBOJ.2008.263 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.88 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 13853 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) : 0.235 REMARK 3 R VALUE (WORKING SET) : 0.232 REMARK 3 FREE R VALUE : 0.280 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 762 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1030 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2330 REMARK 3 BIN FREE R VALUE SET COUNT : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1832 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 38 REMARK 3 SOLVENT ATOMS : 43 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.78000 REMARK 3 B22 (A**2) : 3.32000 REMARK 3 B33 (A**2) : -1.54000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.289 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.233 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.171 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.402 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.920 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.886 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1899 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2552 ; 0.651 ; 1.988 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 222 ; 5.729 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 94 ;35.087 ;24.681 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 371 ;18.916 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;13.174 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 272 ; 0.063 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1395 ; 0.001 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 819 ; 0.217 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1309 ; 0.316 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 75 ; 0.167 ; 0.200 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): 53 ; 0.183 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.166 ; 0.200 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): 1148 ; 0.684 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1771 ; 1.131 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 970 ; 1.687 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 781 ; 2.798 ; 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 : 2 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 6 A 69 4 REMARK 3 1 B 6 B 69 4 REMARK 3 2 A 76 A 110 4 REMARK 3 2 B 76 B 110 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 819 ; 0.77 ; 0.50 REMARK 3 MEDIUM THERMAL 1 A (A**2): 819 ; 0.46 ; 2.