HEADER METAL TRANSPORT 23-FEB-15 4YEA TITLE CRYSTAL STRUCTURE OF CISPLATIN BOUND TO A HUMAN COPPER CHAPERONE TITLE 2 (DIMER) - NEW REFINEMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: COPPER TRANSPORT PROTEIN ATOX1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: METAL TRANSPORT PROTEIN ATX1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ATOX1, HAH1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21B KEYWDS RE-REFINEMENT OF 3IWX, CISPLATIN, PLATINUM, METAL-BINDING, METAL KEYWDS 2 TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR I.G.SHABALIN,Z.DAUTER,M.JASKOLSKI,W.MINOR,A.WLODAWER REVDAT 8 27-SEP-23 4YEA 1 REMARK REVDAT 7 13-APR-22 4YEA 1 AUTHOR JRNL LINK REVDAT 6 25-DEC-19 4YEA 1 REMARK REVDAT 5 06-SEP-17 4YEA 1 REMARK REVDAT 4 16-SEP-15 4YEA 1 JRNL REVDAT 3 09-SEP-15 4YEA 1 JRNL REMARK REVDAT 2 08-JUL-15 4YEA 1 JRNL REVDAT 1 18-MAR-15 4YEA 0 JRNL AUTH I.SHABALIN,Z.DAUTER,M.JASKOLSKI,W.MINOR,A.WLODAWER JRNL TITL CRYSTALLOGRAPHY AND CHEMISTRY SHOULD ALWAYS GO TOGETHER: A JRNL TITL 2 CAUTIONARY TALE OF PROTEIN COMPLEXES WITH CISPLATIN AND JRNL TITL 3 CARBOPLATIN. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 71 1965 2015 JRNL REFN ESSN 1399-0047 JRNL PMID 26327386 JRNL DOI 10.1107/S139900471500629X REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.K.BOAL,A.C.ROSENZWEIG REMARK 1 TITL CRYSTAL STRUCTURES OF CISPLATIN BOUND TO A HUMAN COPPER REMARK 1 TITL 2 CHAPERONE. REMARK 1 REF J.AM.CHEM.SOC. V. 131 14196 2009 REMARK 1 REFN ESSN 1520-5126 REMARK 1 PMID 19807176 REMARK 1 DOI 10.1021/JA906363T REMARK 2 REMARK 2 RESOLUTION. 2.14 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8 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) : 2.14 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.63 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 10030 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) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 503 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) : 2.14 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.20 REMARK 3 REFLECTION IN BIN (WORKING SET) : 726 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.74 REMARK 3 BIN R VALUE (WORKING SET) : 0.2060 REMARK 3 BIN FREE R VALUE SET COUNT : 36 REMARK 3 BIN FREE R VALUE : 0.2600 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1012 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 111 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.10000 REMARK 3 B22 (A**2) : 0.10000 REMARK 3 B33 (A**2) : -0.31000 REMARK 3 B12 (A**2) : 0.05000 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): 0.160 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.145 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.099 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.506 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1046 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1025 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1402 ; 1.469 ; 2.013 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2383 ; 0.884 ; 3.003 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 134 ; 6.937 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 35 ;37.285 ;26.