HEADER OXIDOREDUCTASE 31-OCT-08 3F47
TITLE THE CRYSTAL STRUCTURE OF [FE]-HYDROGENASE (HMD) HOLOENZYME FROM
TITLE 2 METHANOCALDOCOCCUS JANNASCHII
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5,10-METHENYLTETRAHYDROMETHANOPTERIN HYDROGENASE;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: H(2)-FORMING N(5),N(10)-METHYLENETETRAHYDROMETHANOPTERIN
COMPND 5 DEHYDROGENASE, N(5),N(10)-METHENYLTETRAHYDROMETHANOPTERIN
COMPND 6 HYDROGENASE, H(2)-DEPENDENT METHYLENE-H(4)MPT DEHYDROGENASE;
COMPND 7 EC: 1.12.98.2;
COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII;
SOURCE 3 ORGANISM_COMMON: METHANOCOCCUS JANNASCHII;
SOURCE 4 ORGANISM_TAXID: 2190;
SOURCE 5 STRAIN: DSM 2661;
SOURCE 6 GENE: HMD, MJ0784;
SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 9 EXPRESSION_SYSTEM_STRAIN: HMS174(DE3);
SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET-24B(+)
KEYWDS ROSSMANN FOLD, HELIX BUNDLE, COMPLEX WITH IRON GUANYLYL PYRIDINOL
KEYWDS 2 COFACTOR, METHANOGENESIS, ONE-CARBON METABOLISM, OXIDOREDUCTASE
EXPDTA X-RAY DIFFRACTION
AUTHOR T.HIROMOTO,O.PILAK,E.WARKENTIN,R.K.THAUER,S.SHIMA,U.ERMLER
REVDAT 4 01-NOV-23 3F47 1 REMARK LINK
REVDAT 3 25-OCT-17 3F47 1 REMARK
REVDAT 2 13-JUL-11 3F47 1 VERSN
REVDAT 1 10-FEB-09 3F47 0
JRNL AUTH T.HIROMOTO,K.ATAKA,O.PILAK,S.VOGT,M.S.STAGNI,
JRNL AUTH 2 W.MEYER-KLAUCKE,E.WARKENTIN,R.K.THAUER,S.SHIMA,U.ERMLER
JRNL TITL THE CRYSTAL STRUCTURE OF C176A MUTATED [FE]-HYDROGENASE
JRNL TITL 2 SUGGESTS AN ACYL-IRON LIGATION IN THE ACTIVE SITE IRON
JRNL TITL 3 COMPLEX.
JRNL REF FEBS LETT. V. 583 585 2009
JRNL REFN ISSN 0014-5793
JRNL PMID 19162018
JRNL DOI 10.1016/J.FEBSLET.2009.01.017
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH S.SHIMA,O.PILAK,S.VOGT,M.SCHICK,M.S.STAGNI,W.MEYER-KLAUCKE,
REMARK 1 AUTH 2 E.WARKENTIN,R.K.THAUER,U.ERMLER
REMARK 1 TITL THE CRYSTAL STRUCTURE OF [FE]-HYDROGENASE REVEALS THE
REMARK 1 TITL 2 GEOMETRY OF THE ACTIVE SITE
REMARK 1 REF SCIENCE V. 321 572 2008
REMARK 1 REFN ISSN 0036-8075
REMARK 2
REMARK 2 RESOLUTION. 1.75 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) : 1.75
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6
REMARK 3 NUMBER OF REFLECTIONS : 37574
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.174
REMARK 3 R VALUE (WORKING SET) : 0.173
REMARK 3 FREE R VALUE : 0.205
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1887
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) : 1.75
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.80
REMARK 3 REFLECTION IN BIN (WORKING SET) : 2205
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.12
REMARK 3 BIN R VALUE (WORKING SET) : 0.2550
REMARK 3 BIN FREE R VALUE SET COUNT : 98
REMARK 3 BIN FREE R VALUE : 0.3630
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2593
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 42
REMARK 3 SOLVENT ATOMS : 238
REMARK 3
REMARK 3 B VALUES.