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 18 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 2 A 10 REMARK 3 ORIGIN FOR THE GROUP (A): 34.5380 36.2156 48.4598 REMARK 3 T TENSOR REMARK 3 T11: 0.0765 T22: -0.0548 REMARK 3 T33: 0.0968 T12: -0.0735 REMARK 3 T13: 0.0126 T23: -0.0491 REMARK 3 L TENSOR REMARK 3 L11: 12.2559 L22: 8.1259 REMARK 3 L33: 28.9968 L12: -6.8484 REMARK 3 L13: -9.8544 L23: 6.4035 REMARK 3 S TENSOR REMARK 3 S11: 0.0978 S12: -0.4624 S13: 0.1925 REMARK 3 S21: 0.2305 S22: -0.2272 S23: -0.1772 REMARK 3 S31: -0.4230 S32: 0.2490 S33: 0.1294 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 11 A 34 REMARK 3 ORIGIN FOR THE GROUP (A): 22.8049 32.8752 64.6123 REMARK 3 T TENSOR REMARK 3 T11: 0.0655 T22: 0.2169 REMARK 3 T33: 0.1160 T12: -0.0406 REMARK 3 T13: 0.0081 T23: -0.0479 REMARK 3 L TENSOR REMARK 3 L11: 3.2259 L22: 1.7696 REMARK 3 L33: 5.1815 L12: -0.1564 REMARK 3 L13: -2.9824 L23: 1.2800 REMARK 3 S TENSOR REMARK 3 S11: -0.1052 S12: -0.3871 S13: -0.0925 REMARK 3 S21: 0.0726 S22: 0.0264 S23: 0.1886 REMARK 3 S31: 0.4727 S32: -0.4412 S33: 0.0788 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 35 A 51 REMARK 3 ORIGIN FOR THE GROUP (A): 28.6195 26.0497 63.5564 REMARK 3 T TENSOR REMARK 3 T11: 0.2109 T22: 0.1944 REMARK 3 T33: 0.0491 T12: 0.0430 REMARK 3 T13: 0.0288 T23: 0.0107 REMARK 3 L TENSOR REMARK 3 L11: 7.1333 L22: 12.0382 REMARK 3 L33: 10.6275 L12: 4.2598 REMARK 3 L13: 5.1893 L23: 9.0127 REMARK 3 S TENSOR REMARK 3 S11: 0.1528 S12: -0.4296 S13: -0.7236 REMARK 3 S21: 0.2825 S22: 0.0901 S23: -0.4258 REMARK 3 S31: 1.1231 S32: 0.6145 S33: -0.2429 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 52 A 60 REMARK 3 ORIGIN FOR THE GROUP (A): 28.8923 42.7832 66.5509 REMARK 3 T TENSOR REMARK 3 T11: 0.1940 T22: 0.3017 REMARK 3 T33: 0.0472 T12: -0.0623 REMARK 3 T13: -0.0335 T23: 0.0390 REMARK 3 L TENSOR REMARK 3 L11: 23.0502 L22: 9.5229 REMARK 3 L33: 3.5474 L12: -3.4355 REMARK 3 L13: -2.3814 L23: 5.8092 REMARK 3 S TENSOR REMARK 3 S11: -0.2258 S12: -0.3857 S13: 0.4067 REMARK 3 S21: 0.1880 S22: 0.1135 S23: -0.4433 REMARK 3 S31: -0.6906 S32: 0.5167 S33: 0.1122 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 61 A 70 REMARK 3 ORIGIN FOR THE GROUP (A): 21.0523 39.9395 75.6152 REMARK 3 T TENSOR REMARK 3 T11: -0.0357 T22: 0.3981 REMARK 3 T33: 0.1579 T12: 0.0213 REMARK 3 T13: -0.0505 T23: -0.0597 REMARK 3 L TENSOR REMARK 3 L11: 5.5905 L22: 11.7138 REMARK 3 L33: 5.6381 L12: -0.5689 REMARK 3 L13: 3.0539 L23: 4.0688 REMARK 3 S TENSOR REMARK 3 S11: -0.1558 S12: -0.7437 S13: -0.0082 REMARK 3 S21: 0.8427 S22: 0.0981 S23: -0.6983 REMARK 3 S31: 0.1391 S32: -0.0733 S33: 0.0577 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 74 A 81 REMARK 3 ORIGIN FOR THE GROUP (A): 22.3580 35.4631 77.5082 REMARK 3 T TENSOR REMARK 3 T11: -0.0009 T22: 0.3333 REMARK 3 T33: 0.1158 T12: 0.0389 REMARK 3 T13: 0.0533 T23: -0.0262 REMARK 3 L TENSOR REMARK 3 L11: 6.1911 L22: 7.9094 REMARK 3 L33: 16.5187 L12: -3.7701 REMARK 3 L13: 1.1844 L23: -0.3704 REMARK 3 S TENSOR REMARK 3 S11: -0.4133 S12: -0.6329 S13: -0.5114 REMARK 3 S21: 0.4095 S22: 0.4983 S23: -0.3627 REMARK 3 S31: 0.2669 S32: 0.7013 S33: -0.0849 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 82 A 96 REMARK 3 ORIGIN FOR THE GROUP (A): 13.8368 43.9897 58.2011 REMARK 3 T TENSOR REMARK 3 T11: 0.1336 T22: 0.3974 REMARK 3 T33: 0.2189 T12: 0.1046 REMARK 3 T13: 0.0113 T23: -0.0444 