HEADER OXIDOREDUCTASE 17-DEC-15 5FF2
TITLE HYDE FROM T. MARITIMA IN COMPLEX WITH (2R,4R)-TDA
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: [FEFE] HYDROGENASE MATURASE SUBUNIT HYDE;
COMPND 3 CHAIN: A;
COMPND 4 EC: 1.8.-.-;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA;
SOURCE 3 ORGANISM_TAXID: 243274;
SOURCE 4 GENE: TM_1269, THEMA_07990, TMARI_1274;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS RADICAL SAM ENZYME, COMPLEX, FEFE-HYDROGENASE MATURASE,
KEYWDS 2 OXIDOREDUCTASE
EXPDTA X-RAY DIFFRACTION
AUTHOR R.ROHAC,P.AMARA,A.BENJDIA,L.MARTIN,P.RUFFIE,A.FAVIER,O.BERTEAU,
AUTHOR 2 J.M.MOUESCA,J.C.FONTECILLA-CAMPS,Y.NICOLET
REVDAT 3 10-JAN-24 5FF2 1 REMARK
REVDAT 2 04-MAY-16 5FF2 1 JRNL
REVDAT 1 06-APR-16 5FF2 0
JRNL AUTH R.ROHAC,P.AMARA,A.BENJDIA,L.MARTIN,P.RUFFIE,A.FAVIER,
JRNL AUTH 2 O.BERTEAU,J.M.MOUESCA,J.C.FONTECILLA-CAMPS,Y.NICOLET
JRNL TITL CARBON-SULFUR BOND-FORMING REACTION CATALYSED BY THE RADICAL
JRNL TITL 2 SAM ENZYME HYDE.
JRNL REF NAT.CHEM. V. 8 491 2016
JRNL REFN ESSN 1755-4349
JRNL PMID 27102684
JRNL DOI 10.1038/NCHEM.2490
REMARK 2
REMARK 2 RESOLUTION. 1.47 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0131
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) : 1.47
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.47
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4
REMARK 3 NUMBER OF REFLECTIONS : 56772
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) : 0.166
REMARK 3 R VALUE (WORKING SET) : 0.165
REMARK 3 FREE R VALUE : 0.187
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 3009
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) : 1.47
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.51
REMARK 3 REFLECTION IN BIN (WORKING SET) : 4079
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.22
REMARK 3 BIN R VALUE (WORKING SET) : 0.2740
REMARK 3 BIN FREE R VALUE SET COUNT : 222
REMARK 3 BIN FREE R VALUE : 0.3080
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2742
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 212
REMARK 3 SOLVENT ATOMS : 447
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.89
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.84000
REMARK 3 B22 (A**2) : 0.21000
REMARK 3 B33 (A**2) : -1.04000
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): 0.072
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.070
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.053
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.473
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3211 ; 0.022 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 3136 ; 0.004 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4428 ; 2.296 ; 2.078
REMARK 3 BOND ANGLES OTHERS (DEGREES): 7278 ; 1.261 ; 3.001
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 382 ; 6.143 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 134 ;35.188 ;23.209
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 539 ;12.680 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;18.569 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 525 ; 0.157 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3379 ; 0.011 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 668 ; 0.006 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1448 ; 1.682 ; 1.567
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1447 ; 1.682 ; 1.567
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1822 ; 2.286 ; 2.346
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1823 ; 2.285 ; 2.347
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1763 ; 2.744 ; 1.903
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1764 ; 2.743 ; 1.903
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2583 ; 4.014 ; 2.764
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 14287 ; 6.144 ;16.554
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 14286 ; 6.144 ;16.553
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 : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : BABINET MODEL WITH 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 5FF2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-DEC-15.
