HEADER ANTITOXIN 13-FEB-21 7E4J TITLE X-RAY CRYSTAL STRUCTURE OF VAPB12 ANTITOXIN FROM MYCOBACTERIUM TITLE 2 TUBERCULOSIS IN SPACE GROUP P41. COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTITOXIN; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: ANTITOXIN VAPB12,CONSERVED PROTEIN OF UNCHARACTERIZED COMPND 5 FUNCTION,POSSIBLE ANTITOXIN VAPB12; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 GENE: VAPB12, AYJ03_009075, DSI38_08650, E5M52_14165, E5M78_13900, SOURCE 5 ERS007663_00684, ERS007665_03495, ERS007703_02236, ERS007720_02286, SOURCE 6 ERS007722_03650, ERS007741_00752, ERS013471_00074, ERS023446_02694, SOURCE 7 ERS027646_03040, ERS027659_01239, ERS027661_00782, ERS094182_03044, SOURCE 8 F6W99_00284, FRD82_02990, SAMEA2683035_01359; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS VAPBC12, TOXIN-ANTITOXIN, CHOLESTEROL, ANTITOXIN EXPDTA X-RAY DIFFRACTION AUTHOR S.PRATAP,A.K.MEGTA,S.TALWAR,S.CHANDRESH,A.K.PANDEY,V.KRISHNAN REVDAT 1 16-FEB-22 7E4J 0 JRNL AUTH S.PRATAP,A.K.MEGTA,S.TALWAR,C.SHARMA,A.K.PANDEY,V.KRISHNAN JRNL TITL X-RAY CRYSTAL STRUCTURE OF VAPB12 ANTITOXIN FROM JRNL TITL 2 MYCOBACTERIUM TUBERCULOSIS IN SPACE GROUP P41. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.63 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 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) : 1.63 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.56 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 22398 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) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 1106 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) : 1.64 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.68 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1612 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.59 REMARK 3 BIN R VALUE (WORKING SET) : 0.1900 REMARK 3 BIN FREE R VALUE SET COUNT : 91 REMARK 3 BIN FREE R VALUE : 0.2860 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1360 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 121 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -21.21000 REMARK 3 B22 (A**2) : -21.21000 REMARK 3 B33 (A**2) : 42.41000 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): 0.025 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.020 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.062 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.816 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1382 ; 0.011 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 1405 ; 0.002 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1857 ; 1.568 ; 1.633 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3219 ; 1.273 ; 1.578 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 172 ; 6.130 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 79 ;23.897 ;20.886 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 266 ;13.890 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;16.282 