REMARK 3 L TENSOR REMARK 3 L11: 1.1624 L22: 0.2323 REMARK 3 L33: 28.2425 L12: 0.5170 REMARK 3 L13: -4.3532 L23: -1.7697 REMARK 3 S TENSOR REMARK 3 S11: -0.0485 S12: -0.1893 S13: 0.3247 REMARK 3 S21: -0.2990 S22: -0.1586 S23: 0.1923 REMARK 3 S31: -0.5628 S32: -1.3495 S33: 0.2071 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 97 A 108 REMARK 3 ORIGIN FOR THE GROUP (A): 15.7631 41.2808 39.0573 REMARK 3 T TENSOR REMARK 3 T11: 0.0774 T22: 0.1261 REMARK 3 T33: 0.1736 T12: 0.0156 REMARK 3 T13: 0.0325 T23: 0.0110 REMARK 3 L TENSOR REMARK 3 L11: 1.8388 L22: 5.1804 REMARK 3 L33: 39.1523 L12: -2.0046 REMARK 3 L13: -1.3518 L23: 7.0688 REMARK 3 S TENSOR REMARK 3 S11: -0.6057 S12: 0.0971 S13: -0.3073 REMARK 3 S21: 0.3226 S22: 0.1294 S23: 0.0262 REMARK 3 S31: 0.6164 S32: 0.1169 S33: 0.4763 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 109 A 116 REMARK 3 ORIGIN FOR THE GROUP (A): 14.7350 39.6184 22.6877 REMARK 3 T TENSOR REMARK 3 T11: 0.6669 T22: 0.2780 REMARK 3 T33: 0.2059 T12: -0.0353 REMARK 3 T13: -0.0065 T23: -0.0067 REMARK 3 L TENSOR REMARK 3 L11: 10.2095 L22: 11.4264 REMARK 3 L33: 49.0020 L12: -6.8898 REMARK 3 L13: 13.2866 L23: 5.6932 REMARK 3 S TENSOR REMARK 3 S11: 0.9113 S12: 0.4071 S13: -0.2203 REMARK 3 S21: -1.0866 S22: -0.1245 S23: -0.3704 REMARK 3 S31: -0.5959 S32: -1.0243 S33: -0.7868 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 6 B 10 REMARK 3 ORIGIN FOR THE GROUP (A): 25.0319 48.8239 50.8369 REMARK 3 T TENSOR REMARK 3 T11: 0.2430 T22: 0.6270 REMARK 3 T33: 0.3582 T12: -0.0196 REMARK 3 T13: -0.0725 T23: -0.4894 REMARK 3 L TENSOR REMARK 3 L11: 32.1312 L22: 37.1399 REMARK 3 L33: 55.6904 L12: -6.5764 REMARK 3 L13: -8.1404 L23: -2.2889 REMARK 3 S TENSOR REMARK 3 S11: 0.1991 S12: -4.0596 S13: 3.3220 REMARK 3 S21: 1.9543 S22: -0.2923 S23: 0.5815 REMARK 3 S31: -1.1578 S32: -0.4599 S33: 0.0933 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 11 B 34 REMARK 3 ORIGIN FOR THE GROUP (A): 26.1396 45.8743 34.1925 REMARK 3 T TENSOR REMARK 3 T11: 0.1392 T22: 0.0950 REMARK 3 T33: 0.1742 T12: 0.0309 REMARK 3 T13: -0.0067 T23: -0.0177 REMARK 3 L TENSOR REMARK 3 L11: 3.6014 L22: 2.9099 REMARK 3 L33: 4.5050 L12: -0.7530 REMARK 3 L13: -0.4790 L23: -0.8491 REMARK 3 S TENSOR REMARK 3 S11: -0.1132 S12: 0.2059 S13: -0.0471 REMARK 3 S21: -0.0692 S22: 0.1533 S23: -0.0037 REMARK 3 S31: -0.0926 S32: -0.2456 S33: -0.0400 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 35 B 47 REMARK 3 ORIGIN FOR THE GROUP (A): 17.6269 51.4637 35.7054 REMARK 3 T TENSOR REMARK 3 T11: 0.1596 T22: 0.1114 REMARK 3 T33: 0.1699 T12: 0.1385 REMARK 3 T13: 0.0109 T23: -0.0025 REMARK 3 L TENSOR REMARK 3 L11: 12.8871 L22: 7.8082 REMARK 3 L33: 10.8286 L12: 9.9859 REMARK 3 L13: 1.4839 L23: 0.2840 REMARK 3 S TENSOR REMARK 3 S11: -0.0196 S12: -0.6446 S13: 0.6210 REMARK 3 S21: -0.1212 S22: -0.0320 S23: 0.7241 REMARK 3 S31: -0.0232 S32: -0.7686 S33: 0.0516 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 48 B 55 REMARK 3 ORIGIN FOR THE