HEADER OXIDOREDUCTASE 08-AUG-18 6HAV
TITLE CRYSTAL STRUCTURE OF [FE]-HYDROGENASE (HMD) FROM METHANOCOCCUS
TITLE 2 AEOLICUS IN COMPLEX WITH FEGP AND METHENYL-TETRAHYDROMETHANOPTERIN
TITLE 3 (CLOSE FORM A) AT 1.06 A RESOLUTION
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5,10-METHENYLTETRAHYDROMETHANOPTERIN HYDROGENASE;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: H(2)-DEPENDENT METHYLENE-H(4)MPT DEHYDROGENASE,H(2)-FORMING
COMPND 5 N(5),N(10)-METHYLENETETRAHYDROMETHANOPTERIN DEHYDROGENASE,N(5),N(10)-
COMPND 6 METHENYLTETRAHYDROMETHANOPTERIN HYDROGENASE;
COMPND 7 EC: 1.12.98.2;
COMPND 8 ENGINEERED: YES;
COMPND 9 MUTATION: YES;
COMPND 10 OTHER_DETAILS: CYSTEINES 66 AND 118 ARE MAKING A DISULFIDE BRIDGE
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCOCCUS AEOLICUS (STRAIN ATCC BAA-1280 /
SOURCE 3 DSM 17508 / OCM 812 / NANKAI-3);
SOURCE 4 ORGANISM_TAXID: 419665;
SOURCE 5 VARIANT: /;
SOURCE 6 CELL_LINE: /;
SOURCE 7 ATCC: /;
SOURCE 8 ORGAN: /;
SOURCE 9 TISSUE: /;
SOURCE 10 CELL: /;
SOURCE 11 GENE: HMD, MAEO_1025;
SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 13 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 14 EXPRESSION_SYSTEM_VARIANT: /;
SOURCE 15 EXPRESSION_SYSTEM_CELL_LINE: /;
SOURCE 16 EXPRESSION_SYSTEM_ATCC_NUMBER: /;
SOURCE 17 EXPRESSION_SYSTEM_ORGAN: /;
SOURCE 18 EXPRESSION_SYSTEM_TISSUE: /;
SOURCE 19 EXPRESSION_SYSTEM_CELL: /;
SOURCE 20 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 21 EXPRESSION_SYSTEM_PLASMID: PET-24B+
KEYWDS [FE]-HYDROGENASE, CATALYTIC CYCLE, CONFORMATIONAL REARRANGEMENT, FE-
KEYWDS 2 GUANYLYLPYRIDINOL COFACTOR, METHANOGENESIS, HYDRIDE-TRANSFER,
KEYWDS 3 TETRAHYDROMETHANOPTERIN, C1-METABOLISM, ATOMIC RESOLUTION,
KEYWDS 4 OXIDOREDUCTASE
EXPDTA X-RAY DIFFRACTION
AUTHOR G.HUANG,T.WAGNER,M.D.WODRICH,K.ATAKA,E.BILL,U.ERMLER,X.HU,S.SHIMA
REVDAT 4 16-OCT-24 6HAV 1 REMARK
REVDAT 3 17-JAN-24 6HAV 1 LINK
REVDAT 2 04-SEP-19 6HAV 1 JRNL
REVDAT 1 28-AUG-19 6HAV 0
JRNL AUTH G.HUANG,T.WAGNER,M.D.WODRICH,K.ATAKA,E.BILL,U.ERMLER,X.HU,
JRNL AUTH 2 S.SHIMA
JRNL TITL THE ATOMIC-RESOLUTION CRYSTAL STRUCTURE OF ACTIVATED
JRNL TITL 2 [FE]-HYDROGENASE
JRNL REF NAT CATAL 2019
JRNL REFN ESSN 2520-1158
JRNL DOI 10.1038/S41929-019-0289-4
REMARK 2
REMARK 2 RESOLUTION. 1.06 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???)
