HEADER DNA BINDING PROTEIN 05-FEB-12 4DKY TITLE CRYSTAL STRUCTURE ANALYSIS OF N TERMINAL REGION CONTAINING THE TITLE 2 DIMERIZATION DOMAIN AND DNA BINDING DOMAIN OF HU PROTEIN(HISTONE LIKE TITLE 3 PROTEIN-DNA BINDING) FROM MYCOBACTERIUM TUBERCULOSIS [H37RA] COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-BINDING PROTEIN HU HOMOLOG; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: N-TERMINAL BACTERIAL HISTONE-LIKE DOMAIN, UNP RESIDUES 1- COMPND 5 100; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS H37RA; SOURCE 3 ORGANISM_TAXID: 419947; SOURCE 4 GENE: HUPB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET20B KEYWDS NUCLEOID ASSOCIATED PROTEIN, NUCLEOID ARCHITECTURE, HISTONE-LIKE, HU, KEYWDS 2 HU-IHF FOLD, GENOME COMPACTION, GENE REGULATION, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.BHOWMICK,U.A.RAMAGOPAL,S.GHOSH,V.NAGARAJA,S.RAMAKUMAR REVDAT 4 08-NOV-23 4DKY 1 REMARK REVDAT 3 26-JUL-23 4DKY 1 TITLE COMPND SOURCE REMARK REVDAT 3 2 1 DBREF SEQADV LINK REVDAT 2 27-AUG-14 4DKY 1 JRNL REVDAT 1 06-FEB-13 4DKY 0 JRNL AUTH T.BHOWMICK,S.GHOSH,K.DIXIT,V.GANESAN,U.A.RAMAGOPAL,D.DEY, JRNL AUTH 2 S.P.SARMA,S.RAMAKUMAR,V.NAGARAJA JRNL TITL TARGETING MYCOBACTERIUM TUBERCULOSIS NUCLEOID-ASSOCIATED JRNL TITL 2 PROTEIN HU WITH STRUCTURE-BASED INHIBITORS JRNL REF NAT COMMUN V. 5 4124 2014 JRNL REFN ESSN 2041-1723 JRNL PMID 24916461 JRNL DOI 10.1038/NCOMMS5124 REMARK 2 REMARK 2 RESOLUTION. 2.48 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) : 2.48 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.92 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 80.9 REMARK 3 NUMBER OF REFLECTIONS : 6667 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) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 336 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) : 2.48 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 214 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 38.16 REMARK 3 BIN R VALUE (WORKING SET) : 0.2280 REMARK 3 BIN FREE R VALUE SET COUNT : 18 REMARK 3 BIN FREE R VALUE : 0.3130 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1506 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 42 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.09 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -24.93000 REMARK 3 B22 (A**2) : -9.90000 REMARK 3 B33 (A**2) : 34.83000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -3.36000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.191 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.068 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.177 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.309 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.906 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1525 ; 0.026 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1082 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2058 ; 2.390 ; 1.948 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2609 ; 3.844 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 195 ; 7.227 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 67 ;38.065 ;21.642 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 264 ;22.732 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;18.191 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 242 ; 0.133 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1697 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 321 ; 0.007 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL 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 : 0.593 REMARK 3 TWIN DOMAIN : 2 REMARK 3 TWIN OPERATOR : -H, -K, H+L REMARK 3 TWIN FRACTION : 0.407 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 18 REMARK 3 ORIGIN FOR THE GROUP (A): -7.7387 -31.0439 -5.3211 REMARK 3 T TENSOR REMARK 3 T11: 0.2149 T22: 0.1649 REMARK 3 T33: 0.2361 T12: -0.0426 REMARK 3 T13: 0.1638 T23: 0.0096 REMARK 3 L TENSOR REMARK 3 L11: 2.2215 L22: 2.2639 REMARK 3 L33: 3.2745 L12: -1.9222 REMARK 3 L13: 1.8877 L23: -2.6349 REMARK 3 S TENSOR REMARK 3 S11: -0.1616 S12: 0.1478 S13: 0.2105 REMARK 3 S21: -0.0152 S22: 0.0327 S23: -0.1576 REMARK 3 S31: 0.1143 S32: -0.1359 S33: 0.1289 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 19 A 40 REMARK 3 ORIGIN FOR THE GROUP (A): -1.0637 -25.7445 8.1226 REMARK 3 T TENSOR REMARK 3 T11: 0.2605 T22: 0.1732 REMARK 3 T33: 0.1912 T12: -0.0339 REMARK 3 T13: 0.1273 T23: 0.0079 REMARK 3 L TENSOR REMARK 3 L11: 1.5792 L22: 4.4186 REMARK 3 L33: 6.0777 L12: 1.1631 REMARK 3 L13: 2.4023 L23: 4.7041 REMARK 3 S TENSOR REMARK 3 S11: 0.0415 S12: -0.1945 S13: -0.2864 REMARK 3 S21: 0.5563 S22: 0.2129 S23: -0.0143 REMARK 3 S31: 0.4653 S32: -0.0119 S33: -0.2544 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 41 A 54 REMARK 3 ORIGIN FOR THE GROUP (A): 6.1285 -13.7737 4.3846 REMARK 3 T TENSOR REMARK 3 T11: 0.1924 T22: 0.2166 REMARK 3 T33: 0.2747 T12: 0.0054 REMARK 3 T13: 0.1528 T23: 0.0679 REMARK 3 L TENSOR REMARK 3 L11: 5.5138 L22: 2.9677 REMARK 3 L33: 0.5501 L12: -0.4037 REMARK 3 L13: 1.6404 L23: -0.5169 REMARK 3 S TENSOR REMARK 3 S11: 0.1279 S12: -0.0958 S13: -0.0984 REMARK 3 S21: 0.2136 S22: -0.1094 S23: -0.4129 REMARK 3 S31: -0.0102 S32: -0.0509 S33: -0.0185 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 55 A 73 REMARK 3 ORIGIN FOR THE GROUP (A): -9.2122 4.6653 13.7469 REMARK 3 T TENSOR REMARK 3 T11: 0.1683 T22: 0.1754 REMARK 3 T33: 0.2612 T12: 0.0033 REMARK 3 T13: 0.1288 T23: -0.0279 REMARK 3 L TENSOR REMARK 3 L11: 22.1432 L22: 6.6963 REMARK 3 L33: 2.0502 L12: -7.1903 REMARK 3 L13: 5.4691 L23: -0.0379 REMARK 3 S TENSOR REMARK 3 S11: -0.6065 S12: -0.2910 S13: 1.1725 REMARK 3 S21: 0.4167 S22: 0.1093 S23: -0.0370 REMARK 3 S31: -0.0491 S32: -0.0957 S33: 0.4972 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 74 A 90 REMARK 3 ORIGIN FOR THE GROUP (A): 4.2447 -11.7673 -3.0169 REMARK 3 T TENSOR REMARK 3 T11: 0.2099 T22: 0.1911 REMARK 3 T33: 0.1247 