GROUP (A): 32.0577 51.9098 38.6868 REMARK 3 T TENSOR REMARK 3 T11: 0.1791 T22: -0.0422 REMARK 3 T33: 0.1563 T12: -0.0448 REMARK 3 T13: 0.0975 T23: 0.0224 REMARK 3 L TENSOR REMARK 3 L11: 12.1999 L22: 24.7394 REMARK 3 L33: 4.6771 L12: -12.0581 REMARK 3 L13: 2.3921 L23: -9.7096 REMARK 3 S TENSOR REMARK 3 S11: 0.4890 S12: 0.0019 S13: -0.2538 REMARK 3 S21: -0.5785 S22: 0.1383 S23: -0.1632 REMARK 3 S31: -0.0508 S32: -0.2437 S33: -0.6273 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 56 B 63 REMARK 3 ORIGIN FOR THE GROUP (A): 38.6904 42.9300 39.5692 REMARK 3 T TENSOR REMARK 3 T11: 0.0926 T22: 0.1097 REMARK 3 T33: 0.1523 T12: 0.0121 REMARK 3 T13: 0.0547 T23: 0.0282 REMARK 3 L TENSOR REMARK 3 L11: 27.4934 L22: 27.9044 REMARK 3 L33: 6.0353 L12: 0.2904 REMARK 3 L13: 2.5235 L23: 5.5615 REMARK 3 S TENSOR REMARK 3 S11: -0.0992 S12: -0.6492 S13: 0.9949 REMARK 3 S21: 0.6147 S22: -0.0720 S23: -0.7421 REMARK 3 S31: 0.3682 S32: 1.0276 S33: 0.1712 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 64 B 78 REMARK 3 ORIGIN FOR THE GROUP (A): 36.7835 50.8141 22.6159 REMARK 3 T TENSOR REMARK 3 T11: 0.1785 T22: 0.0864 REMARK 3 T33: 0.1618 T12: 0.0434 REMARK 3 T13: 0.0779 T23: -0.0177 REMARK 3 L TENSOR REMARK 3 L11: 3.2214 L22: 9.0217 REMARK 3 L33: 13.5469 L12: 5.3902 REMARK 3 L13: -5.4879 L23: -9.2836 REMARK 3 S TENSOR REMARK 3 S11: 0.1688 S12: 0.3910 S13: -0.1793 REMARK 3 S21: -0.2702 S22: -0.1810 S23: 0.1180 REMARK 3 S31: 0.1146 S32: 0.1746 S33: 0.0122 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 79 B 94 REMARK 3 ORIGIN FOR THE GROUP (A): 31.8111 35.6084 34.9200 REMARK 3 T TENSOR REMARK 3 T11: 0.1491 T22: 0.0151 REMARK 3 T33: 0.1573 T12: 0.0126 REMARK 3 T13: 0.0352 T23: -0.0152 REMARK 3 L TENSOR REMARK 3 L11: 0.0454 L22: 3.3442 REMARK 3 L33: 1.5174 L12: 0.3652 REMARK 3 L13: -0.0746 L23: 0.1518 REMARK 3 S TENSOR REMARK 3 S11: 0.0029 S12: 0.1257 S13: 0.0381 REMARK 3 S21: -0.5553 S22: 0.0173 S23: -0.1441 REMARK 3 S31: 0.4415 S32: 0.1524 S33: -0.0201 REMARK 3 REMARK 3 TLS GROUP : 17 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 95 B 109 REMARK 3 ORIGIN FOR THE GROUP (A): 20.7241 27.1383 53.4677 REMARK 3 T TENSOR REMARK 3 T11: 0.1431 T22: 0.1097 REMARK 3 T33: 0.1190 T12: -0.0649 REMARK 3 T13: -0.0110 T23: -0.0358 REMARK 3 L TENSOR REMARK 3 L11: 6.2092 L22: 6.9228 REMARK 3 L33: 12.9325 L12: 5.9024 REMARK 3 L13: -2.6901 L23: -3.7840 REMARK 3 S TENSOR REMARK 3 S11: 0.0701 S12: 0.2764 S13: -0.7823 REMARK 3 S21: 0.1917 S22: -0.0697 S23: 0.0175 REMARK 3 S31: 0.2040 S32: -0.6616 S33: -0.0003 REMARK 3 REMARK 3 TLS GROUP : 18 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 110 B 115 REMARK 3 ORIGIN FOR THE GROUP (A): 11.1701 21.3921 65.7715 REMARK 3 T TENSOR REMARK 3 T11: 0.0991 T22: 0.7009 REMARK 3 T33: 0.3417 T12: -0.2118 REMARK 3 T13: -0.0494 T23: 0.0692 REMARK 3 L TENSOR REMARK 3 L11: 28.2091 L22: 50.1212 REMARK 3 L33: 49.7736 L12: -24.6800 REMARK 3 L13: -3.8801 L23: -9.3267 REMARK 3 S TENSOR REMARK 3 S11: 1.0683 