HEADER HYDROLASE 09-APR-08 2VRN TITLE THE STRUCTURE OF THE STRESS RESPONSE PROTEIN DR1199 FROM DEINOCOCCUS TITLE 2 RADIODURANS: A MEMBER OF THE DJ-1 SUPERFAMILY COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEASE I; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DR1199; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: CYSTEINE 115 MODIFIED TO CYSTEINE SULFENIC ACID (CSO) SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DEINOCOCCUS RADIODURANS; SOURCE 3 ORGANISM_TAXID: 243230; SOURCE 4 STRAIN: R1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS CYSTEINE SULFENIC ACID, DJ-1/THIJ/PFPI SUPERFAMILY, PROTEASE, KEYWDS 2 HYDROLASE, STRESS RESPONSE EXPDTA X-RAY DIFFRACTION AUTHOR E.FIORAVANTI,M.A.DURA,D.LASCOUX,E.MICOSSI,S.MCSWEENEY REVDAT 6 13-DEC-23 2VRN 1 REMARK LINK REVDAT 5 28-FEB-18 2VRN 1 SOURCE AUTHOR JRNL REVDAT 4 11-JUL-12 2VRN 1 REMARK HETATM REVDAT 3 13-JUL-11 2VRN 1 VERSN REVDAT 2 24-FEB-09 2VRN 1 VERSN REVDAT 1 28-OCT-08 2VRN 0 JRNL AUTH E.FIORAVANTI,M.A.DURA,D.LASCOUX,E.MICOSSI,B.FRANZETTI, JRNL AUTH 2 S.MCSWEENEY JRNL TITL STRUCTURE OF THE STRESS RESPONSE PROTEIN DR1199 FROM JRNL TITL 2 DEINOCOCCUS RADIODURANS: A MEMBER OF THE DJ-1 SUPERFAMILY. JRNL REF BIOCHEMISTRY V. 47 11581 2008 JRNL REFN ISSN 1520-4995 JRNL PMID 18850720 JRNL DOI 10.1021/BI800882V REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.94 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 19890 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) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1077 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) : 2.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.21 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1435 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2690 REMARK 3 BIN FREE R VALUE SET COUNT : 72 REMARK 3 BIN FREE R VALUE : 0.3740 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2778 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 172 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) : 22.31 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.90000 REMARK 3 B22 (A**2) : -0.72000 REMARK 3 B33 (A**2) : -0.18000 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): 0.269 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.221 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.176 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.110 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.912 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2868 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3894 ; 1.313 ; 1.982 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 376 ; 6.049 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 116 ;39.330 ;25.603 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 496 ;15.392 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;13.746 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 443 ; 0.087 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2153 