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.06
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.24
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330
REMARK 3 COMPLETENESS FOR RANGE (%) : 93.2
REMARK 3 NUMBER OF REFLECTIONS : 156000
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.119
REMARK 3 R VALUE (WORKING SET) : 0.118
REMARK 3 FREE R VALUE : 0.134
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960
REMARK 3 FREE R VALUE TEST SET COUNT : 7742
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 45.2816 - 3.2933 1.00 5603 262 0.1342 0.1507
REMARK 3 2 3.2933 - 2.6140 1.00 5372 308 0.1229 0.1337
REMARK 3 3 2.6140 - 2.2836 0.99 5340 285 0.1177 0.1326
REMARK 3 4 2.2836 - 2.0748 0.99 5338 277 0.1077 0.1235
REMARK 3 5 2.0748 - 1.9261 0.99 5333 268 0.1120 0.1115
REMARK 3 6 1.9261 - 1.8125 0.99 5196 312 0.1088 0.1203
REMARK 3 7 1.8125 - 1.7218 0.99 5284 276 0.1046 0.1161
REMARK 3 8 1.7218 - 1.6468 0.99 5237 291 0.0983 0.1117
REMARK 3 9 1.6468 - 1.5834 0.99 5199 284 0.0935 0.1190
REMARK 3 10 1.5834 - 1.5288 0.98 5251 250 0.0896 0.1220
REMARK 3 11 1.5288 - 1.4810 0.98 5207 255 0.0925 0.1145
REMARK 3 12 1.4810 - 1.4386 0.98 5150 300 0.0922 0.1117
REMARK 3 13 1.4386 - 1.4008 0.98 5176 278 0.0947 0.1193
REMARK 3 14 1.4008 - 1.3666 0.98 5209 230 0.0971 0.1309
REMARK 3 15 1.3666 - 1.3355 0.98 5102 280 0.0969 0.1196
REMARK 3 16 1.3355 - 1.3071 0.97 5072 291 0.0993 0.1131
REMARK 3 17 1.3071 - 1.2809 0.96 5124 248 0.0964 0.1366
REMARK 3 18 1.2809 - 1.2568 0.96 5094 252 0.1000 0.1245
REMARK 3 19 1.2568 - 1.2343 0.96 4951 299 0.1058 0.1281
REMARK 3 20 1.2343 - 1.2134 0.95 5057 277 0.1242 0.1474
REMARK 3 21 1.2134 - 1.1938 0.94 4954 225 0.1232 0.1502
REMARK 3 22 1.1938 - 1.1755 0.93 4862 247 0.1284 0.1475
REMARK 3 23 1.1755 - 1.1582 0.92 4895 243 0.1397 0.1524
REMARK 3 24 1.1582 - 1.1418 0.91 4782 235 0.1547 0.1595
REMARK 3 25 1.1418 - 1.1264 0.90 4781 239 0.1659 0.1914
REMARK 3 26 1.1264 - 1.1118 0.91 4790 248 0.1902 0.2182
REMARK 3 27 1.1118 - 1.0979 0.85 4492 203 0.2127 0.2244
REMARK 3 28 1.0979 - 1.0847 0.72 3756 230 0.2997 0.3016
REMARK 3 29 1.0847 - 1.0720 0.64 3345 175 0.3579 0.4332
REMARK 3 30 1.0720 - 1.0600 0.63 3306 174 0.2878 0.2817
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : NULL
REMARK 3 SOLVENT RADIUS : 1.11
REMARK 3 SHRINKAGE RADIUS : 0.90
REMARK 3 K_SOL : NULL
REMARK 3 B_SOL : NULL
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.080
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 12.410
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.10
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : 0.011 3010
REMARK 3 ANGLE : 1.425 4144
REMARK 3 CHIRALITY : 0.097 476
REMARK 3 PLANARITY : 0.010 532
REMARK 3 DIHEDRAL : 21.457 1222
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 6HAV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-AUG-18.
