HEADER TRANSFERASE 05-APR-10 2XB4 TITLE CRYSTAL STRUCTURES OF ZINC CONTAINING ADENYLATE KINASE FROM TITLE 2 DESULFOVIBRIO GIGAS COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADENYLATE KINASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.4.3 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DESULFOVIBRIO GIGAS; SOURCE 3 ORGANISM_TAXID: 879 KEYWDS ATP-BINDING, NUCLEOTIDE-BINDING, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.MUKHOPADHYAY,A.V.KLADOVA,O.Y.GAVEL,J.J.CALVETE,V.L.SHNYROV,I.MOURA, AUTHOR 2 J.J.G.MOURA,S.A.BURSAKOV,M.J.ROMAO,J.TRINCAO REVDAT 3 08-MAY-24 2XB4 1 REMARK LINK REVDAT 2 21-SEP-11 2XB4 1 JRNL REMARK VERSN REVDAT 1 22-SEP-10 2XB4 0 JRNL AUTH A.MUKHOPADHYAY,A.V.KLADOVA,S.A.BURSAKOV,O.Y.GAVEL, JRNL AUTH 2 J.J.CALVETE,V.L.SHNYROV,I.MOURA,J.J.G.MOURA,M.J.ROMAO, JRNL AUTH 3 J.TRINCAO JRNL TITL CRYSTAL STRUCTURE OF THE ZINC-, COBALT-, AND IRON-CONTAINING JRNL TITL 2 ADENYLATE KINASE FROM DESULFOVIBRIO GIGAS: A NOVEL JRNL TITL 3 METAL-CONTAINING ADENYLATE KINASE FROM GRAM-NEGATIVE JRNL TITL 4 BACTERIA. JRNL REF J.BIOL.INORG.CHEM. V. 16 51 2011 JRNL REFN ISSN 0949-8257 JRNL PMID 20821240 JRNL DOI 10.1007/S00775-010-0700-8 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.92 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 31474 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) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1671 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2185 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.46 REMARK 3 BIN R VALUE (WORKING SET) : 0.3380 REMARK 3 BIN FREE R VALUE SET COUNT : 105 REMARK 3 BIN FREE R VALUE : 0.3670 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1718 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 320 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.13000 REMARK 3 B22 (A**2) : -0.08000 REMARK 3 B33 (A**2) : -0.05000 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): 0.097 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.099 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.074 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.375 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1767 ; 0.028 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2381 ; 2.214 ; 1.975 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 225 ; 5.814 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 83 ;34.751 ;25.060 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 314 ;16.215 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;22.409 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 259 ; 0.207 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1347 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 1102 ; 1.276 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1760 ; 2.081 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 665 ; 3.865 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 619 ; 6.289 ; 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 : 10 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 30 REMARK 3 ORIGIN FOR THE GROUP (A): 21.0230 23.3037 16.9859 REMARK 3 T TENSOR REMARK 3 T11: 0.0991 T22: 0.0547 REMARK 3 T33: 0.0951 T12: -0.0356 REMARK 3 T13: 0.0319 T23: -0.0086 REMARK 3 L TENSOR REMARK 3 L11: 2.1724 L22: 0.8486 REMARK 3 L33: 2.4963 L12: -0.2145 REMARK 3 L13: 1.4777 L23: 0.7057 REMARK 3 S TENSOR REMARK 3 S11: -0.0834 S12: 0.2194 S13: 0.1279 REMARK 3 S21: -0.1051 S22: 0.0196 S23: -0.1120 REMARK 3 S31: -0.3443 S32: 0.1978 S33: 0.0638 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 31 A 41 REMARK 3 ORIGIN FOR THE GROUP (A): 31.8169 9.8561 23.5330 REMARK 3 T TENSOR REMARK 3 T11: 0.1225 T22: 0.0478 REMARK 3 T33: 