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 184 ; 0.064 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1524 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 296 ; 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): 700 ; 2.518 ; 3.041 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 699 ; 2.512 ; 3.034 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 868 ; 3.190 ; 4.541 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 869 ; 3.189 ; 4.550 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 682 ; 2.909 ; 3.571 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 683 ; 2.907 ; 3.578 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 990 ; 3.800 ; 5.202 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1508 ; 4.879 ;37.496 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1497 ; 4.738 ;37.339 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 2786 ; 4.025 ; 3.000 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 6 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 1 44 B 1 44 1183 0.06 0.05 REMARK 3 2 A 1 44 C 1 44 1114 0.14 0.05 REMARK 3 3 A 1 44 D 1 44 1110 0.13 0.05 REMARK 3 4 B 1 44 C 1 44 1110 0.13 0.05 REMARK 3 5 B 1 44 D 1 44 1113 0.13 0.05 REMARK 3 6 C 1 44 D 1 44 1163 0.07 0.05 REMARK 3 REMARK 3 TWIN DETAILS REMARK 3 NUMBER OF TWIN DOMAINS : 2 REMARK 3 TWIN DOMAIN : 1 REMARK 3 TWIN OPERATOR : H, K, L REMARK 3 TWIN FRACTION : 0.514 REMARK 3 TWIN DOMAIN : 2 REMARK 3 TWIN OPERATOR : -K, -H, -L REMARK 3 TWIN FRACTION : 0.486 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 1 A 11 REMARK 3 ORIGIN FOR THE GROUP (A): 16.2503 19.9356 11.0760 REMARK 3 T TENSOR REMARK 3 T11: 0.1135 T22: 0.1814 REMARK 3 T33: 0.0513 T12: -0.0062 REMARK 3 T13: -0.0523 T23: 0.0098 REMARK 3 L TENSOR REMARK 3 L11: 1.2849 L22: 0.2151 REMARK 3 L33: 3.4560 L12: 0.2416 REMARK 3 L13: 1.9067 L23: 0.5128 REMARK 3 S TENSOR REMARK 3 S11: -0.2000 S12: 0.1707 S13: 0.2434 REMARK 3 S21: 0.0001 S22: -0.1198 S23: 0.0579 REMARK 3 S31: -0.0614 S32: 0.2492 S33: 0.3199 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 12 A 28 REMARK 3 ORIGIN FOR THE GROUP (A): 3.3109 10.8772 8.1223 REMARK 3 T TENSOR REMARK 3 T11: 0.0563 T22: 0.0579 REMARK 3 T33: 0.0161 T12: -0.0002 REMARK 3 T13: 0.0057 T23: 0.0011 REMARK 3 L TENSOR REMARK 3 L11: 0.0132 L22: 0.8149 REMARK 3 L33: 0.0006 L12: 0.1001 REMARK 3 L13: 0.0004 L23: -0.0013 REMARK 3 S TENSOR REMARK 3 S11: -0.0062 S12: -0.0016 S13: -0.0020 REMARK 3 S21: -0.0403 S22: 0.0027 S23: -0.0414 REMARK 3 S31: 0.0017 S32: -0.0014 S33: 0.0035 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 29 A 44 REMARK 3 ORIGIN FOR THE GROUP (A): 13.5469 7.5041 15.3337 REMARK 3 T TENSOR REMARK 3 T11: 0.0668 T22: 0.0632 REMARK 3 T33: 0.0437 T12: 0.0117 REMARK 3 T13: -0.0087 T23: -0.0086 REMARK 3 L TENSOR REMARK 3 L11: 1.1572 L22: 0.2844 REMARK 3 L33: 0.4783 L12: 0.3394 REMARK 3 L13: 0.3600 L23: 0.3614 REMARK 3 S TENSOR REMARK 3 S11: 0.0247 S12: 0.0270 S13: -0.0866 REMARK 3 S21: 0.0229 S22: 0.0370 S23: -0.0346 REMARK 3 S31: 0.0418 S32: 0.0618 S33: -0.0616 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 : B 1 B 11 REMARK 3 ORIGIN FOR THE GROUP (A): 1.1757 2.6444 29.0761 REMARK 3 T TENSOR REMARK 3 T11: 0.0630 T22: 0.0616 REMARK 3 T33: 0.0254 T12: 0.0055 REMARK 3 T13: -0.0049 T23: -0.0162 REMARK 3 L TENSOR REMARK 3 L11: 0.8995 L22: 0.2850 REMARK 3 L33: 4.0355 L12: -0.3666 REMARK 3 L13: 1.6610 L23: -0.9285 REMARK 3 S TENSOR REMARK 3 S11: -0.1049 S12: -0.1082 S13: 0.1064 REMARK 3 S21: 0.0551 S22: 0.0110 S23: -0.0197 REMARK 3 S31: -0.1862 S32: -0.1853 S33: 0.0940 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 : B 12 B 28 REMARK 3 ORIGIN FOR THE GROUP (A): 14.0914 -6.5244 31.9057 REMARK 3 T TENSOR REMARK 3 T11: 0.0810 T22: 0.0602 REMARK 3 T33: 0.0570 T12: -0.0004 REMARK 3 T13: -0.0218 T23: -0.0063 REMARK 3 L TENSOR REMARK 3 L11: 0.5355 L22: 0.1100 REMARK 3 L33: 0.1568 L12: -0.1694 REMARK 3 L13: -0.2870 L23: 0.0967 REMARK 3 S TENSOR REMARK 3 S11: 0.0052 S12: 0.0189 S13: 0.0093 REMARK 3 S21: 0.0367 S22: 0.0019 S23: -0.0575 REMARK 3 S31: 0.0110 S32: -0.0176 S33: -0.0072 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 : B 29 B 44 REMARK 3 ORIGIN FOR THE GROUP (A): 3.8059 -9.7877 24.8382 REMARK 3 T TENSOR REMARK 3 T11: 0.0632 T22: 0.0607 REMARK 3 T33: 0.0070 T12: -0.0066 REMARK 3 T13: 0.0023 T23: -0.0014 REMARK 3 L TENSOR REMARK 3 L11: 0.5330 L22: 0.5135 REMARK 3 L33: 0.2537 L12: -0.4985 REMARK 3 L13: 0.2497 L23: -0.3138 REMARK 3 S TENSOR REMARK 3 S11: -0.0164 S12: 0.0135 S13: -0.0276 REMARK 3 S21: 0.0006 S22: 0.0179 S23: 0.0181 REMARK 3 S31: 0.0175 S32: -0.0450 S33: -0.0015 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 : C 1 C 11 REMARK 3 ORIGIN FOR THE GROUP (A): 11.8679 19.4031 11.5873 REMARK 3 T TENSOR REMARK 3 T11: 0.0597 T22: 0.0715 REMARK 3 T33: 0.0006 T12: -0.0097 REMARK 3 T13: -0.0019 T23: 0.0019 REMARK 3 L TENSOR REMARK 3 L11: 1.8577 L22: 0.5390 REMARK 3 L33: 3.3026 L12: -0.8062 REMARK 3 L13: 2.0612 L23: -0.4593 REMARK 3 S TENSOR REMARK 3 S11: 0.0239 S12: 0.0870 S13: 0.0127 REMARK 3 S21: -0.0290 S22: -0.0584 S23: 0.0037 REMARK 3 S31: -0.0041 S32: 0.0190 S33: 0.0346 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 : C 12 C 28 REMARK 3 ORIGIN FOR THE GROUP (A): 25.8361 11.7276 12.9184 REMARK 3 T TENSOR REMARK 3 T11: 0.0392 T22: 0.0548 REMARK 3 T33: 0.0316 T12: 0.0025 REMARK 3 T13: 0.0073 T23: 0.0027 REMARK 3 L TENSOR REMARK 3 L11: 0.8030 L22: 0.5096 REMARK 3 L33: 0.9722 L12: 0.0430 REMARK 3 L13: -0.8820 L23: -0.0192 REMARK 3 S TENSOR REMARK 3 S11: -0.0207 S12: 0.0110 S13: -0.0443 REMARK 3 S21: 0.0197 S22: -0.0249 S23: -0.0036 REMARK 3 S31: 0.0215 S32: -0.0046 S33: 0.0456 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 : C 29 C 44 REMARK 3 ORIGIN FOR THE GROUP (A): 15.7256 8.8567 5.9822 REMARK 3 T TENSOR REMARK 3 T11: 0.0790 T22: 0.0585 REMARK 3 T33: 0.0101 T12: -0.0022 REMARK 3 T13: -0.0041 T23: -0.0026 REMARK 3 L