T12: 0.0321 REMARK 3 T13: 0.1384 T23: 0.0113 REMARK 3 L TENSOR REMARK 3 L11: 0.6101 L22: 1.2591 REMARK 3 L33: 15.4484 L12: 0.6336 REMARK 3 L13: -1.7549 L23: 0.6581 REMARK 3 S TENSOR REMARK 3 S11: -0.0416 S12: -0.0342 S13: 0.0111 REMARK 3 S21: -0.1653 S22: 0.0514 S23: 0.0227 REMARK 3 S31: -0.4196 S32: 0.2716 S33: -0.0097 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 91 A 97 REMARK 3 ORIGIN FOR THE GROUP (A): 5.9849 -18.4504 -18.6728 REMARK 3 T TENSOR REMARK 3 T11: 0.9867 T22: 0.3150 REMARK 3 T33: 0.3354 T12: -0.2501 REMARK 3 T13: -0.0656 T23: 0.0458 REMARK 3 L TENSOR REMARK 3 L11: 14.6097 L22: 21.5462 REMARK 3 L33: 45.5259 L12: -17.7185 REMARK 3 L13: -25.7763 L23: 31.3137 REMARK 3 S TENSOR REMARK 3 S11: 0.0904 S12: 1.1552 S13: -1.1206 REMARK 3 S21: -0.2283 S22: -1.7494 S23: 1.2792 REMARK 3 S31: -0.4272 S32: -2.1323 S33: 1.6590 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 1 B 17 REMARK 3 ORIGIN FOR THE GROUP (A): -20.2310 -6.1183 -5.6180 REMARK 3 T TENSOR REMARK 3 T11: 0.1855 T22: 0.1568 REMARK 3 T33: 0.1570 T12: 0.0310 REMARK 3 T13: 0.1142 T23: 0.0271 REMARK 3 L TENSOR REMARK 3 L11: 2.0499 L22: 6.8212 REMARK 3 L33: 0.8678 L12: 0.9966 REMARK 3 L13: -0.7703 L23: -2.2872 REMARK 3 S TENSOR REMARK 3 S11: -0.0103 S12: -0.1995 S13: 0.0240 REMARK 3 S21: -0.1194 S22: -0.0513 S23: -0.2703 REMARK 3 S31: 0.0274 S32: 0.0497 S33: 0.0616 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 18 B 40 REMARK 3 ORIGIN FOR THE GROUP (A): -25.7971 -10.2552 7.3279 REMARK 3 T TENSOR REMARK 3 T11: 0.2441 T22: 0.1507 REMARK 3 T33: 0.1442 T12: 0.0029 REMARK 3 T13: 0.1258 T23: -0.0317 REMARK 3 L TENSOR REMARK 3 L11: 2.9326 L22: 8.4206 REMARK 3 L33: 2.5444 L12: 3.3924 REMARK 3 L13: -1.2187 L23: -3.2088 REMARK 3 S TENSOR REMARK 3 S11: 0.3112 S12: -0.3113 S13: 0.0656 REMARK 3 S21: 0.7389 S22: -0.2781 S23: -0.1851 REMARK 3 S31: -0.3860 S32: 0.0902 S33: -0.0331 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 41 B 54 REMARK 3 ORIGIN FOR THE GROUP (A): -33.6408 -22.9006 4.2965 REMARK 3 T TENSOR REMARK 3 T11: 0.1656 T22: 0.1719 REMARK 3 T33: 0.1410 T12: 0.0583 REMARK 3 T13: 0.1040 T23: -0.0139 REMARK 3 L TENSOR REMARK 3 L11: 2.0701 L22: 11.1903 REMARK 3 L33: 3.1735 L12: -2.2977 REMARK 3 L13: 1.6446 L23: -5.3304 REMARK 3 S TENSOR REMARK 3 S11: 0.1613 S12: 0.0609 S13: -0.1806 REMARK 3 S21: -0.2084 S22: 0.0031 S23: 0.3476 REMARK 3 S31: 0.1590 S32: 0.0766 S33: -0.1644 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 55 B 72 REMARK 3 ORIGIN FOR THE GROUP (A): -18.0105 -41.7328 13.4924 REMARK 3 T TENSOR REMARK 3 T11: 0.6278 T22: 0.3282 REMARK 3 T33: 0.2945 T12: 0.1411 REMARK 3 T13: 0.0338 T23: -0.1381 REMARK 3 L TENSOR REMARK 3 L11: 1.8082 L22: 11.1063 REMARK 3 L33: 0.8693 L12: -0.7433 REMARK 3 L13: -1.2493 L23: 0.7293 REMARK 3 S TENSOR REMARK 3 S11: -1.0009 S12: -0.3548 S13: 0.1645 REMARK 3 S21: 0.1237 S22: 1.0888 S23: -0.3649 REMARK 3 S31: 0.7027 S32: 0.2489 S33: -0.0879 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 