0.0224 T12: 0.0284 REMARK 3 T13: -0.0071 T23: -0.0149 REMARK 3 L TENSOR REMARK 3 L11: 9.8447 L22: 9.1505 REMARK 3 L33: 7.2526 L12: -6.5263 REMARK 3 L13: 0.1115 L23: -1.2546 REMARK 3 S TENSOR REMARK 3 S11: 0.6290 S12: 0.4527 S13: 0.1075 REMARK 3 S21: -0.6223 S22: -0.4053 S23: -0.0460 REMARK 3 S31: 0.4731 S32: 0.0614 S33: -0.2237 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 42 A 69 REMARK 3 ORIGIN FOR THE GROUP (A): 29.9661 5.1335 31.6639 REMARK 3 T TENSOR REMARK 3 T11: 0.0541 T22: 0.0743 REMARK 3 T33: 0.0504 T12: 0.0110 REMARK 3 T13: -0.0087 T23: -0.0131 REMARK 3 L TENSOR REMARK 3 L11: 0.8041 L22: 4.1693 REMARK 3 L33: 1.0673 L12: 0.4185 REMARK 3 L13: 0.5796 L23: 0.5093 REMARK 3 S TENSOR REMARK 3 S11: 0.0374 S12: -0.1652 S13: -0.0216 REMARK 3 S21: 0.1299 S22: 0.0082 S23: 0.1193 REMARK 3 S31: 0.0826 S32: 0.0348 S33: -0.0456 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 70 A 85 REMARK 3 ORIGIN FOR THE GROUP (A): 28.8136 21.2317 25.4687 REMARK 3 T TENSOR REMARK 3 T11: 0.0555 T22: 0.0870 REMARK 3 T33: 0.0816 T12: -0.0437 REMARK 3 T13: 0.0126 T23: -0.0467 REMARK 3 L TENSOR REMARK 3 L11: 2.5720 L22: 3.4029 REMARK 3 L33: 3.3259 L12: -0.5138 REMARK 3 L13: 0.6502 L23: -1.5895 REMARK 3 S TENSOR REMARK 3 S11: -0.0270 S12: 0.0233 S13: 0.1943 REMARK 3 S21: 0.1636 S22: -0.0177 S23: -0.3166 REMARK 3 S31: -0.1484 S32: 0.3898 S33: 0.0447 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 86 A 104 REMARK 3 ORIGIN FOR THE GROUP (A): 20.4258 17.8567 34.6811 REMARK 3 T TENSOR REMARK 3 T11: 0.1748 T22: 0.0897 REMARK 3 T33: 0.0715 T12: -0.0080 REMARK 3 T13: 0.0103 T23: -0.0414 REMARK 3 L TENSOR REMARK 3 L11: 4.5842 L22: 5.6075 REMARK 3 L33: 2.7055 L12: 2.9672 REMARK 3 L13: 3.1215 L23: 3.0231 REMARK 3 S TENSOR REMARK 3 S11: -0.0576 S12: -0.1896 S13: 0.0498 REMARK 3 S21: 0.2700 S22: 0.0842 S23: -0.1302 REMARK 3 S31: -0.1640 S32: -0.0163 S33: -0.0266 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 105 A 119 REMARK 3 ORIGIN FOR THE GROUP (A): 10.7550 21.4588 20.3372 REMARK 3 T TENSOR REMARK 3 T11: 0.0682 T22: 0.0389 REMARK 3 T33: 0.0747 T12: -0.0066 REMARK 3 T13: 0.0306 T23: 0.0169 REMARK 3 L TENSOR REMARK 3 L11: 2.7531 L22: 1.3850 REMARK 3 L33: 2.1496 L12: 0.1362 REMARK 3 L13: 0.6247 L23: 0.6975 REMARK 3 S TENSOR REMARK 3 S11: 0.0068 S12: -0.0884 S13: 0.1196 REMARK 3 S21: 0.0643 S22: -0.0373 S23: 0.1256 REMARK 3 S31: -0.1721 S32: -0.1597 S33: 0.0304 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 120 A 147 REMARK 3 ORIGIN FOR THE GROUP (A): 10.4583 13.2662 -0.6703 REMARK 3 T TENSOR REMARK 3 T11: 0.0254 T22: 0.0937 REMARK 3 T33: 0.0693 T12: -0.0037 REMARK 3 T13: -0.0051 T23: 0.0236 REMARK 3 L TENSOR REMARK 3 L11: 1.9063 L22: 1.1469 REMARK 3 L33: 4.4963 L12: 0.8082 REMARK 3 L13: -1.8940 L23: -0.2921 REMARK 3 S TENSOR REMARK 3 S11: 0.0285 S12: 0.2152 S13: 0.1375 REMARK 3 S21: 0.0147 S22: 0.0225 S23: 0.1156 REMARK 3 S31: 0.0753 S32: -0.2343 S33: -0.0510 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 148 A 170 REMARK 3 ORIGIN FOR THE GROUP (A): 11.6994 7.7966 -0.6102 REMARK 3 T TENSOR REMARK 3 T11: 0.0388 T22: 0.0808 REMARK 3 T33: 0.0418 T12: -0.0158 REMARK 3 T13: 0.0023 T23: -0.0051 REMARK 3 L TENSOR REMARK 3 L11: 0.9501 L22: 1.9802 REMARK 3 L33: 5.5766 L12: 0.5907 REMARK 3 L13: -1.2044 L23: -1.6847 REMARK 3 S TENSOR REMARK 3 S11: -0.0299 S12: 0.1940 S13: 0.0459 REMARK 3 S21: -0.0840 S22: 0.1103 S23: 0.1347 REMARK 3 S31: 0.4161 S32: -0.2445 S33: -0.0804 REMARK 3 REMARK 3 TLS GROUP : 9 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 171 A 208 REMARK 3 ORIGIN FOR THE GROUP (A): 9.5786 18.8483 25.6991 REMARK 3 T TENSOR REMARK 3 T11: 0.0434 T22: 0.0679 REMARK 3 T33: 0.0831 T12: 0.0155 REMARK 