HEADER OXIDOREDUCTASE 25-JUL-17 5OK4 TITLE CRYSTAL STRUCTURE OF NATIVE [FE]-HYDROGENASE HMD FROM TITLE 2 METHANOTHERMOBACTER MARBURGENSIS INACTIVATED BY O2. 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 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOTHERMOBACTER MARBURGENSIS STR. MARBURG; SOURCE 3 ORGANISM_TAXID: 79929; SOURCE 4 CELL_LINE: /; SOURCE 5 ORGAN: /; SOURCE 6 TISSUE: / KEYWDS [FE]-HYDROGENASE, FE-GUANYLYLPYRIDINOL COFACTOR, H2, HYDROGENASE, KEYWDS 2 METHANOGENESIS, METHENYL-TETRAHYDROMETHANOPTERIN, METHYLENE- KEYWDS 3 TETRAHYDROMETHANOPTERIN, HYDROGENATION, O2, INACTIVATION, KEYWDS 4 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR T.WAGNER,G.HUANG,E.BILL,U.ERMLER,K.ATAKA,S.SHIMA REVDAT 3 17-JAN-24 5OK4 1 LINK REVDAT 2 30-MAY-18 5OK4 1 JRNL REVDAT 1 16-MAY-18 5OK4 0 JRNL AUTH G.HUANG,T.WAGNER,U.ERMLER,E.BILL,K.ATAKA,S.SHIMA JRNL TITL DIOXYGEN SENSITIVITY OF [FE]-HYDROGENASE IN THE PRESENCE OF JRNL TITL 2 REDUCING SUBSTRATES. JRNL REF ANGEW. CHEM. INT. ED. ENGL. V. 57 4917 2018 JRNL REFN ESSN 1521-3773 JRNL PMID 29462510 JRNL DOI 10.1002/ANIE.201712293 REMARK 2 REMARK 2 RESOLUTION. 1.29 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) : 1.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 110053 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.128 REMARK 3 R VALUE (WORKING SET) : 0.127 REMARK 3 FREE R VALUE : 0.147 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950 REMARK 3 FREE R VALUE TEST SET COUNT : 5448 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 43.4989 - 4.0073 1.00 3634 205 0.1412 0.1576 REMARK 3 2 4.0073 - 3.1810 1.00 3552 189 0.1261 0.1434 REMARK 3 3 3.1810 - 2.7790 1.00 3538 167 0.1313 0.1257 REMARK 3 4 2.7790 - 2.5250 1.00 3517 194 0.1226 0.1542 REMARK 3 5 2.5250 - 2.3440 1.00 3492 174 0.1162 0.1211 REMARK 3 6 2.3440 - 2.2058 1.00 3521 164 0.1127 0.1299 REMARK 3 7 2.2058 - 2.0953 1.00 3488 189 0.1108 0.1383 REMARK 3 8 2.0953 - 2.0041 1.00 3503 184 0.1111 0.1288 REMARK 3 9 2.0041 - 1.9270 1.00 3478 181 0.1125 0.1438 REMARK 3 10 1.9270 - 1.8605 1.00 3476 190 0.1188 0.1301 REMARK 3 11 1.8605 - 1.8023 1.00 3484 185 0.1059 0.1299 REMARK 3 12 1.8023 - 1.7508 1.00 3463 187 0.1018 0.1277 REMARK 3 13 1.7508 - 1.7047 1.00 3465 196 0.1027 0.1478 REMARK 3 14 1.7047 - 1.6631 1.00 3477 181 0.1028 0.1239 REMARK 3 15 1.6631 - 1.6253 1.00 3486 174 0.1057 0.1338 REMARK 3 16 1.6253 - 1.5907 1.00 3456 172 0.1084 0.1481 REMARK 3 17 1.5907 - 1.5589 1.00 3502 175 0.1105 0.1480 REMARK 3 18 1.5589 - 1.5295 1.00 3462 193 0.1166 0.1411 REMARK 3 19 1.5295 - 1.5021 1.00 3486 171 0.1238 0.1576 REMARK 3 20 1.5021 - 1.4767 1.00 3480 178 0.1283 0.1571 REMARK 3 21 1.4767 - 1.4529 1.00 3439 193 0.1368 0.1902 REMARK 3 22 1.4529 - 1.4305 1.00 3454 172 0.1453 0.1680 REMARK 3 23 1.4305 - 1.4095 1.00 3461 197 0.1589 0.1813 REMARK 3 24 1.4095 - 1.3896 1.00 3481 173 0.1720 0.1996 REMARK 3 25 1.3896 - 1.3708 1.00 3470 191 0.1894 0.2186 REMARK 3 26 1.3708 - 1.3530 1.00 3484 153 0.1987 0.2321 REMARK 3 27 1.3530 - 1.3361 1.00 3486 181 0.2080 0.2425 REMARK 3 28 1.3361 - 1.3200 1.00 3438 186 0.2199 0.2544 REMARK 3 29 1.3200 - 1.3047 1.00 3445 181 0.2434 0.2776 REMARK 3 30 1.3047 - 1.2900 1.00 3487 172 0.2349 0.2186 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.610 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.00 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 : 0.010 2867 REMARK 3 ANGLE : 1.194 3921 REMARK 3 CHIRALITY : 0.086 442 REMARK 3 PLANARITY : 0.009 513 REMARK 3 DIHEDRAL : 24.265 1098 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 5OK4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-JUL-17. REMARK 100 THE DEPOSITION ID IS D_1200005943. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-NOV-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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) : 1.00005 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 : 110077 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.290 REMARK 200 RESOLUTION RANGE LOW (A) : 47.070 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.200 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.36 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.00 REMARK 200 R MERGE FOR SHELL (I) : 1.12800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 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: 2JJF REMARK 200 REMARK 200 REMARK: TRANSPARENT CUBE SHAPE OF ABOUT 100X100 MICROMETER. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1-ML MIXTURE CONTAINING 120 MM REMARK 280 POTASSIUM PHOSPHATE PH 6.0, 1 MM EDTA, 26 UM (1 MG/ML) [FE]- REMARK 280 HYDROGENASE AND 26 UM METHYLENE-H4MPT WAS INCUBATED IN 5-ML REMARK 280 AMBER VIALS WITH RUBBER STOPPERS UNDER A GAS MIXTURE OF N2/O2/H2 REMARK 280 (70%/20%/10%) AT 40 DEGREE CELSIUS FOR 1 H. THE INACTIVATED REMARK 280 ENZYME WAS CONCENTRATED TO 25 MG/ML USING A 30 KDA CENTRIFUGAL REMARK 280 FILTER (MILLIPORE). 0.7-UL OF 25 MG/ML O2-INACTIVATED [FE]- REMARK 280 HYDROGENASE WAS MIXED WITH 0.7 UL OF RESERVOIR SOLUTION OF 2 M REMARK 280 (NH4)2SO4, 100 MM TRIS/HCL, PH 7.0, AND 200 MM LISO4. THE BEST REMARK 280 DIFFRACTING CRYSTAL WAS OBTAINED IN ONE MONTH. PRIOR TO FREEZING REMARK 280 THE CRYSTAL WAS SOAKED FOR 3 SECONDS IN 2 M (NH4)2SO4, 100 MM REMARK 280 TRIS/HCL, PH 7.0, 200 MM LISO4 AND 30% GLYCEROL V/V., VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 281.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 63.70900 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 36.78241 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 47.07033 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 63.70900 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 36.78241 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 47.07033 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 63.70900 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 36.78241 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 47.07033 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 63.70900 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 36.78241 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 47.07033 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 63.70900 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 36.78241 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 47.07033 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 63.70900 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 36.78241 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 47.07033 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 73.56482 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 94.14067 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 73.56482 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 94.14067 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 73.56482 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 94.14067 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 73.56482 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 94.14067 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 73.56482 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 94.14067 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 73.56482 