HEADER TRANSFERASE 10-DEC-09 3L0P TITLE CRYSTAL STRUCTURES OF IRON 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; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DESULFOVIBRIO GIGAS; SOURCE 3 ORGANISM_TAXID: 879; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET-22B(+) KEYWDS ADENYLATE KINASE, GRAM-NEGATIVE BACTERIA, IRON, ATP-BINDING, KINASE, KEYWDS 2 NUCLEOTIDE-BINDING, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.MUKHOPADHYAY,J.TRINCAO,M.J.ROMAO REVDAT 3 20-MAR-24 3L0P 1 REMARK LINK REVDAT 2 12-FEB-14 3L0P 1 JRNL VERSN REVDAT 1 15-DEC-10 3L0P 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. 3.00 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 WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.25 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.1 REMARK 3 NUMBER OF REFLECTIONS : 6444 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) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 297 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) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08 REMARK 3 REFLECTION IN BIN (WORKING SET) : 438 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.74 REMARK 3 BIN R VALUE (WORKING SET) : 0.2860 REMARK 3 BIN FREE R VALUE SET COUNT : 22 REMARK 3 BIN FREE R VALUE : 0.3520 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1668 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 7 REMARK 3 SOLVENT ATOMS : 8 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.27 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.40000 REMARK 3 B22 (A**2) : -0.35000 REMARK 3 B33 (A**2) : 1.75000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.417 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.277 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 33.387 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.931 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.878 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1709 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2309 ; 1.817 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 222 ; 7.011 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 78 ;34.509 ;24.615 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 282 ;20.453 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;11.388 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 256 ; 0.113 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1305 ; 0.007 ; 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): 1095 ; 0.584 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1735 ; 1.169 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 614 ; 2.061 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 573 ; 3.550 ; 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 10 REMARK 3 ORIGIN FOR THE GROUP (A): 16.9801 21.0798 20.5270 REMARK 3 T TENSOR REMARK 3 T11: 0.1535 T22: 0.2384 REMARK 3 T33: 0.1018 T12: -0.0106 REMARK 3 T13: 0.0345 T23: -0.0351 REMARK 3 L TENSOR REMARK 3 L11: 11.6784 L22: 1.3508 REMARK 3 L33: 8.6024 L12: 3.5914 REMARK 3 L13: 6.0400 L23: 2.9626 REMARK 3 S TENSOR REMARK 3 S11: -0.0831 S12: 0.3442 S13: 0.1283 REMARK 3 S21: -0.0586 S22: 0.1783 S23: -0.0198 REMARK 3 S31: -0.0923 S32: 0.1062 S33: -0.0952 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 11 A 36 REMARK 3 ORIGIN FOR THE GROUP (A): 24.0506 20.6055 16.1836 REMARK 3 T TENSOR REMARK 3 T11: 0.2682 T22: 0.1641 REMARK 3 T33: 0.1409 T12: -0.0360 REMARK 3 T13: -0.0024 T23: -0.0134 REMARK 3 L TENSOR REMARK 3 L11: 10.3543 L22: 0.3795 REMARK 3 L33: 6.2523 L12: -1.0992 REMARK 3 L13: 3.2919 L23: 0.8152 REMARK 3 S TENSOR REMARK 3 S11: 0.0991 S12: 0.0234 S13: -0.3428 REMARK 3 S21: -0.0384 S22: 0.0414 S23: 0.0431 REMARK 3 S31: -0.0096 S32: 0.2271 S33: -0.1405 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 37 A 63 REMARK 3 ORIGIN FOR THE GROUP (A): 30.7747 3.7403 30.0813 REMARK 3 T TENSOR REMARK 3 T11: 0.0444 T22: 0.0656 REMARK 3 T33: 0.0683 T12: 0.0339 REMARK 3 T13: -0.0183 T23: -0.0433 REMARK 3 L TENSOR REMARK 3 L11: 3.8293 L22: 13.5286 REMARK 3 L33: 4.2250 L12: 4.2343 REMARK 3 L13: 1.5124 L23: 0.4528 REMARK 3 S TENSOR REMARK 3 S11: 0.0897 S12: 0.0623 S13: -0.1818 REMARK 3 S21: 0.1255 S22: -0.0355 S23: -0.3960 REMARK 3 S31: -0.0803 