3 T13: 0.0451 T23: -0.0075 REMARK 3 L TENSOR REMARK 3 L11: 1.4539 L22: 3.6592 REMARK 3 L33: 2.0126 L12: 0.7088 REMARK 3 L13: 0.3565 L23: 0.8940 REMARK 3 S TENSOR REMARK 3 S11: -0.0578 S12: -0.0427 S13: 0.1409 REMARK 3 S21: 0.0093 S22: 0.0801 S23: 0.1036 REMARK 3 S31: -0.0995 S32: -0.1160 S33: -0.0222 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 : A 209 A 223 REMARK 3 ORIGIN FOR THE GROUP (A): 13.6298 31.1909 11.9383 REMARK 3 T TENSOR REMARK 3 T11: 0.4561 T22: 0.3251 REMARK 3 T33: 0.3001 T12: -0.2175 REMARK 3 T13: 0.0304 T23: 0.1596 REMARK 3 L TENSOR REMARK 3 L11: 7.0576 L22: 17.2890 REMARK 3 L33: 40.8067 L12: -0.3869 REMARK 3 L13: 5.7253 L23: 14.1799 REMARK 3 S TENSOR REMARK 3 S11: -0.8230 S12: 0.8248 S13: 0.6887 REMARK 3 S21: -1.7867 S22: 0.7800 S23: -0.2496 REMARK 3 S31: -2.7718 S32: 0.1337 S33: 0.0431 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B REMARK 3 FACTORS. REMARK 4 REMARK 4 2XB4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-APR-10. REMARK 100 THE DEPOSITION ID IS D_1290043544. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 6.5 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) : 1.7266 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31474 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 23.190 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 0.34000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: AUTOSHARP REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M TARTRATE NA/K, 0.1 M MES (PH REMARK 280 6.5) AND 20% PEG 2K OR 8K (THE PROTEIN:WELL SOLUTION RATIO IN REMARK 280 THE DROP WAS 1:1, 1:2 OR 1:3 WITH THE FINAL DROP VOLUME OF 4, 6 REMARK 280 OR 8 MICRO LITRE) REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 19.69500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 59.72000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 74.79500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 19.69500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 59.72000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 74.79500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 19.69500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 59.72000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 74.79500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 19.69500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 59.72000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 74.79500 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 39410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.4 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 39.39000 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 BIOMT1 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 39.39000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 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 A 101 CG CD OE1 OE2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 48 N CD CE REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 2086 O HOH A 2087 1.75 REMARK 500 O HOH A 2129 O HOH A 2241 2.03 REMARK 500 OE2 GLU A 44 O HOH A 2094 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 GLU A 44 CG GLU A 44 CD 0.103 REMARK 500 LYS A 48 N LYS A 48 CA -0.153 REMARK 500 LYS A 48 CE LYS A 48 NZ -0.465 REMARK 500 GLU A 117 CG GLU A 117 CD 0.090 REMARK 500 ASP A 142 CB ASP A 142 CG 0.134 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 LYS A 48 N - CA - CB ANGL. DEV. = 12.3 DEGREES REMARK 500 LYS A 48 CD - CE - NZ ANGL. DEV. = -19.0 DEGREES REMARK 500 ARG A 55 CG - CD - NE ANGL. DEV. = -16.1 DEGREES REMARK 500 ARG A 55 CD - NE - CZ ANGL. DEV. = 8.9 DEGREES REMARK 500 ARG A 55 NE - CZ - NH1 ANGL. DEV. = 7.4 DEGREES REMARK 500 ARG A 