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1404 ; 0.202 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1934 ; 0.297 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 163 ; 0.143 ; 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): 15 ; 0.148 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.103 ; 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): 1921 ; 0.435 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2981 ; 0.728 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1087 ; 1.322 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 913 ; 1.913 ; 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 : 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 6 A 54 REMARK 3 ORIGIN FOR THE GROUP (A): 20.8453 2.1718 35.5637 REMARK 3 T TENSOR REMARK 3 T11: 0.1622 T22: 0.1250 REMARK 3 T33: 0.2198 T12: 0.0889 REMARK 3 T13: -0.1886 T23: -0.1234 REMARK 3 L TENSOR REMARK 3 L11: 2.1449 L22: 5.2706 REMARK 3 L33: 3.7842 L12: 0.1460 REMARK 3 L13: 1.4705 L23: 1.1432 REMARK 3 S TENSOR REMARK 3 S11: 0.2817 S12: -0.2167 S13: -0.3026 REMARK 3 S21: 0.9850 S22: 0.4289 S23: -0.7776 REMARK 3 S31: 0.7370 S32: 0.1055 S33: -0.7106 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 55 A 80 REMARK 3 ORIGIN FOR THE GROUP (A): 15.6480 2.3910 36.1677 REMARK 3 T TENSOR REMARK 3 T11: 0.1363 T22: 0.2452 REMARK 3 T33: 0.1496 T12: 0.0389 REMARK 3 T13: -0.1653 T23: 0.0428 REMARK 3 L TENSOR REMARK 3 L11: 2.8796 L22: 12.0410 REMARK 3 L33: 11.0394 L12: -0.5224 REMARK 3 L13: -1.1197 L23: 6.0546 REMARK 3 S TENSOR REMARK 3 S11: 0.2569 S12: -0.2985 S13: -0.2897 REMARK 3 S21: 1.3184 S22: 0.1683 S23: -0.1492 REMARK 3 S31: 1.0529 S32: -0.5679 S33: -0.4252 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 81 A 102 REMARK 3 ORIGIN FOR THE GROUP (A): 11.5674 10.8438 30.4377 REMARK 3 T TENSOR REMARK 3 T11: 0.0522 T22: 0.2142 REMARK 3 T33: 0.1674 T12: -0.0049 REMARK 3 T13: 0.0011 T23: -0.0366 REMARK 3 L TENSOR REMARK 3 L11: 3.3096 L22: 6.1487 REMARK 3 L33: 7.6382 L12: -0.9106 REMARK 3 L13: 0.6304 L23: 2.9471 REMARK 3 S TENSOR REMARK 3 S11: 0.2101 S12: -0.2026 S13: -0.2486 REMARK 3 S21: 0.0333 S22: 0.0988 S23: -0.1300 REMARK 3 S31: -0.1324 S32: -0.3646 S33: -0.3089 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 103 A 140 REMARK 3 ORIGIN FOR THE GROUP (A): 18.8844 18.2658 30.4403 REMARK 3 T TENSOR REMARK 3 T11: 0.0414 T22: 0.1196 REMARK 3 T33: 0.1884 T12: -0.0086 REMARK 3 T13: -0.0062 T23: -0.1062 REMARK 3 L TENSOR REMARK 3 L11: 3.2201 L22: 3.4720 REMARK 3 L33: 4.7544 L12: -0.0407 REMARK 3 L13: 0.5411 L23: 1.5278 REMARK 3 S TENSOR REMARK 3 S11: -0.0403 S12: -0.0230 S13: 0.2255 REMARK 3 S21: 0.0628 S22: 0.2890 S23: -0.4443 REMARK 3 S31: -0.3035 S32: 0.1210 S33: -0.2487 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 141 A 173 REMARK 3 ORIGIN FOR THE GROUP (A): 26.9386 18.3430 28.7021 REMARK 3 T TENSOR REMARK 3 T11: -0.0314 T22: 0.1552 REMARK 3 T33: 0.3641 T12: -0.0367 REMARK 3 T13: 0.0389 T23: -0.2665 REMARK 3 L