TENSOR REMARK 3 L11: 3.2183 L22: 1.9531 REMARK 3 L33: 0.2110 L12: 0.0150 REMARK 3 L13: -0.4902 L23: -0.5171 REMARK 3 S TENSOR REMARK 3 S11: -0.0264 S12: 0.0562 S13: -0.1753 REMARK 3 S21: -0.0606 S22: 0.0028 S23: 0.0176 REMARK 3 S31: 0.0142 S32: -0.0063 S33: 0.0236 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 : D 1 D 11 REMARK 3 ORIGIN FOR THE GROUP (A): 5.6894 2.1127 28.5260 REMARK 3 T TENSOR REMARK 3 T11: 0.0644 T22: 0.0529 REMARK 3 T33: 0.0516 T12: 0.0232 REMARK 3 T13: -0.0171 T23: -0.0090 REMARK 3 L TENSOR REMARK 3 L11: 2.1683 L22: 0.4242 REMARK 3 L33: 2.3850 L12: 0.4414 REMARK 3 L13: 1.4552 L23: -0.3887 REMARK 3 S TENSOR REMARK 3 S11: -0.1319 S12: -0.1547 S13: 0.1570 REMARK 3 S21: 0.0305 S22: -0.0481 S23: -0.0010 REMARK 3 S31: -0.2225 S32: -0.0734 S33: 0.1800 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 : D 12 D 28 REMARK 3 ORIGIN FOR THE GROUP (A): -8.4689 -5.6530 27.4934 REMARK 3 T TENSOR REMARK 3 T11: 0.0907 T22: 0.0549 REMARK 3 T33: 0.0194 T12: 0.0025 REMARK 3 T13: -0.0117 T23: -0.0000 REMARK 3 L TENSOR REMARK 3 L11: 0.6722 L22: 0.1249 REMARK 3 L33: 0.5532 L12: 0.2885 REMARK 3 L13: -0.6085 L23: -0.2596 REMARK 3 S TENSOR REMARK 3 S11: 0.0496 S12: 0.0079 S13: 0.0532 REMARK 3 S21: 0.0304 S22: 0.0041 S23: 0.0196 REMARK 3 S31: -0.0332 S32: -0.0094 S33: -0.0537 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 : D 29 D 44 REMARK 3 ORIGIN FOR THE GROUP (A): 1.5181 -8.4056 34.3229 REMARK 3 T TENSOR REMARK 3 T11: 0.0579 T22: 0.0610 REMARK 3 T33: 0.0187 T12: -0.0017 REMARK 3 T13: -0.0056 T23: -0.0088 REMARK 3 L TENSOR REMARK 3 L11: 2.6536 L22: 0.0833 REMARK 3 L33: 1.1321 L12: 0.4694 REMARK 3 L13: 0.7460 L23: 0.1468 REMARK 3 S TENSOR REMARK 3 S11: 0.0291 S12: 0.0073 S13: -0.1938 REMARK 3 S21: 0.0049 S22: -0.0013 S23: -0.0334 REMARK 3 S31: -0.0045 S32: 0.0433 S33: -0.0277 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 7E4J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-FEB-21. REMARK 100 THE DEPOSITION ID IS D_1300020332. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUL-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.3 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) : 0.97951 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23505 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.630 REMARK 200 RESOLUTION RANGE LOW (A) : 40.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : 0.72300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING REMARK 200 SOFTWARE USED: SHELXDE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM CHLORIDE:NAOH PH 6.3, REMARK 280 20% (W/V) PEG3350, VAPOR DIFFUSION, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 81.11350 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 40.55675 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 121.67025 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 3020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 350 REMARK 350 BIOMOLECULE: 2 