S32: 0.0904 S33: -0.0541 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 64 A 90 REMARK 3 ORIGIN FOR THE GROUP (A): 25.4786 17.5466 27.5250 REMARK 3 T TENSOR REMARK 3 T11: 0.1386 T22: 0.1307 REMARK 3 T33: 0.1971 T12: 0.0066 REMARK 3 T13: 0.0241 T23: -0.0840 REMARK 3 L TENSOR REMARK 3 L11: 3.3325 L22: 2.3498 REMARK 3 L33: 5.4227 L12: -1.5735 REMARK 3 L13: -0.9432 L23: -1.3571 REMARK 3 S TENSOR REMARK 3 S11: -0.0131 S12: 0.2442 S13: -0.1543 REMARK 3 S21: -0.0571 S22: -0.0996 S23: -0.3747 REMARK 3 S31: -0.1220 S32: 0.4072 S33: 0.1127 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 91 A 103 REMARK 3 ORIGIN FOR THE GROUP (A): 21.7826 19.5413 36.0872 REMARK 3 T TENSOR REMARK 3 T11: 0.1210 T22: 0.1672 REMARK 3 T33: 0.0837 T12: 0.0136 REMARK 3 T13: 0.0015 T23: -0.0926 REMARK 3 L TENSOR REMARK 3 L11: 16.0481 L22: 24.0758 REMARK 3 L33: 5.5148 L12: 10.3633 REMARK 3 L13: 8.8390 L23: 8.7638 REMARK 3 S TENSOR REMARK 3 S11: -0.0919 S12: -0.6234 S13: 0.4201 REMARK 3 S21: 1.2437 S22: -0.1865 S23: 0.5706 REMARK 3 S31: 0.1647 S32: -0.2656 S33: 0.2784 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 104 A 123 REMARK 3 ORIGIN FOR THE GROUP (A): 10.8659 19.8061 18.3199 REMARK 3 T TENSOR REMARK 3 T11: 0.1506 T22: 0.1761 REMARK 3 T33: 0.0942 T12: -0.0358 REMARK 3 T13: 0.0582 T23: 0.0165 REMARK 3 L TENSOR REMARK 3 L11: 6.3656 L22: 9.3619 REMARK 3 L33: 5.4615 L12: 6.4763 REMARK 3 L13: 4.4934 L23: 4.8288 REMARK 3 S TENSOR REMARK 3 S11: 0.0993 S12: -0.3799 S13: 0.1627 REMARK 3 S21: -0.4398 S22: 0.0374 S23: -0.0552 REMARK 3 S31: -0.2395 S32: -0.5892 S33: -0.1367 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 124 A 147 REMARK 3 ORIGIN FOR THE GROUP (A): 11.5258 12.9554 -2.6323 REMARK 3 T TENSOR REMARK 3 T11: 0.3009 T22: 0.2736 REMARK 3 T33: 0.1717 T12: -0.1090 REMARK 3 T13: -0.0180 T23: 0.0648 REMARK 3 L TENSOR REMARK 3 L11: 3.2887 L22: 8.0045 REMARK 3 L33: 13.9640 L12: 3.8035 REMARK 3 L13: -4.1116 L23: -0.9459 REMARK 3 S TENSOR REMARK 3 S11: -0.1344 S12: 0.5773 S13: 0.4599 REMARK 3 S21: 0.0410 S22: 0.5648 S23: 0.1525 REMARK 3 S31: 0.8589 S32: -1.2793 S33: -0.4304 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 175 REMARK 3 ORIGIN FOR THE GROUP (A): 10.8878 7.2186 3.3829 REMARK 3 T TENSOR REMARK 3 T11: 0.5093 T22: 0.2392 REMARK 3 T33: 0.0139 T12: -0.1671 REMARK 3 T13: 0.0516 T23: -0.0117 REMARK 3 L TENSOR REMARK 3 L11: 0.6843 L22: 2.0662 REMARK 3 L33: 10.8786 L12: 0.1446 REMARK 3 L13: -0.3246 L23: -3.9853 REMARK 3 S TENSOR REMARK 3 S11: -0.2695 S12: 0.3629 S13: 0.0145 REMARK 3 S21: -0.3122 S22: 0.0424 S23: -0.0189 REMARK 3 S31: 1.6435 S32: -0.3217 S33: 0.2271 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 176 A 208 REMARK 3 ORIGIN FOR THE GROUP (A): 9.5913 20.9832 26.6215 REMARK 3 T TENSOR REMARK 3 T11: 0.1688 T22: 0.2032 REMARK 3 T33: 0.3917 T12: 0.0102 REMARK 3 T13: 0.0269 T23: 0.0123 REMARK 3 L TENSOR REMARK 3 L11: 0.6418 L22: 6.9013 REMARK 3 L33: 0.1953 L12: -0.9931 REMARK 3 L13: -0.2829 L23: 1.0340 REMARK 3 S TENSOR REMARK 3 S11: 0.0588 S12: 0.0168 S13: 0.4065 REMARK 3 S21: 0.0025 S22: 0.0398 S23: 0.1967 REMARK 3 S31: -0.0048 S32: -0.0238 S33: -0.0986 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 210 A 223 REMARK 3 ORIGIN FOR THE GROUP (A): 13.3846 31.0811 12.0447 REMARK 3 T TENSOR REMARK 3 T11: 1.0176 T22: 0.6576 REMARK 3 T33: 0.9907 T12: -0.0991 REMARK 3 T13: -0.0327 T23: 0.2825 REMARK 3 L TENSOR REMARK 3 L11: 0.0360 L22: 0.7842 REMARK 3 L33: 24.5577 L12: 0.1315 REMARK 3 L13: 0.7903 L23: 4.3433 REMARK 3 S TENSOR REMARK 3 S11: -0.1702 S12: 0.0124 S13: -0.0289 REMARK 3 S21: -0.3552 S22: 0.1653 S23: 0.1049 REMARK 3 S31: -2.2496 S32: 0.6099 S33: 0.0050 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 3L0P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-DEC-09. REMARK 100 THE DEPOSITION ID IS D_1000056685. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUN-08 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 4.5 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 3.2.25 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6444 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 92.495 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.3 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : 0.07800 REMARK 200 FOR THE DATA SET : 15.