REMARK 100 THE DEPOSITION ID IS D_1000216473.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 12-JUL-13
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : NULL
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ESRF
REMARK 200 BEAMLINE : BM30A
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.979
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XDS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 59781
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.470
REMARK 200 RESOLUTION RANGE LOW (A) : 44.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4
REMARK 200 DATA REDUNDANCY : 2.900
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.0500
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.47
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.56
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.68300
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: REFMAC
REMARK 200 STARTING MODEL: 3IIX
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 43.79
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG4000, LITHIUM SULFATE, CHAPS,
REMARK 280 TRISHCL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X+1/2,-Y,Z+1/2
REMARK 290 3555 -X,Y+1/2,-Z+1/2
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 25.61500
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.05000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.54500
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.05000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.61500
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.54500
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: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 3060 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 14820 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.0 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 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 VAL A 348
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 4 CG CD NE CZ NH1 NH2
REMARK 470 LYS A 9 CE NZ
REMARK 470 GLU A 14 CG CD OE1 OE2
REMARK 470 LYS A 37 CE NZ
REMARK 470 LYS A 80 CD CE NZ
REMARK 470 GLU A 87 CG CD OE1 OE2
REMARK 470 LYS A 188 CD CE NZ
REMARK 470 LYS A 242 CE NZ
REMARK 470 GLN A 304 CG CD OE1 NE2
REMARK 470 LYS A 309 CG CD CE NZ
REMARK 470 LYS A 315 CE NZ
REMARK 470 LYS A 333 CE NZ
REMARK 470 ARG A 336 CD NE CZ NH1 NH2
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 37 CD
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 CD LYS A 37 O HOH A 716 1.67
REMARK 500 O HOH A 617 O HOH A 736 1.78
REMARK 500 O HOH A 772 O HOH A 822 1.83
REMARK 500 O HOH A 873 O HOH A 922 1.89
REMARK 500 O HOH A 764 O HOH A 916 1.91
REMARK 500 CB LYS A 309 O HOH A 860 1.93
REMARK 500 O HOH A 826 O HOH A 855 1.96
REMARK 500 O HOH A 581 O HOH A 928 2.03
REMARK 500 O HOH A 791 O HOH A 869 2.05
REMARK 500 O HOH A 523 O HOH A 790 2.09
REMARK 500 NH2 ARG A 44 O HOH A 501 2.09
REMARK 500 O HOH A 719 O HOH A 900 2.11
REMARK 500 O HOH A 942 O HOH A 946 2.14
REMARK 500 O HOH A 681 O HOH A 802 2.16
REMARK 500 CZ ARG A 44 O HOH A 501 2.16
REMARK 500 O HOH A 867 O HOH A 894 2.17
REMARK 500 O HOH A 550 O HOH A 807 2.18