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 203 ;12.750 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 2 ; 7.048 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 168 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1121 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 189 ; 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): 536 ; 0.627 ; 1.648 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 535 ; 0.624 ; 1.646 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 667 ; 1.015 ; 2.465 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): 1 ;17.818 ; 0.100 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 : 12 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 15 REMARK 3 ORIGIN FOR THE GROUP (A): 19.7580 -4.2390 1.2040 REMARK 3 T TENSOR REMARK 3 T11: 0.1003 T22: 0.1524 REMARK 3 T33: 0.2167 T12: 0.0016 REMARK 3 T13: -0.0192 T23: 0.0022 REMARK 3 L TENSOR REMARK 3 L11: 1.0921 L22: 10.0651 REMARK 3 L33: 3.7398 L12: -2.8037 REMARK 3 L13: 0.8403 L23: -1.3133 REMARK 3 S TENSOR REMARK 3 S11: 0.0674 S12: 0.2286 S13: -0.0842 REMARK 3 S21: -0.3260 S22: -0.2737 S23: 0.1482 REMARK 3 S31: -0.1603 S32: -0.0867 S33: 0.2062 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 16 A 22 REMARK 3 ORIGIN FOR THE GROUP (A): 24.6160 -9.3720 9.1260 REMARK 3 T TENSOR REMARK 3 T11: 0.1630 T22: 0.1672 REMARK 3 T33: 0.1736 T12: 0.0183 REMARK 3 T13: 0.0072 T23: 0.0278 REMARK 3 L TENSOR REMARK 3 L11: 18.4696 L22: 12.6364 REMARK 3 L33: 4.4095 L12: 6.8445 REMARK 3 L13: 3.9190 L23: 7.4636 REMARK 3 S TENSOR REMARK 3 S11: -0.0509 S12: -0.5514 S13: -0.3739 REMARK 3 S21: 0.8132 S22: 0.0017 S23: 0.0833 REMARK 3 S31: 0.4850 S32: 0.0052 S33: 0.0492 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 23 A 38 REMARK 3 ORIGIN FOR THE GROUP (A): 19.5050 -4.1200 7.7460 REMARK 3 T TENSOR REMARK 3 T11: 0.1243 T22: 0.0750 REMARK 3 T33: 0.1484 T12: 0.0187 REMARK 3 T13: 0.0104 T23: 0.0323 REMARK 3 L TENSOR REMARK 3 L11: 4.1614 L22: 5.0346 REMARK 3 L33: 8.2591 L12: 0.9862 REMARK 3 L13: 1.9943 L23: 1.4274 REMARK 3 S TENSOR REMARK 3 S11: -0.1147 S12: -0.1477 S13: -0.0227 REMARK 3 S21: 0.1943 S22: 0.1121 S23: -0.0120 REMARK 3 S31: -0.0803 S32: -0.2390 S33: 0.0025 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 39 A 47 REMARK 3 ORIGIN FOR THE GROUP (A): 19.8540 4.0320 7.2620 REMARK 3 T TENSOR REMARK 3 T11: 0.2305 T22: 0.1734 REMARK 3 T33: 0.4061 T12: 0.1057 REMARK 3 T13: -0.0923 T23: -0.1051 REMARK 3 L TENSOR REMARK 3 L11: 1.6792 L22: 12.3235 REMARK 3 L33: 3.9433 L12: -0.8536 REMARK 3 L13: -2.2154 L23: 1.1759 REMARK 3 S TENSOR REMARK 3 S11: 0.0029 S12: 0.0222 S13: 0.4155 REMARK 3 S21: 0.5489 S22: 0.0326 S23: 0.2000 REMARK 3 S31: -0.3060 S32: -0.3377 