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: 2960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 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 B 43 CG CD OE1 OE2 REMARK 470 GLU D 13 CG CD OE1 OE2 REMARK 470 GLU D 42 CG CD OE1 OE2 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 B 229 DISTANCE = 6.04 ANGSTROMS REMARK 525 HOH B 230 DISTANCE = 6.78 ANGSTROMS REMARK 525 HOH D 128 DISTANCE = 5.92 ANGSTROMS REMARK 525 HOH D 129 DISTANCE = 5.98 ANGSTROMS 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 ZN B 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 12 OD1 REMARK 620 2 ASP A 12 OD2 65.1 REMARK 620 3 HIS A 16 NE2 105.2 104.7 REMARK 620 4 ASP B 12 OD1 102.5 82.6 23.2 REMARK 620 5 HIS B 16 NE2 98.9 80.4 24.8 3.6 REMARK 620 N 1 2 3 4 DBREF1 7E4J A 1 44 UNP A0A045KH53_MYCTX DBREF2 7E4J A A0A045KH53 1 44 DBREF1 7E4J B 1 44 UNP A0A045KH53_MYCTX DBREF2 7E4J B A0A045KH53 1 44 DBREF1 7E4J C 1 44 UNP A0A045KH53_MYCTX DBREF2 7E4J C A0A045KH53 1 44 DBREF1 7E4J D 1 44 UNP A0A045KH53_MYCTX DBREF2 7E4J D A0A045KH53 1 44 SEQRES 1 A 44 MET SER ALA MET VAL GLN ILE ARG ASN VAL PRO ASP GLU SEQRES 2 A 44 LEU LEU HIS GLU LEU LYS ALA ARG ALA ALA ALA GLN ARG SEQRES 3 A 44 MET SER LEU SER ASP PHE LEU LEU ALA ARG LEU ALA GLU SEQRES 4 A 44 ILE ALA GLU GLU PRO SEQRES 1 B 44 MET SER ALA MET VAL GLN ILE ARG ASN VAL PRO ASP GLU SEQRES 2 B 44 LEU LEU HIS GLU LEU LYS ALA ARG ALA ALA ALA GLN ARG SEQRES 3 B 44 MET SER LEU SER ASP PHE LEU LEU ALA ARG LEU ALA GLU SEQRES 4 B 44 ILE ALA GLU GLU PRO SEQRES 1 C 44 MET SER ALA MET VAL GLN ILE ARG ASN VAL PRO ASP GLU SEQRES 2 C 44 LEU LEU HIS GLU LEU LYS ALA ARG ALA ALA ALA GLN ARG SEQRES 3 C 44 MET SER LEU SER ASP PHE LEU LEU ALA ARG LEU ALA GLU SEQRES 4 C 44 ILE ALA GLU GLU PRO SEQRES 1 D 44 MET SER ALA MET VAL GLN ILE ARG ASN VAL PRO ASP GLU SEQRES 2 D 44 LEU LEU HIS GLU LEU LYS ALA ARG ALA ALA ALA GLN ARG SEQRES 3 D 44 MET SER LEU SER ASP PHE LEU LEU ALA ARG LEU ALA GLU SEQRES 4 D 44 ILE ALA GLU GLU PRO HET ZN B 101 1 HETNAM ZN ZINC ION FORMUL 5 ZN ZN 2+ FORMUL 6 HOH *121(H2 O) HELIX 1 AA1 ASP A 12 GLN A 25 1 14 HELIX 2 AA2 SER A 28 GLU A 43 1 16 HELIX 3 AA3 ASP B 12 GLN B 25 1 14 HELIX 4 AA4 SER B 28 GLU B 43 1 16 HELIX 5 AA5 ASP C 12 GLN C 25 1 14 HELIX 6 AA6 SER C 28 GLU C 43 1 16 HELIX 7 AA7 ASP D 12 GLN D 25 1 14 HELIX 8 AA8 SER D 28 GLU D 43 1 16 SHEET 1 AA1 2 SER A 2 PRO A 11 0 SHEET 2 AA1 2 SER C 2 PRO C 11 -1 O ILE C 7 N VAL A 5 SHEET 1 AA2 2 SER B 2 PRO B 11 0 SHEET 2 AA2 2 SER D 2 PRO D 11 -1 O VAL D 5 N ILE B 7 LINK OD1 ASP A 12 ZN ZN B 101 1555 4564 2.20 LINK OD2 ASP A 12 ZN ZN B 101 1555 4564 1.98 LINK NE2 HIS A 16 ZN ZN B 101 1555 4564 2.26 LINK OD1 ASP B 12 ZN ZN B 101 1555 1555 1.88 LINK NE2 HIS B 16 ZN ZN B 101 1555 1555 2.03 CRYST1 34.660 34.660 162.227 90.00 90.00 90.00 P 41 16 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 0.028852 0.000000 0.000000 0.00000 SCALE2 0.000000 0.028852 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006164 0.00000