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 O HOH A 725 O HOH A 881 2655 2.08
REMARK 500 O HOH A 842 O HOH A 872 4555 2.09
REMARK 500 O HOH A 604 O HOH A 858 2655 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 ARG A 92 CZ ARG A 92 NH1 0.079
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 ARG A 29 NE - CZ - NH1 ANGL. DEV. = -4.1 DEGREES
REMARK 500 ARG A 29 NE - CZ - NH2 ANGL. DEV. = 4.8 DEGREES
REMARK 500 ARG A 92 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES
REMARK 500 TYR A 113 CB - CG - CD1 ANGL. DEV. = -3.9 DEGREES
REMARK 500 MET A 129 CG - SD - CE ANGL. DEV. = -23.1 DEGREES
REMARK 500 ARG A 172 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES
REMARK 500 ASP A 212 CB - CG - OD2 ANGL. DEV. = -6.2 DEGREES
REMARK 500 MET A 291 CG - SD - CE ANGL. DEV. = -18.4 DEGREES
REMARK 500 ARG A 332 NE - CZ - NH2 ANGL. DEV. = -3.9 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 ASN A 78 37.74 -94.60
REMARK 500 ASN A 78 30.82 -89.03
REMARK 500 GLU A 161 -59.43 78.64
REMARK 500 THR A 175 -159.63 -151.93
REMARK 500 ALA A 196 -154.41 -123.25
REMARK 500 ASN A 288 11.43 -143.93
REMARK 500 GLN A 304 79.36 -117.54
REMARK 500 CYS A 311 -2.54 78.14
REMARK 500 ASP A 337 -159.90 -132.45
REMARK 500 GLU A 346 -158.39 -121.06
REMARK 500
REMARK 500 REMARK: NULL
REMARK 610
REMARK 610 MISSING HETEROATOM
REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 610 I=INSERTION CODE):
REMARK 610 M RES C SSEQI
REMARK 610 CPS A 404
REMARK 610 CPS A 405
REMARK 610 CPS A 406
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 SF4 A 401 FE2
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 63 SG
REMARK 620 2 SF4 A 401 S1 105.4
REMARK 620 3 SF4 A 401 S3 116.9 106.4
REMARK 620 4 SF4 A 401 S4 118.9 103.9 104.1
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 SF4 A 401 FE3
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 67 SG
REMARK 620 2 SF4 A 401 S1 115.8
REMARK 620 3 SF4 A 401 S2 117.4 103.7
REMARK 620 4 SF4 A 401 S4 108.4 103.4 107.0
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 SF4 A 401 FE1
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 70 SG
REMARK 620 2 SF4 A 401 S2 110.8
REMARK 620 3 SF4 A 401 S3 118.6 106.7
REMARK 620 4 SF4 A 401 S4 108.7 105.1 106.0
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 SF4 A 401 FE4
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 SAH A 408 N
REMARK 620 2 SF4 A 401 S1 98.6
REMARK 620 3 SF4 A 401 S2 156.9 98.4
REMARK 620 4 SF4 A 401 S3 92.5 101.3 99.4
REMARK 620 5 SAH A 408 OXT 70.2 95.2 92.7 157.7
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 SF4 A 401
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CPS A 402
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CPS A 403
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CPS A 404
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CPS A 405
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CPS A 406
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 407
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SAH A 408
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 5XB A 409
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue H2S A 410
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue H2S A 411