S33: -0.0355 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 48 A 57 REMARK 3 ORIGIN FOR THE GROUP (A): 28.3240 2.0400 2.9520 REMARK 3 T TENSOR REMARK 3 T11: 0.1193 T22: 0.0918 REMARK 3 T33: 0.2506 T12: -0.0195 REMARK 3 T13: -0.0063 T23: 0.0305 REMARK 3 L TENSOR REMARK 3 L11: 8.2729 L22: 19.6299 REMARK 3 L33: 9.0051 L12: -6.5190 REMARK 3 L13: 2.9758 L23: 6.7968 REMARK 3 S TENSOR REMARK 3 S11: 0.1086 S12: 0.4560 S13: 0.5071 REMARK 3 S21: -0.2368 S22: -0.0295 S23: -0.7434 REMARK 3 S31: -0.2147 S32: 0.4176 S33: -0.0791 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 58 A 68 REMARK 3 ORIGIN FOR THE GROUP (A): 21.4360 0.6660 -1.2870 REMARK 3 T TENSOR REMARK 3 T11: 0.1623 T22: 0.0561 REMARK 3 T33: 0.1553 T12: -0.0325 REMARK 3 T13: 0.0404 T23: 0.0546 REMARK 3 L TENSOR REMARK 3 L11: 13.0633 L22: 17.1221 REMARK 3 L33: 5.2581 L12: -12.3804 REMARK 3 L13: 2.8449 L23: 0.0280 REMARK 3 S TENSOR REMARK 3 S11: -0.1824 S12: -0.1720 S13: -0.0882 REMARK 3 S21: 0.0569 S22: 0.1503 S23: 0.2733 REMARK 3 S31: -0.3387 S32: -0.0835 S33: 0.0321 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 : B 2 B 11 REMARK 3 ORIGIN FOR THE GROUP (A): 39.3970 -20.1910 5.4910 REMARK 3 T TENSOR REMARK 3 T11: 0.2359 T22: 0.1283 REMARK 3 T33: 0.0746 T12: 0.0218 REMARK 3 T13: 0.0198 T23: 0.0126 REMARK 3 L TENSOR REMARK 3 L11: 14.2042 L22: 4.8889 REMARK 3 L33: 4.6256 L12: 3.5088 REMARK 3 L13: 5.6103 L23: 0.3442 REMARK 3 S TENSOR REMARK 3 S11: -0.1627 S12: 0.1218 S13: 0.0773 REMARK 3 S21: -0.1237 S22: 0.0955 S23: -0.0164 REMARK 3 S31: 0.2189 S32: 0.1166 S33: 0.0672 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 : B 12 B 23 REMARK 3 ORIGIN FOR THE GROUP (A): 32.1670 -13.7480 -2.1770 REMARK 3 T TENSOR REMARK 3 T11: 0.1527 T22: 0.1038 REMARK 3 T33: 0.1150 T12: 0.0095 REMARK 3 T13: 0.0217 T23: 0.0121 REMARK 3 L TENSOR REMARK 3 L11: 8.8455 L22: 6.6145 REMARK 3 L33: 3.0444 L12: 1.8840 REMARK 3 L13: 1.1006 L23: -0.0102 REMARK 3 S TENSOR REMARK 3 S11: -0.0627 S12: 0.2858 S13: 0.2163 REMARK 3 S21: 0.0094 S22: 0.0735 S23: 0.2596 REMARK 3 S31: -0.2965 S32: -0.0853 S33: -0.0109 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 24 B 38 REMARK 3 ORIGIN FOR THE GROUP (A): 38.5650 -17.8390 -1.2200 REMARK 3 T TENSOR REMARK 3 T11: 0.1637 T22: 0.1454 REMARK 3 T33: 0.0892 T12: -0.0092 REMARK 3 T13: -0.0026 T23: 0.0112 REMARK 3 L TENSOR REMARK 3 L11: 5.3811 L22: 8.4606 REMARK 3 L33: 3.9671 L12: 4.0587 REMARK 3 L13: -1.6489 L23: -2.0611 REMARK 3 S TENSOR REMARK 3 S11: -0.1318 S12: 0.0490 S13: -0.0467 REMARK 3 S21: -0.3050 S22: 0.0546 S23: -0.1933 REMARK 3 S31: -0.0217 S32: 0.1667 S33: 0.0771 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 39 B 54 REMARK 3 ORIGIN FOR THE GROUP (A): 44.8950 -14.4010 5.0180 REMARK 3 T TENSOR REMARK 3 T11: 0.1333 T22: 0.1688 REMARK 3 T33: 0.1571 T12: -0.0250 REMARK 3 T13: -0.0008 T23: -0.0195 REMARK 3 L TENSOR REMARK 3 L11: 4.4069 L22: 4.6560 REMARK 3 L33: 2.5444 L12: 2.4783 REMARK 3 L13: 1.3472 L23: -0.2479 REMARK 3 S TENSOR REMARK 3 S11: -0.1208 S12: 0.2550 S13: 0.0116 REMARK 3 S21: -0.1130 S22: 0.2868 S23: -0.4501 REMARK 3 S31: -0.0276 S32: 0.2836 S33: -0.1661 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 55 B 63 REMARK 3 ORIGIN FOR THE GROUP (A): 34.0950 -12.8750 8.4350 REMARK 3 T TENSOR REMARK 3 T11: 0.1321 T22: 0.1199 REMARK 3 T33: 0.1325 T12: -0.0001 REMARK 3 T13: 0.0172 T23: 0.0086 REMARK 3 L TENSOR REMARK 3 L11: 20.2630 L22: 3.2285 REMARK 3 L33: 2.5863 L12: -3.0537 REMARK 3 L13: 0.8185 L23: 0.3204 REMARK 3 S TENSOR REMARK 3 S11: 0.0827 S12: 0.3001 S13: 0.9076 REMARK 3 S21: -0.0860 S22: -0.0481 S23: 0.1489 REMARK 3 S31: -0.2091 S32: -0.1652 S33: -0.0345 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 64 B 68 REMARK 3 ORIGIN FOR THE GROUP (A): 45.7930 -23.0410 9.0370 REMARK 3 T TENSOR REMARK 3 T11: 0.2804 T22: 0.2678 REMARK 3 T33: 0.1340 T12: 0.0486 REMARK 3 T13: -0.0507 T23: -0.0704 REMARK 3 L TENSOR REMARK 3 L11: 9.6060 L22: 8.1811 REMARK 3 L33: 5.3949 L12: -2.2659 REMARK 3 L13: -2.2568 L23: -0.6967 REMARK 3 S TENSOR REMARK 3 S11: 0.0902 S12: 0.7120 S13: -0.2337 REMARK 3 S21: -0.0232 S22: 0.0848 S23: -0.6913 REMARK 3 S31: 0.7913 S32: 0.5213 S33: -0.1751 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS REMARK 3 THIS DEPOSIT RESULTED FROM AN ANALYSIS OF A NUMBER OF PDB ENTRIES REMARK 3 THAT CONTAIN CISPLATIN OR CARBOPLATIN IN COMPLEX WITH PROTEINS, REMARK 3 CONDUCTED IN THE SPIRIT OF THE TERWILLIGER-BRICOGNE MOTTO REMARK 3 ADVOCATING CONTINUOUS IMPROVEMENT OF THE MACROMOLECULAR MODELS IN REMARK 3 THE PDB (ACTA CRYST. D70, 2533, 2014). THE STRUCTURE FACTORS AND REMARK 3 COORDINATES, ORIGINALLY DEPOSITED AS 3IWX (BOAL, A. K. & REMARK 3 ROSENZWEIG, A. C. 2009. J. AM. CHEM. SOC. 131, 14196-14197), WERE REMARK 3 USED AS THE STARTING POINT FOR AN INDEPENDENT RE-REFINEMENT. THE REMARK 3 NEW MODEL INCLUDES SOME REINTERPRETATION OF THE LIGANDS, HAS LOWER REMARK 3 R FACTORS, AND IMPROVED STATISTICS DESCRIBING THE AGREEMENT WITH REMARK 3 THE EXPERIMENTAL DATA. REMARK 4 REMARK 4 4YEA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1000207203. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-APR-09 REMARK 200 TEMPERATURE (KELVIN) : 113.0 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10562 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.140 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : 0.07800 REMARK 200 FOR THE DATA SET : 23.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.14 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.40100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3IWX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5 M LITHIUM SULFATE, 0.1M MES, 50 MM REMARK 280 NACL, PH 6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K, PH REMARK 280 6.