TENSOR REMARK 3 L11: 3.1974 L22: 2.4893 REMARK 3 L33: 3.8902 L12: -0.0121 REMARK 3 L13: 1.9407 L23: 0.7218 REMARK 3 S TENSOR REMARK 3 S11: -0.1394 S12: 0.2900 S13: 0.3636 REMARK 3 S21: -0.1347 S22: 0.5000 S23: -0.8485 REMARK 3 S31: -0.1323 S32: 0.6743 S33: -0.3606 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 174 A 190 REMARK 3 ORIGIN FOR THE GROUP (A): 26.3447 18.0058 43.3235 REMARK 3 T TENSOR REMARK 3 T11: 0.1295 T22: 0.0700 REMARK 3 T33: 0.2584 T12: 0.0625 REMARK 3 T13: -0.2288 T23: -0.3080 REMARK 3 L TENSOR REMARK 3 L11: 9.8531 L22: 15.0610 REMARK 3 L33: 11.6171 L12: -6.0761 REMARK 3 L13: -2.4250 L23: 5.0174 REMARK 3 S TENSOR REMARK 3 S11: -0.4115 S12: -0.3305 S13: 0.6449 REMARK 3 S21: 1.1079 S22: 1.0330 S23: -1.4303 REMARK 3 S31: 0.2517 S32: 0.5022 S33: -0.6215 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 6 B 54 REMARK 3 ORIGIN FOR THE GROUP (A): 10.5136 4.4711 1.3462 REMARK 3 T TENSOR REMARK 3 T11: 0.3417 T22: 0.2127 REMARK 3 T33: 0.0747 T12: 0.0409 REMARK 3 T13: 0.1106 T23: -0.0639 REMARK 3 L TENSOR REMARK 3 L11: 2.2451 L22: 2.7476 REMARK 3 L33: 4.2788 L12: 0.2676 REMARK 3 L13: 0.6580 L23: 0.0996 REMARK 3 S TENSOR REMARK 3 S11: 0.2213 S12: 0.5810 S13: -0.1263 REMARK 3 S21: -0.6727 S22: 0.1146 S23: -0.3415 REMARK 3 S31: -0.1765 S32: 0.3634 S33: -0.3359 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 55 B 63 REMARK 3 ORIGIN FOR THE GROUP (A): 14.0438 -3.3346 9.7778 REMARK 3 T TENSOR REMARK 3 T11: 0.0817 T22: 0.0049 REMARK 3 T33: 0.1432 T12: 0.0658 REMARK 3 T13: -0.0719 T23: -0.1874 REMARK 3 L TENSOR REMARK 3 L11: 9.1945 L22: 9.1028 REMARK 3 L33: 10.6527 L12: -3.2269 REMARK 3 L13: -1.4084 L23: 3.5035 REMARK 3 S TENSOR REMARK 3 S11: 0.4283 S12: 0.3240 S13: -0.5877 REMARK 3 S21: -0.1637 S22: -0.0056 S23: -0.0534 REMARK 3 S31: 0.3636 S32: 0.5606 S33: -0.4227 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 64 B 93 REMARK 3 ORIGIN FOR THE GROUP (A): 16.4297 11.6119 2.5387 REMARK 3 T TENSOR REMARK 3 T11: 0.3420 T22: 0.1538 REMARK 3 T33: 0.0010 T12: -0.1112 REMARK 3 T13: 0.2280 T23: -0.0360 REMARK 3 L TENSOR REMARK 3 L11: 3.7818 L22: 1.5389 REMARK 3 L33: 6.5801 L12: -0.3090 REMARK 3 L13: 2.7370 L23: 2.4149 REMARK 3 S TENSOR REMARK 3 S11: -0.0064 S12: 0.6087 S13: 0.1895 REMARK 3 S21: -0.8724 S22: 0.1969 S23: -0.5539 REMARK 3 S31: -0.7776 S32: 1.1886 S33: -0.1904 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 94 B 109 REMARK 3 ORIGIN FOR THE GROUP (A): 15.7698 20.6052 1.2796 REMARK 3 T TENSOR REMARK 3 T11: 0.6759 T22: 0.3366 REMARK 3 T33: 0.1827 T12: -0.2774 REMARK 3 T13: 0.3313 T23: 0.1577 REMARK 3 L TENSOR REMARK 3 L11: 17.8292 L22: 20.1535 REMARK 3 L33: 22.3222 L12: -13.1100 REMARK 3 L13: 17.7172 L23: -6.8770 REMARK 3 S TENSOR REMARK 3 S11: -0.7570 S12: 0.1572 S13: 1.0357 REMARK 3 S21: -0.9875 S22: 0.5731 S23: -0.8490 REMARK 3 S31: -1.1467 S32: 0.7808 S33: 0.1839 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 110 B 172 REMARK 3 ORIGIN FOR THE GROUP (A): 4.1146 16.8961 12.5296 