73 B 91 REMARK 3 ORIGIN FOR THE GROUP (A): -31.5757 -25.6393 -2.2711 REMARK 3 T TENSOR REMARK 3 T11: 0.2360 T22: 0.2251 REMARK 3 T33: 0.1702 T12: 0.0344 REMARK 3 T13: 0.1445 T23: -0.0028 REMARK 3 L TENSOR REMARK 3 L11: 0.0417 L22: 1.1775 REMARK 3 L33: 0.9931 L12: -0.1094 REMARK 3 L13: -0.0838 L23: 1.0767 REMARK 3 S TENSOR REMARK 3 S11: -0.0161 S12: -0.0643 S13: -0.0459 REMARK 3 S21: -0.2240 S22: -0.0646 S23: 0.0973 REMARK 3 S31: -0.2293 S32: -0.1049 S33: 0.0807 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 92 B 104 REMARK 3 ORIGIN FOR THE GROUP (A): -30.9366 -19.4688 -20.6017 REMARK 3 T TENSOR REMARK 3 T11: 0.4832 T22: 0.0168 REMARK 3 T33: 0.2216 T12: 0.0818 REMARK 3 T13: 0.0080 T23: -0.0243 REMARK 3 L TENSOR REMARK 3 L11: 28.2178 L22: 3.5348 REMARK 3 L33: 11.9398 L12: 4.6010 REMARK 3 L13: -0.5199 L23: 5.6787 REMARK 3 S TENSOR REMARK 3 S11: -1.0160 S12: -0.1133 S13: -0.3925 REMARK 3 S21: -0.8019 S22: -0.2574 S23: 0.5777 REMARK 3 S31: -1.3342 S32: -0.3825 S33: 1.2734 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 4DKY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1000070459. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-OCT-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 (CRYOGENICALLY COOLED) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8546 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.478 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 81.3 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.57500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.3.0 REMARK 200 STARTING MODEL: PDB ENTRY 3C4I REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL, PH 6.7, 2.5M SODIUM REMARK 280 FORMATE, 10MM MNCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 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: 4470 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -51.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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: 4490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -51.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 -55.11500 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 GLU A 98 REMARK 465 GLY A 99 REMARK 465 PRO A 100 REMARK 465 HIS A 101 REMARK 465 HIS A 102 REMARK 465 HIS A 103 REMARK 465 HIS A 104 REMARK 465 HIS A 105 REMARK 465 HIS A 106 REMARK 465 GLY B 99 REMARK 465 PRO B 100 REMARK 465 HIS B 101 REMARK 465 HIS B 105 REMARK 465 HIS B 106 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 HIS B 102 CG ND1 CD2 CE1 NE2 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 PHE A 47 -77.74 -127.27 REMARK 500 PHE B 47 -66.99 -106.43 REMARK 500 HIS B 103 70.96 -117.97 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 MN B 201 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 98 OE1 REMARK 620 2 GLU B 98 OE2 60.0 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3C4I RELATED DB: PDB DBREF 4DKY A 1 100 UNP A5U6Z7 A5U6Z7_MYCTA 