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.22333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 18.11167 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 27.16750 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 9.05583 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 45.27917 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: 1490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 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 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 ARG A 21 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG B 21 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 400 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 12 SG REMARK 620 2 CYS A 15 SG 116.6 REMARK 620 3 CYS B 12 SG 96.2 109.1 REMARK 620 4 CYS B 15 SG 108.9 109.0 117.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CU A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3IWX RELATED DB: PDB REMARK 900 THE CURRENT DEPOSIT IS RE-REFINEMENT OF 3IWX DBREF 4YEA A 2 68 UNP O00244 ATOX1_HUMAN 2 68 DBREF 4YEA B 2 68 UNP O00244 ATOX1_HUMAN 2 68 SEQRES 1 A 67 PRO LYS HIS GLU PHE SER VAL ASP MET THR CYS GLY GLY SEQRES 2 A 67 CYS ALA GLU ALA VAL SER ARG VAL LEU ASN LYS LEU GLY SEQRES 3 A 67 GLY VAL LYS TYR ASP ILE ASP LEU PRO ASN LYS LYS VAL SEQRES 4 A 67 CYS ILE GLU SER GLU HIS SER MET ASP THR LEU LEU ALA SEQRES 5 A 67 THR LEU LYS LYS THR GLY LYS THR VAL SER TYR LEU GLY SEQRES 6 A 67 LEU GLU SEQRES 1 B 67 PRO LYS HIS GLU PHE SER VAL ASP MET THR CYS GLY GLY SEQRES 2 B 67 CYS ALA GLU ALA VAL SER ARG VAL LEU ASN LYS LEU GLY SEQRES 3 B 67 GLY VAL LYS TYR ASP ILE ASP LEU PRO ASN LYS LYS VAL SEQRES 4 B 67 CYS ILE GLU SER GLU HIS SER MET ASP THR LEU LEU ALA SEQRES 5 B 67 THR LEU LYS LYS THR GLY LYS THR VAL SER TYR LEU GLY SEQRES 6 B 67 LEU GLU HET CU A 400 1 HET SO4 A 401 5 HET SO4 B 101 5 HET SO4 B 102 5 HETNAM CU COPPER (II) ION HETNAM SO4 SULFATE ION FORMUL 3 CU CU 2+ FORMUL 4 SO4 3(O4 S 2-) FORMUL 7 HOH *111(H2 O) HELIX 1 AA1 CYS A 12 GLY A 27 1 16 HELIX 2 AA2 SER A 47 LYS A 57 1 11 HELIX 3 AA3 CYS B 12 GLY B 27 1 16 HELIX 4 AA4 SER B 47 LYS B 57 1 11 SHEET 1 AA1 4 VAL A 29 ASP A 34 0 SHEET 2 AA1 4 LYS A 39 SER A 44 -1 O GLU A 43 N LYS A 30 SHEET 3 AA1 4 LYS A 3 VAL A 8 -1 N HIS A 4 O ILE A 42 SHEET 4 AA1 4 VAL A 62 LEU A 67 -1 O GLY A 66 N GLU A 5 SHEET 1 AA2 4 VAL B 29 ASP B 34 0 SHEET 2 AA2 4 LYS B 39 SER B 44 -1 O GLU B 43 N LYS B 30 SHEET 3 AA2 4 LYS B 3 VAL B 8 -1 N HIS B 4 O ILE B 42 SHEET 4 AA2 4 VAL B 62 LEU B 67 -1 O LEU B 65 N GLU B 5 LINK SG CYS A 12 CU CU A 400 1555 1555 2.33 LINK SG CYS A 15 CU CU A 400 1555 1555 2.35 LINK CU CU A 400 SG CYS B 12 1555 1555 2.33 LINK CU CU A 400 SG CYS B 15 1555 1555 2.31 SITE 1 AC1 4 CYS A 12 CYS A 15 CYS B 12 CYS B 15 SITE 1 AC2 3 HIS A 46 SER A 47 THR A 50 SITE 1 AC3 3 GLY B 28 HOH B 257 HOH B 263 SITE 1 AC4 3 HIS B 46 SER B 47 THR B 50 CRYST1 78.289 78.289 54.335 90.00 90.00 120.00 P 65 12 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 0.012773 0.007375 0.000000 0.00000 SCALE2 0.000000 0.014749 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018404 0.00000