REMARK 3 T TENSOR REMARK 3 T11: 0.1886 T22: 0.0672 REMARK 3 T33: 0.0615 T12: 0.0393 REMARK 3 T13: 0.0336 T23: 0.0058 REMARK 3 L TENSOR REMARK 3 L11: 3.4148 L22: 4.4951 REMARK 3 L33: 4.6856 L12: 0.7800 REMARK 3 L13: 1.7107 L23: 2.0923 REMARK 3 S TENSOR REMARK 3 S11: -0.0308 S12: -0.0378 S13: 0.4259 REMARK 3 S21: -0.3728 S22: -0.1093 S23: 0.1201 REMARK 3 S31: -0.4963 S32: -0.0663 S33: 0.1401 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 173 B 190 REMARK 3 ORIGIN FOR THE GROUP (A): 0.4728 18.6602 -2.0935 REMARK 3 T TENSOR REMARK 3 T11: 0.8156 T22: 0.3780 REMARK 3 T33: 0.3070 T12: 0.0932 REMARK 3 T13: -0.1120 T23: 0.0324 REMARK 3 L TENSOR REMARK 3 L11: 14.1309 L22: 23.2712 REMARK 3 L33: 4.8807 L12: 11.4634 REMARK 3 L13: -6.0596 L23: -4.1953 REMARK 3 S TENSOR REMARK 3 S11: -0.1822 S12: 0.4359 S13: 2.0174 REMARK 3 S21: -1.6234 S22: 0.4583 S23: 1.1715 REMARK 3 S31: -1.2989 S32: -0.3338 S33: -0.2761 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. THE SIDE-CHAIN ATOMS WITHOUT VISIBLE ELECTRON DENSITY REMARK 3 AT 1. 0 SIGMA WERE REMOVED FROM THE MODEL. A PEAK TO 6.0 SIGMA REMARK 3 (POSSIBLY AN ION) NEAR RESIDUES A22 AND A59 WAS NOT MODELLED DUE REMARK 3 TO LACK OF COORDINATION. REMARK 4 REMARK 4 2VRN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-APR-08. REMARK 100 THE DEPOSITION ID IS D_1290035906. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.93 REMARK 200 MONOCHROMATOR : DIAMOND (111), GE(220) REMARK 200 OPTICS : TOROIDAL MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20998 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 4.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.52000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1GSI REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM FORMATE PH 5.9, 20% REMARK 280 (W/V) PEG 3350 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 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 SMTRY1 3 -1.000000 0.000000 0.000000 32.91900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.28100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.91900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.28100 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: 2120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.9 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 MET A 1 REMARK 465 THR A 2 REMARK 465 LYS A 3 REMARK 465 ALA A 4 REMARK 465 LYS A 5 REMARK 465 MET B 1 REMARK 465 THR B 2 REMARK 465 LYS B 3 REMARK 465 ALA B 4 REMARK 465 LYS B 5 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 ARG A 63 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 99 CD CE NZ REMARK 470 LYS A 165 CE NZ REMARK 470 LYS A 175 CD CE NZ REMARK 470 ARG A 188 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 190 CG CD CE NZ REMARK 470 GLU B 70 CG CD OE1 OE2 REMARK 470 GLU B 95 CG CD OE1 OE2 REMARK 470 ARG B 188 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 190 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ASP B 103 CG ASP B 103 OD2 0.193 REMARK 500 REMARK 500 REMARK: NULL 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 ASP B 103 CB - CG - OD2 ANGL. DEV. = -11.