REMARK 3 B VALUE TYPE : LIKELY RESIDUAL
REMARK 3 FROM WILSON PLOT (A**2) : 32.68
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.55
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.82000
REMARK 3 B22 (A**2) : 0.82000
REMARK 3 B33 (A**2) : -1.65000
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): 0.111
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.107
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.074
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.613
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2818 ; 0.016 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3853 ; 1.578 ; 2.007
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 370 ; 5.255 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 102 ;36.713 ;25.784
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 493 ;13.397 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;21.905 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 442 ; 0.110 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2110 ; 0.007 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1381 ; 0.203 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1981 ; 0.302 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 235 ; 0.124 ; 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): 67 ; 0.196 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 19 ; 0.144 ; 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): 1802 ; 0.749 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2933 ; 1.294 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1047 ; 2.474 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 920 ; 3.978 ; 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 : 4
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 154
REMARK 3 ORIGIN FOR THE GROUP (A): 20.6872 -1.6043 33.0099
REMARK 3 T TENSOR
REMARK 3 T11: -0.0641 T22: -0.1625
REMARK 3 T33: -0.1500 T12: 0.0104
REMARK 3 T13: -0.0431 T23: 0.0043
REMARK 3 L TENSOR
REMARK 3 L11: 3.2611 L22: 1.4131
REMARK 3 L33: 1.9771 L12: 0.2209
REMARK 3 L13: -0.1466 L23: 0.0266
REMARK 3 S TENSOR
REMARK 3 S11: 0.0277 S12: -0.2190 S13: -0.1425
REMARK 3 S21: 0.1816 S22: 0.0232 S23: 0.0095
REMARK 3 S31: 0.2777 S32: 0.0370 S33: -0.0509
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 155 A 240
REMARK 3 ORIGIN FOR THE GROUP (A): 32.6133 6.2578 20.5073
REMARK 3 T TENSOR
REMARK 3 T11: -0.1533 T22: -0.1026
REMARK 3 T33: -0.1168 T12: 0.0302
REMARK 3 T13: -0.0276 T23: -0.0195
REMARK 3 L TENSOR
REMARK 3 L11: 2.5241 L22: 2.1824
REMARK 3 L33: 2.1095 L12: 0.8359
REMARK 3 L13: 0.2562 L23: -0.2206
REMARK 3 S TENSOR
REMARK 3 S11: -0.0110 S12: 0.1280 S13: 0.0820
REMARK 3 S21: -0.0687 S22: 0.0133 S23: -0.2375
REMARK 3 S31: 0.0672 S32: 0.3241 S33: -0.0024
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 241 A 286
REMARK 3 ORIGIN FOR THE GROUP (A): 19.0845 8.5403 -2.5684
REMARK 3 T TENSOR
REMARK 3 T11: -0.1176 T22: -0.1351
REMARK 3 T33: -0.1443 T12: -0.0166
REMARK 3 T13: 0.0020 T23: -0.0060
REMARK 3 L TENSOR
REMARK 3 L11: 2.7778 L22: 2.0010
REMARK 3 L33: 4.6790 L12: -0.1081
REMARK 3 L13: 1.3762 L23: -0.1603
REMARK 3 S TENSOR
REMARK 3 S11: 0.0836 S12: 0.2550 S13: -0.0414
REMARK 3 S21: -0.2346 S22: -0.0172 S23: -0.0301
REMARK 3 S31: 0.1142 S32: 0.1588 S33: -0.0664
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 287 A 345
REMARK 3 ORIGIN FOR THE GROUP (A): 5.2014 17.7320 -3.6195
REMARK 3 T TENSOR
REMARK 3 T11: -0.1356 T22: -0.0812
REMARK 3 T33: -0.1658 T12: -0.0318
REMARK 3 T13: -0.0075 T23: 0.0483
REMARK 3 L TENSOR
REMARK 3 L11: 2.6679 L22: 4.4697
REMARK 3 L33: 4.3531 L12: 0.3991
REMARK 3 L13: 1.0204 L23: 0.8168
REMARK 3 S TENSOR
REMARK 3 S11: 0.0150 S12: -0.0122 S13: -0.0097
REMARK 3 S21: -0.0063 S22: 0.1239 S23: 0.2245
REMARK 3 S31: 0.0132 S32: -0.3498 S33: -0.1389
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: NULL
REMARK 4
REMARK 4 3F47 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-NOV-08.