55 NE - CZ - NH2 ANGL. DEV. = -10.3 DEGREES REMARK 500 ASP A 62 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 142 CB - CG - OD2 ANGL. DEV. = 8.3 DEGREES REMARK 500 ARG A 152 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 173 NE - CZ - NH1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG A 173 NE - CZ - NH2 ANGL. DEV. = -5.1 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 182 19.69 -150.94 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 ZN A1224 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 129 SG REMARK 620 2 HIS A 135 ND1 119.5 REMARK 620 3 CYS A 151 SG 108.8 108.6 REMARK 620 4 CYS A 154 SG 97.4 106.6 115.9 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 ZN A 1224 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SRT A 1225 DBREF 2XB4 A 1 223 UNP C7U112 C7U112_DESGI 1 223 SEQADV 2XB4 ASP A 142 UNP C7U112 GLU 142 CONFLICT SEQRES 1 A 223 MET ASN ILE LEU ILE PHE GLY PRO ASN GLY SER GLY LYS SEQRES 2 A 223 GLY THR GLN GLY ASN LEU VAL LYS ASP LYS TYR SER LEU SEQRES 3 A 223 ALA HIS ILE GLU SER GLY GLY ILE PHE ARG GLU HIS ILE SEQRES 4 A 223 GLY GLY GLY THR GLU LEU GLY LYS LYS ALA LYS GLU PHE SEQRES 5 A 223 ILE ASP ARG GLY ASP LEU VAL PRO ASP ASP ILE THR ILE SEQRES 6 A 223 PRO MET VAL LEU GLU THR LEU GLU SER LYS GLY LYS ASP SEQRES 7 A 223 GLY TRP LEU LEU ASP GLY PHE PRO ARG ASN THR VAL GLN SEQRES 8 A 223 ALA GLN LYS LEU PHE GLU ALA LEU GLN GLU LYS GLY MET SEQRES 9 A 223 LYS ILE ASN PHE VAL ILE GLU ILE LEU LEU PRO ARG GLU SEQRES 10 A 223 VAL ALA LYS ASN ARG ILE MET GLY ARG ARG ILE CYS LYS SEQRES 11 A 223 ASN ASN PRO ASN HIS PRO ASN ASN ILE PHE ILE ASP ALA SEQRES 12 A 223 ILE LYS PRO ASN GLY ASP VAL CYS ARG VAL CYS GLY GLY SEQRES 13 A 223 ALA LEU SER ALA ARG ALA ASP ASP GLN ASP GLU GLY ALA SEQRES 14 A 223 ILE ASN LYS ARG HIS ASP ILE TYR TYR ASN THR VAL ASP SEQRES 15 A 223 GLY THR LEU ALA ALA ALA TYR TYR TYR LYS ASN MET ALA SEQRES 16 A 223 ALA LYS GLU GLY PHE VAL TYR ILE GLU LEU ASP GLY GLU SEQRES 17 A 223 GLY SER ILE ASP SER ILE LYS ASP THR LEU LEU ALA GLN SEQRES 18 A 223 LEU ALA HET ZN A1224 1 HET SRT A1225 10 HETNAM ZN ZINC ION HETNAM SRT S,R MESO-TARTARIC ACID FORMUL 2 ZN ZN 2+ FORMUL 3 SRT C4 H6 O6 FORMUL 4 HOH *320(H2 O) HELIX 1 1 GLY A 12 SER A 25 1 14 HELIX 2 2 SER A 31 ILE A 39 1 9 HELIX 3 3 THR A 43 ASP A 54 1 12 HELIX 4 4 PRO A 60 GLY A 76 1 17 HELIX 5 5 ASN A 88 LYS A 102 1 15 HELIX 6 6 PRO A 115 GLY A 125 1 11 HELIX 7 7 ILE A 141 LYS A 145 5 5 HELIX 8 8 ARG A 161 GLN A 165 5 5 HELIX 9 9 ASP A 166 TYR A 178 1 13 HELIX 10 10 GLY A 183 ASN A 193 1 11 HELIX 11 11 MET A 194 GLY A 199 1 6 HELIX 12 12 SER A 210 ALA A 223 1 14 SHEET 1 AA 5 ALA A 27 GLU A 30 0 SHEET 2 AA 5 TRP A 80 ASP A 83 1 O LEU A 81 N ILE A 29 SHEET 3 AA 5 ASN A 2 PHE A 6 1 O ILE A 3 N LEU A 82 SHEET 4 AA 5 PHE A 108 LEU A 113 1 O PHE A 108 N LEU A 4 SHEET 5 AA 5 VAL A 201 ASP A 206 1 O VAL A 201 N VAL A 109 SHEET 1 AB 2 ILE A 128 CYS A 129 0 SHEET 2 AB 2 LEU A 158 SER A 159 -1 O SER A 159 N ILE A 128 LINK SG CYS A 129 ZN ZN A1224 1555 1555 2.32 LINK ND1 HIS A 135 ZN ZN A1224 1555 1555 2.03 LINK SG CYS A 151 ZN ZN A1224 1555 1555 2.34 LINK SG CYS A 154 ZN ZN A1224 1555 1555 2.35 CISPEP 1 PHE A 85 PRO A 86 0 7.68 SITE 1 AC1 4 CYS A 129 HIS A 135 CYS A 151 CYS A 154 SITE 1 AC2 14 PRO A 8 ASN A 9 GLY A 10 SER A 11 SITE 2 AC2 14 GLY A 12 LYS A 13 ARG A 126 ASN A 131 SITE 3 AC2 14 ASN A 132 HOH A2021 HOH A2317 HOH A2318 SITE 4 AC2 14 HOH A2319 HOH A2320 CRYST1 39.390 119.440 149.590 90.00 90.00 90.00 I 2 2 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 0.025387 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008372 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006685 0.00000