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 55 -32.63 82.75 REMARK 500 GLN A 59 -135.23 -115.34 REMARK 500 CSO A 115 -107.01 76.20 REMARK 500 ASP B 55 -32.43 74.29 REMARK 500 GLN B 59 -137.42 -106.96 REMARK 500 SER B 69 46.32 -90.86 REMARK 500 GLU B 70 -10.17 -156.00 REMARK 500 CSO B 115 -110.09 72.30 REMARK 500 PRO B 118 -9.30 -55.81 REMARK 500 ASP B 184 94.57 55.69 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 MG A1191 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 179 OE1 REMARK 620 2 GLU A 182 OE2 70.6 REMARK 620 3 HIS A 185 NE2 75.2 59.1 REMARK 620 4 HOH A2073 O 109.3 174.8 115.7 REMARK 620 5 HOH A2085 O 155.2 85.3 87.5 94.0 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1191 DBREF 2VRN A 1 190 UNP Q9RV31 Q9RV31_DEIRA 1 190 DBREF 2VRN B 1 190 UNP Q9RV31 Q9RV31_DEIRA 1 190 SEQADV 2VRN SER A 136 UNP Q9RV31 PRO 136 CONFLICT SEQADV 2VRN SER B 136 UNP Q9RV31 PRO 136 CONFLICT SEQRES 1 A 190 MET THR LYS ALA LYS ASP LEU THR GLY LYS LYS ILE ALA SEQRES 2 A 190 ILE LEU ALA ALA ASP GLY VAL GLU GLU ILE GLU LEU THR SEQRES 3 A 190 SER PRO ARG ALA ALA ILE GLU ALA ALA GLY GLY THR THR SEQRES 4 A 190 GLU LEU ILE SER LEU GLU PRO GLY GLU ILE GLN SER MET SEQRES 5 A 190 LYS GLY ASP ILE GLU PRO GLN GLU LYS TYR ARG VAL ASP SEQRES 6 A 190 HIS VAL VAL SER GLU VAL GLN VAL SER ASP TYR ASP GLY SEQRES 7 A 190 LEU LEU LEU PRO GLY GLY THR VAL ASN PRO ASP LYS LEU SEQRES 8 A 190 ARG LEU GLU GLU GLY ALA MET LYS PHE VAL ARG ASP MET SEQRES 9 A 190 TYR ASP ALA GLY LYS PRO ILE ALA ALA ILE CSO HIS GLY SEQRES 10 A 190 PRO TRP SER LEU SER GLU THR GLY ILE ALA GLN GLY LEU SEQRES 11 A 190 LYS MET THR SER TRP SER SER LEU LYS ARG GLU LEU THR SEQRES 12 A 190 LEU ALA GLY ALA GLN TRP VAL ASP GLU GLU CYS VAL THR SEQRES 13 A 190 ASP LYS GLY VAL VAL THR SER ARG LYS PRO ASP ASP LEU SEQRES 14 A 190 PRO ALA PHE ASN LYS LYS ILE VAL GLU GLU PHE ALA GLU SEQRES 15 A 190 GLY ASP HIS SER SER ARG ARG LYS SEQRES 1 B 190 MET THR LYS ALA LYS ASP LEU THR GLY LYS LYS ILE ALA SEQRES 2 B 190 ILE LEU ALA ALA ASP GLY VAL GLU GLU ILE GLU LEU THR SEQRES 3 B 190 SER PRO ARG ALA ALA ILE GLU ALA ALA GLY GLY THR THR SEQRES 4 B 190 GLU LEU ILE SER LEU GLU PRO GLY GLU ILE GLN SER MET SEQRES 5 B 190 LYS GLY ASP ILE GLU PRO GLN GLU LYS TYR ARG VAL ASP SEQRES 6 B 190 HIS VAL VAL SER GLU VAL GLN VAL SER ASP TYR ASP GLY SEQRES 7 B 190 LEU LEU LEU PRO GLY GLY THR VAL ASN PRO ASP LYS LEU SEQRES 8 B 190 ARG LEU GLU GLU GLY ALA MET LYS PHE VAL ARG ASP MET SEQRES 9 B 190 TYR ASP ALA GLY LYS PRO ILE ALA ALA ILE CSO HIS GLY SEQRES 10 B 190 PRO TRP SER LEU SER GLU THR GLY ILE ALA GLN GLY LEU SEQRES 11 B 190 LYS MET THR SER TRP SER SER LEU LYS ARG GLU LEU THR SEQRES 12 B 190 LEU ALA GLY ALA GLN TRP VAL ASP GLU GLU CYS VAL THR SEQRES 13 B 190 ASP LYS GLY VAL VAL THR SER ARG LYS PRO ASP ASP LEU SEQRES 14 B 190 PRO ALA PHE