REMARK 100 THE DEPOSITION ID IS D_1200011319.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 17-FEB-17
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : /
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) : 1.00001
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.22
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 156432
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.060
REMARK 200 RESOLUTION RANGE LOW (A) : 46.980
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 93.7
REMARK 200 DATA REDUNDANCY : 6.100
REMARK 200 R MERGE (I) : 0.04900
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.4000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.06
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.12
REMARK 200 COMPLETENESS FOR SHELL (%) : 74.8
REMARK 200 DATA REDUNDANCY IN SHELL : 4.00
REMARK 200 R MERGE FOR SHELL (I) : 0.98100
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.400
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: 6HAC
REMARK 200
REMARK 200 REMARK: LARGE ORTHORHOMBIC ROD
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 51.17
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALLIZATION OF [FE]-HYDROGENASE
REMARK 280 -METHENYL-H4MPT+ COMPLEX WAS PERFORMED IN THE ANAEROBIC TENT
REMARK 280 WITH GAS PHASE 100%N2 AT ROOM TEMPERATURE UNDER DARK CONDITION.
REMARK 280 THE RECONSTITUTED [FE]-HYDROGENASE HOLOENZYME (50 MG/ML) WAS
REMARK 280 MIXED WITH 10 MM METHENYL-H4MPT+, BOTH OF WHICH CONTAINED 10 MM
REMARK 280 MOPS/KOH PH 7.0. THE FINAL CONCENTRATIONS OF [FE]-HYDROGENASE
REMARK 280 AND METHENYL-H4MPT+ WERE 24 MG/ML AND 3 MM, RESPECTIVELY. AFTER
REMARK 280 INCUBATING THE MIXTURE IN THIS TENT UNDER DARK CONDITION FOR 5
REMARK 280 MIN, THE ENZYME SOLUTION WAS CENTRIFUGED AT 8000 RPM FOR 5 MIN
REMARK 280 BY USING CENTRIFUGAL FILTERS MADE OF POLYVINYLIDENE FLUORIDE
REMARK 280 (PVDF, MILLIPORE). THE CRYSTALLIZATION SOLUTION CONTAINED 20% W/
REMARK 280 V POLYETHYLENE GLYCOL 3350 AND 200 MM SODIUM THIOCYANATE WITH A
REMARK 280 RATIO OF PROTEIN MIXTURE AND CRYSTALLIZATION RESERVOIR OF 2 UL /
REMARK 280 2 UL DROPS SPOTTED ON A 24 WELL JUNIOR CLOVER PLATE. THE CRYSTAL
REMARK 280 WAS SOAKED FOR A COUPLE OF SECONDS IN 20% W/V POLYETHYLENE
REMARK 280 GLYCOL 3350, 20% V/V GLYCEROL AND 200 MM SODIUM THIOCYANATE
REMARK 280 BEFORE FREEZING IN LIQUID NITROGEN., VAPOR DIFFUSION, SITTING
REMARK 280 DROP, TEMPERATURE 298K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z+1/2
REMARK 290 3555 -X,Y,-Z+1/2
REMARK 290 4555 X,-Y,-Z
REMARK 290 5555 X+1/2,Y+1/2,Z
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
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 83.79950
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 83.79950
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 33.32400
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.12300
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 33.32400
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.12300
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 83.79950
REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 33.32400
REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 33.12300
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 83.79950
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 33.32400
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 33.12300
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 12560 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 24270 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -152.0 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 1.000000 0.000000 0.000000 0.00000
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 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375 HOH A 989 LIES ON A SPECIAL POSITION.