1 100 DBREF 4DKY B 1 100 UNP A5U6Z7 A5U6Z7_MYCTA 1 100 SEQADV 4DKY HIS A 101 UNP A5U6Z7 EXPRESSION TAG SEQADV 4DKY HIS A 102 UNP A5U6Z7 EXPRESSION TAG SEQADV 4DKY HIS A 103 UNP A5U6Z7 EXPRESSION TAG SEQADV 4DKY HIS A 104 UNP A5U6Z7 EXPRESSION TAG SEQADV 4DKY HIS A 105 UNP A5U6Z7 EXPRESSION TAG SEQADV 4DKY HIS A 106 UNP A5U6Z7 EXPRESSION TAG SEQADV 4DKY HIS B 101 UNP A5U6Z7 EXPRESSION TAG SEQADV 4DKY HIS B 102 UNP A5U6Z7 EXPRESSION TAG SEQADV 4DKY HIS B 103 UNP A5U6Z7 EXPRESSION TAG SEQADV 4DKY HIS B 104 UNP A5U6Z7 EXPRESSION TAG SEQADV 4DKY HIS B 105 UNP A5U6Z7 EXPRESSION TAG SEQADV 4DKY HIS B 106 UNP A5U6Z7 EXPRESSION TAG SEQRES 1 A 106 MET ASN LYS ALA GLU LEU ILE ASP VAL LEU THR GLN LYS SEQRES 2 A 106 LEU GLY SER ASP ARG ARG GLN ALA THR ALA ALA VAL GLU SEQRES 3 A 106 ASN VAL VAL ASP THR ILE VAL ARG ALA VAL HIS LYS GLY SEQRES 4 A 106 ASP SER VAL THR ILE THR GLY PHE GLY VAL PHE GLU GLN SEQRES 5 A 106 ARG ARG ARG ALA ALA ARG VAL ALA ARG ASN PRO ARG THR SEQRES 6 A 106 GLY GLU THR VAL LYS VAL LYS PRO THR SER VAL PRO ALA SEQRES 7 A 106 PHE ARG PRO GLY ALA GLN PHE LYS ALA VAL VAL SER GLY SEQRES 8 A 106 ALA GLN ARG LEU PRO ALA GLU GLY PRO HIS HIS HIS HIS SEQRES 9 A 106 HIS HIS SEQRES 1 B 106 MET ASN LYS ALA GLU LEU ILE ASP VAL LEU THR GLN LYS SEQRES 2 B 106 LEU GLY SER ASP ARG ARG GLN ALA THR ALA ALA VAL GLU SEQRES 3 B 106 ASN VAL VAL ASP THR ILE VAL ARG ALA VAL HIS LYS GLY SEQRES 4 B 106 ASP SER VAL THR ILE THR GLY PHE GLY VAL PHE GLU GLN SEQRES 5 B 106 ARG ARG ARG ALA ALA ARG VAL ALA ARG ASN PRO ARG THR SEQRES 6 B 106 GLY GLU THR VAL LYS VAL LYS PRO THR SER VAL PRO ALA SEQRES 7 B 106 PHE ARG PRO GLY ALA GLN PHE LYS ALA VAL VAL SER GLY SEQRES 8 B 106 ALA GLN ARG LEU PRO ALA GLU GLY PRO HIS HIS HIS HIS SEQRES 9 B 106 HIS HIS HET MN A 201 1 HET MN B 201 1 HETNAM MN MANGANESE (II) ION FORMUL 3 MN 2(MN 2+) FORMUL 5 HOH *42(H2 O) HELIX 1 1 ASN A 2 GLY A 15 1 14 HELIX 2 2 ASP A 17 LYS A 38 1 22 HELIX 3 3 GLY A 82 SER A 90 1 9 HELIX 4 4 ASN B 2 GLY B 15 1 14 HELIX 5 5 ASP B 17 LYS B 38 1 22 HELIX 6 6 GLY B 82 SER B 90 1 9 SHEET 1 A 3 VAL A 42 ILE A 44 0 SHEET 2 A 3 GLY A 48 ARG A 55 -1 O PHE A 50 N VAL A 42 SHEET 3 A 3 THR A 74 PRO A 81 -1 O VAL A 76 N ARG A 53 SHEET 1 B 2 ARG A 58 ARG A 61 0 SHEET 2 B 2 THR A 68 VAL A 71 -1 O VAL A 69 N ALA A 60 SHEET 1 C 3 VAL B 42 ILE B 44 0 SHEET 2 C 3 GLY B 48 ARG B 55 -1 O GLY B 48 N ILE B 44 SHEET 3 C 3 THR B 74 PRO B 81 -1 O VAL B 76 N ARG B 53 SHEET 1 D 2 ARG B 58 ARG B 61 0 SHEET 2 D 2 THR B 68 VAL B 71 -1 O VAL B 69 N ALA B 60 LINK MN MN A 201 O HOH A 322 1555 1555 2.36 LINK OE1 GLU B 98 MN MN B 201 1555 1555 2.14 LINK OE2 GLU B 98 MN MN B 201 1555 1555 2.32 SITE 1 AC1 2 ARG A 94 HOH A 322 SITE 1 AC2 3 ARG B 94 GLU B 98 HIS B 104 CRYST1 55.115 37.052 64.854 90.00 115.29 90.00 P 1 2 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.018144 0.000000 0.008573 0.00000 SCALE2 0.000000 0.026989 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017054 0.00000