S12: -0.7718 S13: -1.0108 REMARK 3 S21: 0.5521 S22: -1.7405 S23: -1.9328 REMARK 3 S31: 3.3078 S32: -3.1847 S33: 0.6722 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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: AUTHOR CHECKED USING MOLPROBITY AND IN REMARK 3 COOT FOR TORSION ANGLES OUTSIDE AND ALL RESIDUES ARE WITHIN THE REMARK 3 ALLOWED CONFORMATIONS. THERE ARE NO OUTLIERS. REMARK 4 REMARK 4 3F8F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-NOV-08. REMARK 100 THE DEPOSITION ID IS D_1000050276. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-NOV-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.2.25 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14655 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 49.884 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.27300 REMARK 200 R SYM FOR SHELL (I) : 0.27300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.700 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: 3F8B REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG1500, 0.1M MALONIC REMARK 280 ACID/IMIDAZOL/BORIC (MIB) BUFFER, PH 7, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 17.72500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 73.55800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.51250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 73.55800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.72500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.51250 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 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: 4090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 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 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 SER A 71 REMARK 465 GLN A 72 REMARK 465 SER A 117 REMARK 465 ARG A 118 REMARK 465 TRP A 119 REMARK 465 SER A 120 REMARK 465 HIS A 121 REMARK 465 PRO A 122 REMARK 465 GLN A 123 REMARK 465 PHE A 124 REMARK 465 GLU A 125 REMARK 465 LYS A 126 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 GLU B 3 REMARK 465 ILE B 4 REMARK 465 LYS B 116 REMARK 465 SER B 117 REMARK 465 ARG B 118 REMARK 465 TRP B 119 REMARK 465 SER B 120 REMARK 465 HIS B 121 REMARK 465 PRO B 122 REMARK 465 GLN B 123 REMARK 465 PHE B 124 REMARK 465 GLU B 125 REMARK 465 LYS B 126 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 MET A 1 CB CG SD CE 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 ARG B 75 89.51 -165.63 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 DM1 A 127 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3F8B RELATED DB: PDB REMARK 900 LMRR IN DRUG FREE STATE REMARK 900 RELATED ID: 3F8C RELATED DB: PDB DBREF 3F8F A 1 116 UNP A2RI36 A2RI36_LACLM 1 116 DBREF 3F8F B 1 116 UNP A2RI36 A2RI36_LACLM 1 116 SEQADV 3F8F SER A 117 UNP A2RI36 EXPRESSION TAG SEQADV 3F8F ARG A 118 UNP A2RI36 EXPRESSION TAG SEQADV 3F8F TRP A 119 UNP A2RI36 EXPRESSION TAG SEQADV 3F8F SER A 120 UNP A2RI36 EXPRESSION TAG SEQADV 3F8F