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 CYS A 66 CA - CB - SG ANGL. DEV. = 6.7 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 SER A 42 -136.10 57.62
REMARK 500 TRP A 148 64.97 -150.44
REMARK 500 PRO A 150 -178.68 -63.49
REMARK 500 LYS A 151 138.43 -37.25
REMARK 500 ALA A 175 -144.23 -134.61
REMARK 500 CYS A 204 177.70 178.61
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH A1004 DISTANCE = 6.20 ANGSTROMS
REMARK 525 HOH A1005 DISTANCE = 6.59 ANGSTROMS
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 407 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 LEU A 51 O
REMARK 620 2 VAL A 54 O 125.9
REMARK 620 3 ILE A 57 O 103.9 91.0
REMARK 620 4 HOH A 648 O 118.8 113.5 87.3
REMARK 620 5 HOH A 807 O 88.6 84.9 166.7 82.8
REMARK 620 N 1 2 3 4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 FE9 A 401 FE
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 176 SG
REMARK 620 2 FE9 A 401 N1 84.2
REMARK 620 3 FE9 A 401 C1F 172.4 89.2
REMARK 620 4 FE9 A 401 C8 77.3 85.2 98.4
REMARK 620 5 FE9 A 401 C2F 91.8 176.0 94.7 93.4
REMARK 620 N 1 2 3 4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA A 408 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH A 842 O
REMARK 620 2 HOH A 989 O 90.0
REMARK 620 3 HOH A 989 O 90.0 0.0
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 FE9 A 401
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 402
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 403
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 404
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 405
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 406
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 407
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 408
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SCN A 409
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SCN A 410
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SCN A 411
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue E4M A 412
DBREF 6HAV A 1 342 UNP A6UVT1 A6UVT1_META3 1 342
SEQRES 1 A 342 MET LYS VAL ALA ILE LEU GLY ALA GLY CYS TYR ARG SER
SEQRES 2 A 342 HIS ALA ALA CYS GLY ILE THR ASN PHE SER ARG ALA ALA
SEQRES 3 A 342 GLU VAL ALA ASN LYS VAL GLY ILE PRO GLU ILE THR MET
SEQRES 4 A 342 THR HIS SER THR ILE THR MET GLY ALA GLU LEU LEU HIS
SEQRES 5 A 342 LEU VAL ASP GLU ILE ASP GLU VAL VAL VAL SER ASP PRO
SEQRES 6 A 342 CYS PHE ALA GLU GLU PRO GLY LEU ILE ILE ILE ASP GLU
SEQRES 7 A 342 PHE ASP CYS LYS GLU VAL MET GLU ALA HIS LEU ALA GLY
SEQRES 8 A 342 LYS ALA GLU ASP VAL MET PRO ALA ILE ARG ASP ALA VAL
SEQRES 9 A 342 LYS ALA LYS ALA LYS ASP SER PRO LYS PRO PRO LYS GLY
SEQRES 10 A 342 CYS ILE HIS PHE VAL ASN PRO GLU LYS VAL GLY LEU LYS
SEQRES 11 A 342 VAL THR SER ASP ASP ARG GLU ALA ILE GLU GLY ALA ASP