ASN LYS LYS ILE VAL GLU GLU PHE ALA GLU SEQRES 15 B 190 GLY ASP HIS SER SER ARG ARG LYS MODRES 2VRN CSO A 115 CYS S-HYDROXYCYSTEINE MODRES 2VRN CSO B 115 CYS S-HYDROXYCYSTEINE HET CSO A 115 7 HET CSO B 115 7 HET MG A1191 1 HETNAM CSO S-HYDROXYCYSTEINE HETNAM MG MAGNESIUM ION FORMUL 1 CSO 2(C3 H7 N O3 S) FORMUL 3 MG MG 2+ FORMUL 4 HOH *172(H2 O) HELIX 1 1 GLU A 21 ALA A 35 1 15 HELIX 2 2 SER A 69 VAL A 71 5 3 HELIX 3 3 GLN A 72 TYR A 76 5 5 HELIX 4 4 THR A 85 ARG A 92 1 8 HELIX 5 5 GLU A 94 ALA A 107 1 14 HELIX 6 6 PRO A 118 THR A 124 1 7 HELIX 7 7 TRP A 135 SER A 137 5 3 HELIX 8 8 LEU A 138 ALA A 145 1 8 HELIX 9 9 LYS A 165 ASP A 167 5 3 HELIX 10 10 ASP A 168 GLY A 183 1 16 HELIX 11 11 HIS A 185 ARG A 189 5 5 HELIX 12 12 GLU B 22 ALA B 35 1 14 HELIX 13 13 SER B 69 VAL B 71 5 3 HELIX 14 14 GLN B 72 TYR B 76 5 5 HELIX 15 15 THR B 85 ARG B 92 1 8 HELIX 16 16 GLU B 94 ALA B 107 1 14 HELIX 17 17 PRO B 118 THR B 124 1 7 HELIX 18 18 TRP B 135 SER B 137 5 3 HELIX 19 19 LEU B 138 ALA B 145 1 8 HELIX 20 20 LYS B 165 ASP B 167 5 3 HELIX 21 21 ASP B 168 GLY B 183 1 16 SHEET 1 AA 7 HIS A 66 VAL A 67 0 SHEET 2 AA 7 THR A 38 SER A 43 1 N SER A 43 O HIS A 66 SHEET 3 AA 7 LYS A 11 LEU A 15 1 O ILE A 12 N GLU A 40 SHEET 4 AA 7 GLY A 78 LEU A 81 1 O GLY A 78 N ALA A 13 SHEET 5 AA 7 ILE A 111 ALA A 113 1 O ALA A 112 N LEU A 81 SHEET 6 AA 7 VAL A 160 THR A 162 1 O VAL A 161 N ALA A 113 SHEET 7 AA 7 VAL A 155 ASP A 157 -1 O VAL A 155 N THR A 162 SHEET 1 AB 2 GLU A 48 LYS A 53 0 SHEET 2 AB 2 GLU A 57 ARG A 63 -1 O GLU A 57 N LYS A 53 SHEET 1 AC 2 LYS A 131 MET A 132 0 SHEET 2 AC 2 GLN A 148 TRP A 149 1 O GLN A 148 N MET A 132 SHEET 1 BA 7 HIS B 66 VAL B 67 0 SHEET 2 BA 7 THR B 38 SER B 43 1 N SER B 43 O HIS B 66 SHEET 3 BA 7 LYS B 11 LEU B 15 1 O ILE B 12 N GLU B 40 SHEET 4 BA 7 GLY B 78 LEU B 81 1 O GLY B 78 N ALA B 13 SHEET 5 BA 7 ILE B 111 ALA B 113 1 O ALA B 112 N LEU B 81 SHEET 6 BA 7 VAL B 160 SER B 163 1 O VAL B 161 N ALA B 113 SHEET 7 BA 7 CYS B 154 ASP B 157 -1 O VAL B 155 N THR B 162 SHEET 1 BB 3 VAL B 20 GLU B 21 0 SHEET 2 BB 3 GLU B 48 LYS B 53 1 N MET B 52 O VAL B 20 SHEET 3 BB 3 GLU B 57 ARG B 63 -1 O GLU B 57 N LYS B 53 SHEET 1 BC 2 LYS B 131 MET B 132 0 SHEET 2 BC 2 GLN B 148 TRP B 149 1 O GLN B 148 N MET B 132 LINK C ILE A 114 N CSO A 115 1555 1555 1.33 LINK C CSO A 115 N HIS A 116 1555 1555 1.34 LINK C ILE B 114 N CSO B 115 1555 1555 1.33 LINK C CSO B 115 N HIS B 116 1555 1555 1.34 LINK OE1 GLU A 179 MG MG A1191 1555 1555 2.28 LINK OE2 GLU A 182 MG MG A1191 1555 1555 1.90 LINK NE2 HIS A 185 MG MG A1191 1555 1555 2.86 LINK MG MG A1191 O HOH A2073 1555 1555 2.11 LINK MG MG A1191 O HOH A2085 1555 1555 2.80 SITE 1 AC1 5 GLU A 179 GLU A 182 HIS A 185 HOH A2073 SITE 2 AC1 5 HOH A2085 CRYST1 65.838 88.562 64.088 90.00 90.00 90.00 P 21 21 2 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 0.015189 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011292 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015604 0.00000