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 94.14067 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 39050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 70370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -438.0 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 4 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 5 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 6 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 FE FE A 403 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 766 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 871 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1002 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 691 O HOH A 764 1.73 REMARK 500 O HOH A 613 O HOH A 669 2.00 REMARK 500 O HOH A 612 O HOH A 965 2.17 REMARK 500 O HOH A 781 O HOH A 958 2.18 REMARK 500 O HOH A 719 O HOH A 728 2.19 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 613 O HOH A 780 15554 1.90 REMARK 500 O HOH A 802 O HOH A 918 17555 2.03 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 -138.16 57.51 REMARK 500 ASN A 68 -132.52 -117.17 REMARK 500 GLN A 69 61.46 -101.98 REMARK 500 GLU A 87 -57.64 -126.11 REMARK 500 PRO A 146 -171.33 -46.70 REMARK 500 LYS A 186 -86.42 -101.10 REMARK 500 THR A 200 -159.74 -158.68 REMARK 500 ALA A 206 -133.77 50.97 REMARK 500 GLN A 213 157.36 83.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE A 403 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 153 OD2 REMARK 620 2 ASP A 153 OD2 0.0 REMARK 620 3 HOH A 871 O 113.2 113.2 REMARK 620 4 HOH A 871 O 113.4 113.4 0.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE A 401 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 172 SG REMARK 620 2 ASP A 189 OD2 56.7 REMARK 620 3 HIS A 203 NE2 108.6 77.5 REMARK 620 4 FEG A 404 O18 85.3 36.7 86.8 REMARK 620 5 FEG A 404 O28 108.5 85.7 120.1 51.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE A 402 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 187 ND1 REMARK 620 2 GLY A 249 O 31.9 REMARK 620 3 CYS A 252 SG 29.1 4.1 REMARK 620 4 CYS A 255 SG 28.9 4.4 5.9 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FEG 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 DBREF 5OK4 A 1 344 UNP P32440 HMD_METTM 1 344 SEQRES 1 A 344 MET LYS LEU ALA ILE LEU GLY ALA GLY CYS TYR ARG THR SEQRES 2 A 344 HIS ALA ALA SER GLY ILE THR ASN PHE SER ARG ALA CYS SEQRES 3 A 344 GLU VAL ALA GLU MET VAL GLY LYS PRO GLU ILE ALA MET SEQRES 4 A 344 THR HIS SER THR ILE THR MET GLY ALA GLU LEU LYS GLU SEQRES 5 A 344 LEU ALA GLY VAL ASP GLU VAL VAL VAL ALA ASP PRO VAL SEQRES 6 A 344 PHE ASP ASN GLN PHE THR VAL ILE ASP ASP PHE ALA TYR SEQRES 7 A 344 GLU ASP VAL ILE GLU ALA HIS LYS GLU ASP PRO GLU LYS SEQRES 8 A 344 ILE MET PRO GLN ILE ARG GLU LYS VAL ASN GLU VAL ALA SEQRES 9 A 344 LYS GLU LEU PRO LYS PRO PRO GLU GLY ALA ILE HIS PHE SEQRES 10 A 344 THR HIS PRO GLU ASP LEU GLY PHE GLU ILE THR THR ASP SEQRES 11 A 344 ASP ARG GLU ALA VAL ALA ASP ALA ASP PHE ILE MET THR SEQRES 12 A 344 TRP PHE PRO LYS GLY ASP MET GLN PRO ASP ILE ILE ASN SEQRES 13 A 344 LYS PHE ILE ASP ASP ILE LYS PRO GLY ALA ILE VAL THR SEQRES 14 A 344 HIS ALA CYS THR ILE PRO THR THR LYS PHE TYR LYS ILE SEQRES 15 A 344 PHE GLU GLN LYS HIS GLY ASP LEU VAL THR LYS PRO GLU SEQRES 16 A 344 THR LEU ASN VAL THR SER TYR HIS PRO GLY ALA VAL PRO SEQRES 17 A 344 GLU MET LYS GLY GLN VAL TYR ILE ALA GLU GLY TYR ALA SEQRES 18 A 344 SER GLU ASP ALA ILE GLU THR LEU PHE GLU LEU GLY GLN SEQRES 19 A 344 LYS ALA ARG GLY ASN ALA TYR ARG LEU PRO ALA GLU LEU SEQRES 20 A 344 LEU GLY PRO VAL CYS ASP MET CYS SER ALA LEU THR ALA SEQRES 