SEQRES 12 A 342 ILE VAL ILE THR TRP LEU PRO LYS GLY GLY SER GLN PRO
SEQRES 13 A 342 ALA ILE ILE GLU LYS PHE VAL ASP ALA ILE LYS GLU GLY
SEQRES 14 A 342 ALA ILE VAL THR HIS ALA CYS THR ILE PRO THR PRO LYS
SEQRES 15 A 342 PHE ALA LYS ILE PHE LYS ASP LEU GLY ARG GLU ASP LEU
SEQRES 16 A 342 ASN ILE VAL SER PHE HIS PRO GLY CYS VAL PRO GLU MET
SEQRES 17 A 342 LYS GLY GLN VAL TYR LEU SER GLU GLY TYR ALA SER GLU
SEQRES 18 A 342 GLU ALA VAL GLU LYS LEU TYR LYS ILE ALA LYS ILE SER
SEQRES 19 A 342 ARG GLY THR ALA PHE LYS MET PRO ALA ASN LEU ILE SER
SEQRES 20 A 342 PRO VAL CYS ASP MET GLY SER ALA VAL THR ALA PRO VAL
SEQRES 21 A 342 TYR ALA ALA ILE LEU SER TYR ARG ASP ALA VAL THR ASN
SEQRES 22 A 342 ILE LEU GLY ALA PRO ALA ASP PHE ALA GLN MET MET ALA
SEQRES 23 A 342 ASP GLU ALA ILE THR GLN MET LEU GLU LEU MET ARG ASN
SEQRES 24 A 342 GLU GLY ILE GLN ASN MET GLU ASN LYS LEU ASN PRO GLY
SEQRES 25 A 342 ALA LEU THR GLY THR ALA ASP SER MET CYS PHE GLY PRO
SEQRES 26 A 342 LEU SER GLU LEU LEU PRO ALA SER LEU LYS VAL LEU GLU
SEQRES 27 A 342 GLU HIS LYS LYS
HET FE9 A 401 41
HET GOL A 402 6
HET GOL A 403 6
HET GOL A 404 6
HET GOL A 405 6
HET GOL A 406 6
HET NA A 407 1
HET NA A 408 1
HET SCN A 409 3
HET SCN A 410 3
HET SCN A 411 3
HET E4M A 412 54
HETNAM FE9 IRON-GUANYLYL PYRIDINOL COFACTOR
HETNAM GOL GLYCEROL
HETNAM NA SODIUM ION
HETNAM SCN THIOCYANATE ION
HETNAM E4M 1-{4-[(6S,6AR,7R)-3-AMINO-6,7-DIMETHYL-1-OXO-1,2,5,6,
HETNAM 2 E4M 6A,7-HEXAHYDRO-8H-IMIDAZO[1,5-F]PTERIDIN-10-IUM-8-
HETNAM 3 E4M YL]PHENYL}-1-DEOXY-5-O-{5-O-[(S)-{[(1S)-1,3-
HETNAM 4 E4M DICARBOXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]-ALPHA-D-
HETNAM 5 E4M RIBOFURANOSYL}-D-RIBITOL
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 2 FE9 C21 H23 FE N6 O13 P S 4+
FORMUL 3 GOL 5(C3 H8 O3)
FORMUL 8 NA 2(NA 1+)
FORMUL 10 SCN 3(C N S 1-)
FORMUL 13 E4M C31 H44 N6 O16 P 1+
FORMUL 14 HOH *505(H2 O)
HELIX 1 AA1 TYR A 11 GLY A 18 1 8
HELIX 2 AA2 PHE A 22 GLY A 33 1 12
HELIX 3 AA3 ILE A 34 THR A 40 5 7
HELIX 4 AA4 HIS A 41 VAL A 54 1 14
HELIX 5 AA5 PRO A 65 GLU A 69 5 5
HELIX 6 AA6 ASP A 80 ALA A 90 1 11
HELIX 7 AA7 LYS A 92 ASP A 95 5 4
HELIX 8 AA8 VAL A 96 ASP A 110 1 15
HELIX 9 AA9 ASN A 123 GLY A 128 5 6
HELIX 10 AB1 ASP A 134 GLU A 140 1 7
HELIX 11 AB2 LYS A 151 GLY A 153 5 3
HELIX 12 AB3 SER A 154 VAL A 163 1 10
HELIX 13 AB4 ASP A 164 ILE A 166 5 3
HELIX 14 AB5 PRO A 179 LEU A 190 1 12
HELIX 15 AB6 SER A 220 GLY A 236 1 17
HELIX 16 AB7 LEU A 245 ASP A 251 1 7
HELIX 17 AB8 GLY A 253 ILE A 274 1 22
HELIX 18 AB9 PRO A 278 GLY A 301 1 24
HELIX 19 AC1 ASN A 304 LEU A 309 1 6
HELIX 20 AC2 ASN A 310 THR A 315 5 6
HELIX 21 AC3 THR A 317 CYS A 322 5 6
HELIX 22 AC4 PHE A 323 SER A 327 5 5
HELIX 23 AC5 GLU A 328 HIS A 340 1 13
SHEET 1 AA1 6 LYS A 130 THR A 132 0
SHEET 2 AA1 6 GLU A 59 SER A 63 1 N VAL A 62 O LYS A 130
SHEET 3 AA1 6 LYS A 2 LEU A 6 1 N ILE A 5 O SER A 63