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3IIX RELATED DB: PDB
REMARK 900 RELATED ID: 3IIZ RELATED DB: PDB
REMARK 900 RELATED ID: 5FEP RELATED DB: PDB
REMARK 900 RELATED ID: 5FES RELATED DB: PDB
REMARK 900 RELATED ID: 5FEW RELATED DB: PDB
REMARK 900 RELATED ID: 5FEX RELATED DB: PDB
REMARK 900 RELATED ID: 5FEZ RELATED DB: PDB
REMARK 900 RELATED ID: 5FF0 RELATED DB: PDB
DBREF 5FF2 A 1 348 UNP Q9X0Z6 HYDE_THEMA 1 348
SEQRES 1 A 348 MET THR GLY ARG GLU ILE LEU GLU LYS LEU GLU ARG ARG
SEQRES 2 A 348 GLU PHE THR ARG GLU VAL LEU LYS GLU ALA LEU SER ILE
SEQRES 3 A 348 ASN ASP ARG GLY PHE ASN GLU ALA LEU PHE LYS LEU ALA
SEQRES 4 A 348 ASP GLU ILE ARG ARG LYS TYR VAL GLY ASP GLU VAL HIS
SEQRES 5 A 348 ILE ARG ALA ILE ILE GLU PHE SER ASN VAL CYS ARG LYS
SEQRES 6 A 348 ASN CYS LEU TYR CYS GLY LEU ARG ARG ASP ASN LYS ASN
SEQRES 7 A 348 LEU LYS ARG TYR ARG MET THR PRO GLU GLU ILE VAL GLU
SEQRES 8 A 348 ARG ALA ARG LEU ALA VAL GLN PHE GLY ALA LYS THR ILE
SEQRES 9 A 348 VAL LEU GLN SER GLY GLU ASP PRO TYR TYR MET PRO ASP
SEQRES 10 A 348 VAL ILE SER ASP ILE VAL LYS GLU ILE LYS LYS MET GLY
SEQRES 11 A 348 VAL ALA VAL THR LEU SER LEU GLY GLU TRP PRO ARG GLU
SEQRES 12 A 348 TYR TYR GLU LYS TRP LYS GLU ALA GLY ALA ASP ARG TYR
SEQRES 13 A 348 LEU LEU ARG HIS GLU THR ALA ASN PRO VAL LEU HIS ARG
SEQRES 14 A 348 LYS LEU ARG PRO ASP THR SER PHE GLU ASN ARG LEU ASN
SEQRES 15 A 348 CYS LEU LEU THR LEU LYS GLU LEU GLY TYR GLU THR GLY
SEQRES 16 A 348 ALA GLY SER MET VAL GLY LEU PRO GLY GLN THR ILE ASP
SEQRES 17 A 348 ASP LEU VAL ASP ASP LEU LEU PHE LEU LYS GLU HIS ASP
SEQRES 18 A 348 PHE ASP MET VAL GLY ILE GLY PRO PHE ILE PRO HIS PRO
SEQRES 19 A 348 ASP THR PRO LEU ALA ASN GLU LYS LYS GLY ASP PHE THR
SEQRES 20 A 348 LEU THR LEU LYS MET VAL ALA LEU THR ARG ILE LEU LEU
SEQRES 21 A 348 PRO ASP SER ASN ILE PRO ALA THR THR ALA MET GLY THR
SEQRES 22 A 348 ILE VAL PRO GLY GLY ARG GLU ILE THR LEU ARG CYS GLY
SEQRES 23 A 348 ALA ASN VAL ILE MET PRO ASN TRP THR PRO SER PRO TYR
SEQRES 24 A 348 ARG GLN LEU TYR GLN LEU TYR PRO GLY LYS ILE CYS VAL
SEQRES 25 A 348 PHE GLU LYS ASP THR ALA CYS ILE PRO CYS VAL MET LYS
SEQRES 26 A 348 MET ILE GLU LEU LEU GLY ARG LYS PRO GLY ARG ASP TRP
SEQRES 27 A 348 GLY GLY ARG LYS ARG VAL PHE GLU THR VAL
HET SF4 A 401 8
HET CPS A 402 42
HET CPS A 403 42
HET CPS A 404 29
HET CPS A 405 26
HET CPS A 406 50
HET CL A 407 1
HET SAH A 408 26
HET 5XB A 409 11
HET H2S A 410 1
HET H2S A 411 1
HETNAM SF4 IRON/SULFUR CLUSTER
HETNAM CPS 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-
HETNAM 2 CPS PROPANESULFONATE
HETNAM CL CHLORIDE ION
HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE
HETNAM 5XB (2~{R},4~{R})-1,3-THIAZOLIDINE-2,4-DICARBOXYLIC ACID
HETNAM H2S HYDROSULFURIC ACID
HETSYN CPS CHAPS
HETSYN H2S HYDROGEN SULFIDE
FORMUL 2 SF4 FE4 S4
FORMUL 3 CPS 5(C32 H58 N2 O7 S)
FORMUL 8 CL CL 1-
FORMUL 9 SAH C14 H20 N6 O5 S
FORMUL 10 5XB C5 H7 N O4 S
FORMUL 11 H2S 2(H2 S)
FORMUL 13 HOH *447(H2 O)
HELIX 1 AA1 THR A 2 ARG A 12 1 11
HELIX 2 AA2 THR A 16 ILE A 26 1 11
HELIX 3 AA3 ASP A 28 GLY A 48 1 21
HELIX 4 AA4 THR A 85 PHE A 99 1 15
HELIX 5 AA5 ASP A 111 MET A 115 5 5
HELIX 6 AA6 PRO A 116 LYS A 128 1 13
HELIX 7 AA7 PRO A 141 ALA A 151 1 11