21 A 344 ILE THR TYR ALA GLY ILE LEU SER TYR ARG ASP SER VAL SEQRES 22 A 344 THR GLN VAL LEU GLY ALA PRO ALA SER PHE ALA GLN MET SEQRES 23 A 344 MET ALA LYS GLU SER LEU GLU GLN ILE THR ALA LEU MET SEQRES 24 A 344 GLU LYS VAL GLY ILE ASP LYS MET GLU GLU ASN LEU ASP SEQRES 25 A 344 PRO GLY ALA LEU LEU GLY THR ALA ASP SER MET ASN PHE SEQRES 26 A 344 GLY ALA SER ALA GLU ILE LEU PRO THR VAL PHE GLU ILE SEQRES 27 A 344 LEU GLU LYS ARG LYS LYS HET FE A 401 1 HET FE A 402 1 HET FE A 403 1 HET FEG A 404 37 HET GOL A 405 6 HETNAM FE FE (III) ION HETNAM FEG 5'-O-[(S)-{[2-(CARBOXYMETHYL)-6-HYDROXY-3,5- HETNAM 2 FEG DIMETHYLPYRIDIN-4-YL]OXY}(HYDROXY)PHOSPHORYL]GUANOSINE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 FE 3(FE 3+) FORMUL 5 FEG C19 H23 N6 O11 P FORMUL 6 GOL C3 H8 O3 FORMUL 7 HOH *516(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 LYS A 34 THR A 40 5 7 HELIX 4 AA4 HIS A 41 ALA A 54 1 14 HELIX 5 AA5 PRO A 64 ASN A 68 5 5 HELIX 6 AA6 ALA A 77 ASP A 88 1 12 HELIX 7 AA7 PRO A 89 LYS A 91 5 3 HELIX 8 AA8 ILE A 92 LEU A 107 1 16 HELIX 9 AA9 HIS A 119 GLY A 124 5 6 HELIX 10 AB1 ASP A 130 ALA A 136 1 7 HELIX 11 AB2 LYS A 147 ASP A 149 5 3 HELIX 12 AB3 MET A 150 ASN A 156 1 7 HELIX 13 AB4 LYS A 157 ILE A 162 5 6 HELIX 14 AB5 PRO A 175 GLU A 184 1 10 HELIX 15 AB6 SER A 222 GLY A 238 1 17 HELIX 16 AB7 GLU A 246 CYS A 252 5 7 HELIX 17 AB8 CYS A 255 VAL A 276 1 22 HELIX 18 AB9 PRO A 280 GLY A 303 1 24 HELIX 19 AC1 ILE A 304 ASN A 310 5 7 HELIX 20 AC2 ASP A 312 ALA A 315 5 4 HELIX 21 AC3 LEU A 316 ASP A 321 1 6 HELIX 22 AC4 SER A 322 ASN A 324 5 3 HELIX 23 AC5 PHE A 325 GLY A 326 5 2 HELIX 24 AC6 ALA A 327 LYS A 343 1 17 SHEET 1 AA1 6 GLU A 126 THR A 128 0 SHEET 2 AA1 6 GLU A 58 ALA A 62 1 N VAL A 61 O GLU A 126 SHEET 3 AA1 6 LYS A 2 LEU A 6 1 N ILE A 5 O VAL A 60 SHEET 4 AA1 6 PHE A 140 THR A 143 1 O MET A 142 N ALA A 4 SHEET 5 AA1 6 ILE A 167 THR A 169 1 O ILE A 167 N ILE A 141 SHEET 6 AA1 6 ASN A 198 THR A 200 1 O ASN A 198 N VAL A 168 SHEET 1 AA2 2 GLN A 69 VAL A 72 0 SHEET 2 AA2 2 GLY A 113 HIS A 116 1 O ALA A 114 N THR A 71 SHEET 1 AA3 2 TYR A 215 GLU A 218 0 SHEET 2 AA3 2 TYR A 241 PRO A 244 1 O TYR A 241 N ILE A 216 LINK OD2 ASP A 153 FE FE A 403 1555 1555 1.95 LINK OD2 ASP A 153 FE FE A 403 1555 2555 1.95 LINK SG CYS A 172 FE FE A 401 1555 1555 2.27 LINK ND1 HIS A 187 FE FE A 402 1555 2555 2.00 LINK OD2 ASP A 189 FE FE A 401 1555 2555 1.95 LINK NE2 HIS A 203 FE FE A 401 1555 1555 2.00 LINK O GLY A 249 FE FE A 402 1555 1555 2.13 LINK SG CYS A 252 FE FE A 402 1555 1555 2.23 LINK SG CYS A 255 FE FE A 402 1555 1555 2.27 LINK FE FE A 401 O18 FEG A 404 1555 1555 2.78 LINK FE FE A 401 O28 FEG A 404 1555 1555 1.98 LINK FE FE A 403 O HOH A 871 1555 1555 2.03 LINK FE FE A 403 O HOH A 871 1555 2555 2.03 CISPEP 1 PRO A 110 PRO A 111 0 7.46 SITE 1 AC1 4 CYS A 172 ASP A 189 HIS A 203 FEG A 404 SITE 1 AC2 4 HIS A 187 GLY A 249 CYS A 252 CYS A 255 SITE 1 AC3 2 ASP A 153 HOH A 871 SITE 1 AC4 29 LEU A 6 GLY A 7 GLY A 9 CYS A 10 SITE 2 AC4 29 THR A 13 HIS A 14 ALA A 62 ASP A 63 SITE 3 AC4 29 PRO A 64 PRO A 110 PRO A 111 ASP A 131 SITE 4 AC4 29 TRP A 144 PHE A 145 PRO A 146 ILE A 154 SITE 5 AC4 29 ALA A 171 CYS A 172 ASP A 189 HIS A 203 SITE 6 AC4 29 FE A 401 HOH A 546 HOH A 560 HOH A 563 SITE 7 AC4 29 HOH A 578 HOH A 659 HOH A 701 HOH A 807 SITE 8 AC4 29 HOH A 820 SITE 1 AC5 3 VAL A 276 HOH A 520 HOH A 543 CRYST1 127.418 127.418 141.211 90.00 90.00 120.00 H 3 2 18 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 0.007848 0.004531 0.000000 0.00000 SCALE2 0.000000 0.009062 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007082 0.00000