REMARK 100 THE DEPOSITION ID IS D_1000050125.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 01-FEB-07
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 8.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SLS
REMARK 200 BEAMLINE : X10SA
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9920
REMARK 200 MONOCHROMATOR : LN2 COOLED FIXED-EXIT SI(111)
REMARK 200 MONOCHROMATOR
REMARK 200 OPTICS : DYNAMICALLY BENDABLE MIRROR
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XSCALE
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37583
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750
REMARK 200 RESOLUTION RANGE LOW (A) : 26.200
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5
REMARK 200 DATA REDUNDANCY : 5.200
REMARK 200 R MERGE (I) : 0.05600
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.0000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80
REMARK 200 COMPLETENESS FOR SHELL (%) : 81.6
REMARK 200 DATA REDUNDANCY IN SHELL : 3.60
REMARK 200 R MERGE FOR SHELL (I) : 0.50800
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS
REMARK 200 SOFTWARE USED: REFMAC 5.2.0019
REMARK 200 STARTING MODEL: 3DAG
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 50.04
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 50% MPD, 100MM TRIS-HCL, 20MM AMMONIUM
REMARK 280 DIHYDROGEN PHOSPHATE, 1MM DTT , PH 8.5, VAPOR DIFFUSION, SITTING
REMARK 280 DROP, TEMPERATURE 283K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 2 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2
REMARK 290 3555 -Y,X+1/2,Z+1/4
REMARK 290 4555 Y+1/2,-X,Z+3/4
REMARK 290 5555 -X+1/2,Y,-Z+3/4
REMARK 290 6555 X,-Y+1/2,-Z+1/4
REMARK 290 7555 Y+1/2,X+1/2,-Z+1/2
REMARK 290 8555 -Y,-X,-Z
REMARK 290 9555 X+1/2,Y+1/2,Z+1/2
REMARK 290 10555 -X,-Y,Z
REMARK 290 11555 -Y+1/2,X,Z+3/4
REMARK 290 12555 Y,-X+1/2,Z+1/4
REMARK 290 13555 -X,Y+1/2,-Z+1/4
REMARK 290 14555 X+1/2,-Y,-Z+3/4
REMARK 290 15555 Y,X,-Z
REMARK 290 16555 -Y+1/2,-X+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 47.96500
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 47.96500
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 82.90500
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 47.96500
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 41.45250
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 47.96500
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 124.35750
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 47.96500
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 124.35750
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.96500
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 41.45250
REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 47.96500
REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 47.96500
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 82.90500
REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 47.96500
REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 47.96500
REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 82.90500
REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 47.96500
REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 124.35750
REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 47.96500
REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 41.45250
REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 47.96500
REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 41.45250
REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 47.96500
REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 124.35750
REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 47.96500
REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 47.96500
REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 82.90500
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: 8480 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 26600 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -127.0 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 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT2 2 1.000000 0.000000 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 345
REMARK 465 GLU A 346
REMARK 465 GLY A 347
REMARK 465 LYS A 348
REMARK 465 THR A 349
REMARK 465 LYS A 350
REMARK 465 CYS A 351
REMARK 465 GLU A 352
REMARK 465 ILE A 353
REMARK 465 MET A 354
REMARK 465 SER A 355
REMARK 465 GLN A 356
REMARK 465 LYS A 357
REMARK 465 GLU A 358
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 SER A 42 -131.41 54.27
REMARK 500 ASN A 153 31.76 -85.72
REMARK 500 ALA A 175 -146.31 -121.07
REMARK 500 CYS A 204 -172.84 -173.08
REMARK 500 CYS A 204 175.70 173.17
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 NA A 363 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 LEU A 51 O
REMARK 620 2 VAL A 54 O 98.5
REMARK 620 3 VAL A 57 O 97.3 90.1
REMARK 620 N 1 2
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 FE2 A 360 FE
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 176 SG
REMARK 620 2 I2C A 359 N1 87.5
REMARK 620 3 I2C A 359 C8 74.3 83.7
REMARK 620 4 CMO A 361 C 171.3 91.5 97.1
REMARK 620 5 CMO A 362 C 91.2 175.1 91.4 89.0
REMARK 620 6 HOH A 364 O 91.4 95.3 165.7 97.2 89.5
REMARK 620 N 1 2 3 4 5
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE I2C A 359
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE2 A 360
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CMO A 361
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CMO A 362
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 363
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2B0J RELATED DB: PDB
REMARK 900 THE HMD APOENZYME.
REMARK 900 RELATED ID: 3DAG RELATED DB: PDB
REMARK 900 THE HMD HOLOENZYME, RECONSTITUTED WITH IRON GUANYLYL PYRIDINOL
REMARK 900 COFACTOR.
REMARK 900 RELATED ID: 3DAF RELATED DB: PDB
REMARK 900 THE HMD HOLOENZYME, INHIBITED BY CYANIDE.