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.17 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.24600 REMARK 200 R SYM FOR SHELL (I) : 0.24600 REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: DM 6.0, PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M TARTRATE NA/K, 0.1M MES (PH 6.5), REMARK 280 20% PEG 2000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K, REMARK 280 PH 4.5 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 19.40000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 59.58000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 73.35500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 19.40000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 59.58000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 73.35500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 19.40000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 59.58000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 73.35500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 19.40000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 59.58000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 73.35500 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 GLY A 209 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 LYS A 23 CG CD CE NZ REMARK 470 LYS A 75 CG CD CE NZ REMARK 470 LYS A 77 CG CD CE NZ REMARK 470 ASP A 83 CG OD1 OD2 REMARK 470 GLU A 117 CG CD OE1 OE2 REMARK 470 LYS A 120 CG CD CE NZ REMARK 470 LYS A 145 CG CD CE NZ REMARK 470 ASP A 149 CG OD1 OD2 REMARK 470 LYS A 197 CG CD CE NZ REMARK 470 GLU A 208 CG CD OE1 OE2 REMARK 470 SER A 210 OG REMARK 470 ASP A 212 CG OD1 OD2 REMARK 470 SER A 213 OG REMARK 470 LYS A 215 CG CD CE NZ REMARK 470 LEU A 219 CG CD1 CD2 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 GLY A 40 N GLY A 42 2.08 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 LEU A 158 CA - CB - CG ANGL. DEV. = 14.1 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 HIS A 38 -79.56 -70.19 REMARK 500 ASP A 54 2.54 -66.98 REMARK 500 ASP A 149 30.77 -85.73 REMARK 500 ASP A 166 72.99 -102.30 REMARK 500 ASP A 182 13.00 -144.04 REMARK 500 ASP A 206 105.35 -58.39 REMARK 500 ILE A 211 -37.66 6.27 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 FE A 224 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 129 SG REMARK 620 2 HIS A 135 ND1 120.1 REMARK 620 3 CYS A 151 SG 114.0 112.9 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE A 224 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 225 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3L0S RELATED DB: PDB DBREF 3L0P A 1 223 UNP C7U112 C7U112_DESGI 1 223 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 GLU 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 FE A 224 1 HET GOL A 225 6 HETNAM FE FE (III) ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 FE FE 3+ FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *8(H2 O) HELIX 1 1 GLY A 12 TYR A 24 1 13 HELIX 2 2 SER A 31 GLY A 40 1 10 HELIX 3 3 THR A 43 ASP A 54 1 12 HELIX 4 4 PRO A 60 LYS A 75 1 16 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 ASP A 166 TYR A 178 1 13 HELIX 9 9 GLY A 183 ASN A 193 1 11 HELIX 10 10 MET A 194 GLY A 199 1 6 HELIX 11 11 ASP A 216 GLN A 221 1 6 SHEET 1 A 5 ALA A 27 GLU A 30 0 SHEET 2 A 5 TRP A 80 ASP A 83 1 O LEU A 81 N ILE A 29 SHEET 3 A 5 ASN A 2 PHE A 6 1 N ILE A 3 O TRP A 80 SHEET 4 A 5 PHE A 108 LEU A 113 1 O ILE A 110 N PHE A 6 SHEET 5 A 5 VAL A 201 ASP A 206 1 O ILE A 203 N VAL A 109 SHEET 1 B 3 PRO A 136 ASN A 138 0 SHEET 2 B 3 ARG A 126 CYS A 129 -1 N ARG A 127 O ASN A 137 SHEET 3 B 3 LEU A 158 SER A 159 -1 O SER A 159 N ILE A 128 LINK SG CYS A 129 FE FE A 224 1555 1555 2.14 LINK ND1 HIS A 135 FE FE A 224 1555 1555 2.13 LINK SG CYS A 151 FE FE A 224 1555 1555 2.25 CISPEP 1 PHE A 85 PRO A 86 0 11.79 SITE 1 AC1 4 CYS A 129 HIS A 135 CYS A 151 CYS A 154 SITE 1 AC2 8 PRO A 8 ASN A 9 GLY A 10 SER A 11 SITE 2 AC2 8 GLY A 12 LYS A 13 ASN A 131 ASN A 132 CRYST1 38.800 119.160 146.710 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 0.025773 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008392 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006816 0.00000