SHEET 4 AA1 6 ILE A 144 THR A 147 1 O ILE A 146 N ALA A 4
SHEET 5 AA1 6 ILE A 171 THR A 173 1 O ILE A 171 N VAL A 145
SHEET 6 AA1 6 ASN A 196 ILE A 197 1 O ASN A 196 N VAL A 172
SHEET 1 AA2 2 GLY A 72 ILE A 75 0
SHEET 2 AA2 2 GLY A 117 HIS A 120 1 O HIS A 120 N ILE A 74
SHEET 1 AA3 2 TYR A 213 GLU A 216 0
SHEET 2 AA3 2 PHE A 239 PRO A 242 1 O PHE A 239 N LEU A 214
SSBOND 1 CYS A 66 CYS A 118 1555 1555 2.12
LINK O LEU A 51 NA NA A 407 1555 1555 2.24
LINK O VAL A 54 NA NA A 407 1555 1555 2.30
LINK O ILE A 57 NA NA A 407 1555 1555 2.30
LINK SG CYS A 176 FE FE9 A 401 1555 1555 2.41
LINK NA NA A 407 O HOH A 648 1555 3555 2.26
LINK NA NA A 407 O HOH A 807 1555 3555 2.45
LINK NA NA A 408 O HOH A 842 1555 1555 3.06
LINK NA NA A 408 O AHOH A 989 1555 1555 2.71
LINK NA NA A 408 O AHOH A 989 1555 3555 2.71
CISPEP 1 GLU A 70 PRO A 71 0 -0.09
CISPEP 2 PRO A 114 PRO A 115 0 4.18
SITE 1 AC1 32 LEU A 6 GLY A 7 GLY A 9 CYS A 10
SITE 2 AC1 32 SER A 13 HIS A 14 SER A 63 ASP A 64
SITE 3 AC1 32 PRO A 65 CYS A 66 PRO A 114 PRO A 115
SITE 4 AC1 32 CYS A 118 ASP A 135 TRP A 148 LEU A 149
SITE 5 AC1 32 PRO A 150 ILE A 158 ALA A 175 CYS A 176
SITE 6 AC1 32 THR A 177 HIS A 201 PRO A 202 GLY A 203
SITE 7 AC1 32 CYS A 204 VAL A 205 PRO A 206 E4M A 412
SITE 8 AC1 32 HOH A 545 HOH A 579 HOH A 598 HOH A 632
SITE 1 AC2 11 ILE A 76 ASP A 77 GLU A 78 GLY A 217
SITE 2 AC2 11 TYR A 218 ALA A 219 SER A 220 HOH A 512
SITE 3 AC2 11 HOH A 553 HOH A 619 HOH A 620
SITE 1 AC3 6 PHE A 239 HOH A 533 HOH A 574 HOH A 657
SITE 2 AC3 6 HOH A 804 HOH A 846
SITE 1 AC4 11 GLU A 78 ASP A 102 ALA A 103 GLY A 217
SITE 2 AC4 11 TYR A 218 ASN A 244 HOH A 513 HOH A 529
SITE 3 AC4 11 HOH A 605 HOH A 693 HOH A 749
SITE 1 AC5 11 ALA A 29 ASN A 30 GLY A 33 ILE A 34
SITE 2 AC5 11 PRO A 35 ASP A 58 LYS A 82 MET A 85
SITE 3 AC5 11 HOH A 519 HOH A 559 HOH A 648
SITE 1 AC6 4 LEU A 294 GLU A 295 ARG A 298 HOH A 785
SITE 1 AC7 5 LEU A 51 VAL A 54 ILE A 57 HOH A 648
SITE 2 AC7 5 HOH A 807
SITE 1 AC8 5 HIS A 52 VAL A 127 GLY A 128 HOH A 842
SITE 2 AC8 5 HOH A 989
SITE 1 AC9 3 GLY A 152 HOH A 651 HOH A 825
SITE 1 AD1 3 GLY A 153 PHE A 281 HOH A 948
SITE 1 AD2 3 GLY A 324 PRO A 325 HOH A 531
SITE 1 AD3 30 SER A 13 CYS A 17 LYS A 113 PRO A 114
SITE 2 AD3 30 PRO A 150 LYS A 151 CYS A 176 GLY A 203
SITE 3 AD3 30 CYS A 250 ASP A 251 MET A 252 SER A 254
SITE 4 AD3 30 PRO A 278 PHE A 281 THR A 317 SER A 320
SITE 5 AD3 30 MET A 321 FE9 A 401 HOH A 505 HOH A 508
SITE 6 AD3 30 HOH A 539 HOH A 545 HOH A 547 HOH A 593
SITE 7 AD3 30 HOH A 629 HOH A 632 HOH A 667 HOH A 731
SITE 8 AD3 30 HOH A 796 HOH A 806
CRYST1 66.648 66.246 167.599 90.00 90.00 90.00 C 2 2 21 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 0.015004 0.000000 0.000000 0.00000
SCALE2 0.000000 0.015095 0.000000 0.00000
SCALE3 0.000000 0.000000 0.005967 0.00000