REMARK 900 RELATED ID: 3F46 RELATED DB: PDB
DBREF 3F47 A 1 358 UNP Q58194 HMD_METJA 1 358
SEQRES 1 A 358 MET LYS ILE ALA ILE LEU GLY ALA GLY CYS TYR ARG THR
SEQRES 2 A 358 HIS ALA ALA ALA GLY ILE THR ASN PHE MET ARG ALA CYS
SEQRES 3 A 358 GLU VAL ALA LYS GLU VAL GLY LYS PRO GLU ILE ALA LEU
SEQRES 4 A 358 THR HIS SER SER ILE THR TYR GLY ALA GLU LEU LEU HIS
SEQRES 5 A 358 LEU VAL PRO ASP VAL LYS GLU VAL ILE VAL SER ASP PRO
SEQRES 6 A 358 CYS PHE ALA GLU GLU PRO GLY LEU VAL VAL ILE ASP GLU
SEQRES 7 A 358 PHE ASP PRO LYS GLU VAL MET GLU ALA HIS LEU SER GLY
SEQRES 8 A 358 ASN PRO GLU SER ILE MET PRO LYS ILE ARG GLU VAL VAL
SEQRES 9 A 358 LYS ALA LYS ALA LYS GLU LEU PRO LYS PRO PRO LYS ALA
SEQRES 10 A 358 CYS ILE HIS LEU VAL HIS PRO GLU ASP VAL GLY LEU LYS
SEQRES 11 A 358 VAL THR SER ASP ASP ARG GLU ALA VAL GLU GLY ALA ASP
SEQRES 12 A 358 ILE VAL ILE THR TRP LEU PRO LYS GLY ASN LYS GLN PRO
SEQRES 13 A 358 ASP ILE ILE LYS LYS PHE ALA ASP ALA ILE PRO GLU GLY
SEQRES 14 A 358 ALA ILE VAL THR HIS ALA CYS THR ILE PRO THR THR LYS
SEQRES 15 A 358 PHE ALA LYS ILE PHE LYS ASP LEU GLY ARG GLU ASP LEU
SEQRES 16 A 358 ASN ILE THR SER TYR HIS PRO GLY CYS VAL PRO GLU MET
SEQRES 17 A 358 LYS GLY GLN VAL TYR ILE ALA GLU GLY TYR ALA SER GLU
SEQRES 18 A 358 GLU ALA VAL ASN LYS LEU TYR GLU ILE GLY LYS ILE ALA
SEQRES 19 A 358 ARG GLY LYS ALA PHE LYS MET PRO ALA ASN LEU ILE GLY
SEQRES 20 A 358 PRO VAL CYS ASP MET CYS SER ALA VAL THR ALA THR VAL
SEQRES 21 A 358 TYR ALA GLY LEU LEU ALA TYR ARG ASP ALA VAL THR LYS
SEQRES 22 A 358 ILE LEU GLY ALA PRO ALA ASP PHE ALA GLN MET MET ALA
SEQRES 23 A 358 ASP GLU ALA LEU THR GLN ILE HIS ASN LEU MET LYS GLU
SEQRES 24 A 358 LYS GLY ILE ALA ASN MET GLU GLU ALA LEU ASP PRO ALA
SEQRES 25 A 358 ALA LEU LEU GLY THR ALA ASP SER MET CYS PHE GLY PRO
SEQRES 26 A 358 LEU ALA GLU ILE LEU PRO THR ALA LEU LYS VAL LEU GLU
SEQRES 27 A 358 LYS HIS LYS VAL VAL GLU GLU GLU GLY LYS THR LYS CYS
SEQRES 28 A 358 GLU ILE MET SER GLN LYS GLU
HET I2C A 359 36
HET FE2 A 360 1
HET CMO A 361 2
HET CMO A 362 2
HET NA A 363 1
HETNAM I2C 5'-O-[(S)-HYDROXY{[2-HYDROXY-3,5-DIMETHYL-6-(2-
HETNAM 2 I2C OXOETHYL)PYRIDIN-4-YL]OXY}PHOSPHORYL]GUANOSINE
HETNAM FE2 FE (II) ION
HETNAM CMO CARBON MONOXIDE
HETNAM NA SODIUM ION
FORMUL 2 I2C C19 H23 N6 O10 P
FORMUL 3 FE2 FE 2+
FORMUL 4 CMO 2(C O)
FORMUL 6 NA NA 1+
FORMUL 7 HOH *238(H2 O)
HELIX 1 1 TYR A 11 GLY A 18 1 8
HELIX 2 2 PHE A 22 GLY A 33 1 12
HELIX 3 3 LYS A 34 THR A 40 5 7
HELIX 4 4 HIS A 41 VAL A 54 1 14
HELIX 5 5 PRO A 65 GLU A 69 5 5