HIS A 121 UNP A2RI36 EXPRESSION TAG SEQADV 3F8F PRO A 122 UNP A2RI36 EXPRESSION TAG SEQADV 3F8F GLN A 123 UNP A2RI36 EXPRESSION TAG SEQADV 3F8F PHE A 124 UNP A2RI36 EXPRESSION TAG SEQADV 3F8F GLU A 125 UNP A2RI36 EXPRESSION TAG SEQADV 3F8F LYS A 126 UNP A2RI36 EXPRESSION TAG SEQADV 3F8F SER B 117 UNP A2RI36 EXPRESSION TAG SEQADV 3F8F ARG B 118 UNP A2RI36 EXPRESSION TAG SEQADV 3F8F TRP B 119 UNP A2RI36 EXPRESSION TAG SEQADV 3F8F SER B 120 UNP A2RI36 EXPRESSION TAG SEQADV 3F8F HIS B 121 UNP A2RI36 EXPRESSION TAG SEQADV 3F8F PRO B 122 UNP A2RI36 EXPRESSION TAG SEQADV 3F8F GLN B 123 UNP A2RI36 EXPRESSION TAG SEQADV 3F8F PHE B 124 UNP A2RI36 EXPRESSION TAG SEQADV 3F8F GLU B 125 UNP A2RI36 EXPRESSION TAG SEQADV 3F8F LYS B 126 UNP A2RI36 EXPRESSION TAG SEQRES 1 A 126 MET ALA GLU ILE PRO LYS GLU MET LEU ARG ALA GLN THR SEQRES 2 A 126 ASN VAL ILE LEU LEU ASN VAL LEU LYS GLN GLY ASP ASN SEQRES 3 A 126 TYR VAL TYR GLY ILE ILE LYS GLN VAL LYS GLU ALA SER SEQRES 4 A 126 ASN GLY GLU MET GLU LEU ASN GLU ALA THR LEU TYR THR SEQRES 5 A 126 ILE PHE LYS ARG LEU GLU LYS ASP GLY ILE ILE SER SER SEQRES 6 A 126 TYR TRP GLY ASP GLU SER GLN GLY GLY ARG ARG LYS TYR SEQRES 7 A 126 TYR ARG LEU THR GLU ILE GLY HIS GLU ASN MET ARG LEU SEQRES 8 A 126 ALA PHE GLU SER TRP SER ARG VAL ASP LYS ILE ILE GLU SEQRES 9 A 126 ASN LEU GLU ALA ASN LYS LYS SER GLU ALA ILE LYS SER SEQRES 10 A 126 ARG TRP SER HIS PRO GLN PHE GLU LYS SEQRES 1 B 126 MET ALA GLU ILE PRO LYS GLU MET LEU ARG ALA GLN THR SEQRES 2 B 126 ASN VAL ILE LEU LEU ASN VAL LEU LYS GLN GLY ASP ASN SEQRES 3 B 126 TYR VAL TYR GLY ILE ILE LYS GLN VAL LYS GLU ALA SER SEQRES 4 B 126 ASN GLY GLU MET GLU LEU ASN GLU ALA THR LEU TYR THR SEQRES 5 B 126 ILE PHE LYS ARG LEU GLU LYS ASP GLY ILE ILE SER SER SEQRES 6 B 126 TYR TRP GLY ASP GLU SER GLN GLY GLY ARG ARG LYS TYR SEQRES 7 B 126 TYR ARG LEU THR GLU ILE GLY HIS GLU ASN MET ARG LEU SEQRES 8 B 126 ALA PHE GLU SER TRP SER ARG VAL ASP LYS ILE ILE GLU SEQRES 9 B 126 ASN LEU GLU ALA ASN LYS LYS SER GLU ALA ILE LYS SER SEQRES 10 B 126 ARG TRP SER HIS PRO GLN PHE GLU LYS HET DM1 A 127 38 HETNAM DM1 DAUNOMYCIN HETSYN DM1 DAUNORUBICIN FORMUL 3 DM1 C27 H29 N O10 FORMUL 4 HOH *43(H2 O) HELIX 1 1 PRO A 5 GLY A 24 1 20 HELIX 2 2 TYR A 27 SER A 39 1 13 HELIX 3 3 ASN A 46 ASP A 60 1 15 HELIX 4 4 THR A 82 LYS A 116 1 35 HELIX 5 5 PRO B 5 GLY B 24 1 20 HELIX 6 6 TYR B 27 ALA B 38 1 12 HELIX 7 7 ASN B 46 ASP B 60 1 15 HELIX 8 8 THR B 82 GLU B 113 1 32 SHEET 1 A 2 ILE A 63 TRP A 67 0 SHEET 2 A 2 LYS A 77 LEU A 81 -1 O TYR A 78 N TYR A 66 SHEET 1 B 2 ILE B 63 GLY B 68 0 SHEET 2 B 2 ARG B 76 LEU B 81 -1 O TYR B 78 N TYR B 66 SITE 1 AC1 8 MET A 8 VAL A 15 MET A 89 PHE A 93 SITE 2 AC1 8 TRP A 96 HOH A 147 VAL B 15 TRP B 96 CRYST1 35.450 53.025 147.116 90.00 90.00 90.00 P 21 21 21 8 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 0.028209 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018859 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006797 0.00000