HELIX 8 AA8 ASN A 164 ARG A 172 1 9
HELIX 9 AA9 SER A 176 LEU A 190 1 15
HELIX 10 AB1 THR A 206 ASP A 221 1 16
HELIX 11 AB2 ASP A 245 LEU A 260 1 16
HELIX 12 AB3 THR A 268 VAL A 275 1 8
HELIX 13 AB4 GLY A 277 ARG A 284 1 8
HELIX 14 AB5 TYR A 299 TYR A 303 5 5
HELIX 15 AB6 ALA A 318 LEU A 330 1 13
SHEET 1 AA1 7 MET A 224 PRO A 229 0
SHEET 2 AA1 7 GLU A 193 VAL A 200 1 N ALA A 196 O GLY A 226
SHEET 3 AA1 7 ARG A 155 LEU A 157 1 N TYR A 156 O GLY A 195
SHEET 4 AA1 7 ALA A 132 SER A 136 1 N LEU A 135 O LEU A 157
SHEET 5 AA1 7 THR A 103 SER A 108 1 N ILE A 104 O THR A 134
SHEET 6 AA1 7 GLU A 50 SER A 60 1 N ILE A 57 O VAL A 105
SHEET 7 AA1 7 VAL A 289 ILE A 290 1 O ILE A 290 N HIS A 52
SHEET 1 AA2 7 MET A 224 PRO A 229 0
SHEET 2 AA2 7 GLU A 193 VAL A 200 1 N ALA A 196 O GLY A 226
SHEET 3 AA2 7 ARG A 155 LEU A 157 1 N TYR A 156 O GLY A 195
SHEET 4 AA2 7 ALA A 132 SER A 136 1 N LEU A 135 O LEU A 157
SHEET 5 AA2 7 THR A 103 SER A 108 1 N ILE A 104 O THR A 134
SHEET 6 AA2 7 GLU A 50 SER A 60 1 N ILE A 57 O VAL A 105
SHEET 7 AA2 7 LYS A 333 PRO A 334 1 O LYS A 333 N VAL A 51
LINK SG CYS A 63 FE2 SF4 A 401 1555 1555 2.26
LINK SG CYS A 67 FE3 SF4 A 401 1555 1555 2.33
LINK SG CYS A 70 FE1 SF4 A 401 1555 1555 2.29
LINK FE4 SF4 A 401 N SAH A 408 1555 1555 2.31
LINK FE4 SF4 A 401 OXT SAH A 408 1555 1555 2.33
CISPEP 1 MET A 115 PRO A 116 0 -5.60
CISPEP 2 SER A 297 PRO A 298 0 8.14
SITE 1 AC1 4 CYS A 63 CYS A 67 CYS A 70 SAH A 408
SITE 1 AC2 19 GLN A 98 PHE A 99 GLY A 100 PRO A 276
SITE 2 AC2 19 GLY A 277 GLU A 280 ARG A 284 MET A 324
SITE 3 AC2 19 LEU A 330 CPS A 405 CPS A 406 HOH A 540
SITE 4 AC2 19 HOH A 543 HOH A 561 HOH A 571 HOH A 599
SITE 5 AC2 19 HOH A 657 HOH A 662 HOH A 776
SITE 1 AC3 17 LYS A 37 ASP A 40 LYS A 170 ARG A 284
SITE 2 AC3 17 SER A 297 LYS A 315 ASP A 316 THR A 317
SITE 3 AC3 17 HOH A 603 HOH A 616 HOH A 623 HOH A 648
SITE 4 AC3 17 HOH A 653 HOH A 737 HOH A 803 HOH A 840
SITE 5 AC3 17 HOH A 903
SITE 1 AC4 8 ARG A 29 GLU A 33 THR A 247 CPS A 405
SITE 2 AC4 8 HOH A 521 HOH A 614 HOH A 615 HOH A 687
SITE 1 AC5 12 ARG A 29 LYS A 315 THR A 317 ALA A 318
SITE 2 AC5 12 CPS A 402 CPS A 404 CPS A 406 HOH A 626
SITE 3 AC5 12 HOH A 679 HOH A 743 HOH A 755 HOH A 757
SITE 1 AC6 15 LYS A 128 PRO A 321 MET A 324 GLU A 328
SITE 2 AC6 15 CPS A 402 CPS A 405 HOH A 505 HOH A 551
SITE 3 AC6 15 HOH A 571 HOH A 585 HOH A 597 HOH A 670
SITE 4 AC6 15 HOH A 702 HOH A 721 HOH A 842
SITE 1 AC7 3 ARG A 54 THR A 134 ARG A 155
SITE 1 AC8 17 TYR A 69 SER A 108 ARG A 159 GLU A 161
SITE 2 AC8 17 ARG A 180 MET A 199 PRO A 229 ILE A 231
SITE 3 AC8 17 TYR A 303 LEU A 305 TYR A 306 SF4 A 401
SITE 4 AC8 17 HOH A 589 HOH A 608 HOH A 629 HOH A 633
SITE 5 AC8 17 HOH A 739
SITE 1 AC9 13 GLN A 107 ARG A 159 GLY A 226 THR A 268
SITE 2 AC9 13 THR A 269 ALA A 270 MET A 291 TYR A 306
SITE 3 AC9 13 HOH A 535 HOH A 547 HOH A 607 HOH A 768
SITE 4 AC9 13 HOH A 800
SITE 1 AD1 2 CYS A 311 CYS A 319
SITE 1 AD2 2 CYS A 322 HOH A 915
CRYST1 51.230 79.090 86.100 90.00 90.00 90.00 P 21 21 21 4
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.019520 0.000000 0.000000 0.00000
SCALE2 0.000000 0.012644 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011614 0.00000