HELIX 6 6 ASP A 80 SER A 90 1 11
HELIX 7 7 ASN A 92 SER A 95 5 4
HELIX 8 8 ILE A 96 LYS A 109 1 14
HELIX 9 9 HIS A 123 GLY A 128 5 6
HELIX 10 10 ASP A 134 GLU A 140 1 7
HELIX 11 11 LYS A 154 LYS A 161 1 8
HELIX 12 12 PHE A 162 ILE A 166 5 5
HELIX 13 13 PRO A 179 LEU A 190 1 12
HELIX 14 14 SER A 220 GLY A 236 1 17
HELIX 15 15 LEU A 245 ASP A 251 1 7
HELIX 16 16 CYS A 253 ILE A 274 1 22
HELIX 17 17 PRO A 278 GLY A 301 1 24
HELIX 18 18 ILE A 302 ALA A 308 5 7
HELIX 19 19 ASP A 310 CYS A 322 5 13
HELIX 20 20 PHE A 323 ALA A 327 5 5
HELIX 21 21 GLU A 328 HIS A 340 1 13
SHEET 1 A 6 LYS A 130 THR A 132 0
SHEET 2 A 6 GLU A 59 SER A 63 1 N VAL A 62 O LYS A 130
SHEET 3 A 6 LYS A 2 LEU A 6 1 N ILE A 5 O ILE A 61
SHEET 4 A 6 ILE A 144 THR A 147 1 O ILE A 146 N ALA A 4
SHEET 5 A 6 ILE A 171 HIS A 174 1 O THR A 173 N VAL A 145
SHEET 6 A 6 ASN A 196 SER A 199 1 O ASN A 196 N VAL A 172
SHEET 1 B 2 GLY A 72 VAL A 75 0
SHEET 2 B 2 ALA A 117 HIS A 120 1 O HIS A 120 N VAL A 74
SHEET 1 C 2 VAL A 212 GLU A 216 0
SHEET 2 C 2 ALA A 238 PRO A 242 1 O PHE A 239 N ILE A 214
LINK O LEU A 51 NA NA A 363 1555 1555 2.71
LINK O VAL A 54 NA NA A 363 1555 1555 2.66
LINK O VAL A 57 NA NA A 363 1555 1555 2.59
LINK SG CYS A 176 FE FE2 A 360 1555 1555 2.38
LINK N1 I2C A 359 FE FE2 A 360 1555 1555 2.01
LINK C8 I2C A 359 FE FE2 A 360 1555 1555 1.91
LINK FE FE2 A 360 C CMO A 361 1555 1555 1.83
LINK FE FE2 A 360 C CMO A 362 1555 1555 1.86
LINK FE FE2 A 360 O HOH A 364 1555 1555 2.33
CISPEP 1 GLU A 70 PRO A 71 0 -4.91
CISPEP 2 GLU A 70 PRO A 71 0 2.14
CISPEP 3 PRO A 114 PRO A 115 0 3.53
SITE 1 AC1 30 LEU A 6 GLY A 7 GLY A 9 CYS A 10
SITE 2 AC1 30 THR A 13 SER A 63 ASP A 64 PRO A 65
SITE 3 AC1 30 PRO A 114 PRO A 115 CYS A 118 ASP A 135
SITE 4 AC1 30 TRP A 148 LEU A 149 PRO A 150 ILE A 158
SITE 5 AC1 30 ALA A 175 CYS A 176 THR A 177 PRO A 202
SITE 6 AC1 30 FE2 A 360 CMO A 361 CMO A 362 HOH A 364
SITE 7 AC1 30 HOH A 373 HOH A 385 HOH A 404 HOH A 471
SITE 8 AC1 30 HOH A 487 HOH A 493
SITE 1 AC2 5 CYS A 176 I2C A 359 CMO A 361 CMO A 362
SITE 2 AC2 5 HOH A 364
SITE 1 AC3 7 TRP A 148 CYS A 204 VAL A 205 PRO A 206
SITE 2 AC3 7 I2C A 359 FE2 A 360 CMO A 362
SITE 1 AC4 8 CYS A 176 HIS A 201 PRO A 202 CYS A 204
SITE 2 AC4 8 I2C A 359 FE2 A 360 CMO A 361 HOH A 364
SITE 1 AC5 4 LEU A 51 VAL A 54 PRO A 55 VAL A 57
CRYST1 95.930 95.930 165.810 90.00 90.00 90.00 I 41 2 2 16
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.010424 0.000000 0.000000 0.00000
SCALE2 0.000000 0.010424 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006031 0.00000