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 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 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 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