HEADER OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR 05-NOV-13 4NHX TITLE CRYSTAL STRUCTURE OF HUMAN OGFOD1, 2-OXOGLUTARATE AND IRON-DEPENDENT TITLE 2 OXYGENASE DOMAIN CONTAINING 1, IN COMPLEX WITH N-OXALYLGLYCINE (NOG) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2-OXOGLUTARATE AND IRON-DEPENDENT OXYGENASE DOMAIN- COMPND 3 CONTAINING PROTEIN 1; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: TERMINATION AND POLYADENYLATION 1 HOMOLOG; COMPND 6 EC: 1.14.11.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: OGFOD1, KIAA1612, TPA1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS JELLY-ROLL FOLD, TRANSLATION, RIBOSOME, DOUBLE-STRANDED BETA HELIX, KEYWDS 2 OXYGEN SENSING, OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.HORITA,M.A.MCDONOUGH,C.J.SCHOFIELD REVDAT 6 20-SEP-23 4NHX 1 REMARK SEQADV LINK REVDAT 5 17-JUL-19 4NHX 1 REMARK REVDAT 4 22-NOV-17 4NHX 1 REMARK REVDAT 3 29-APR-15 4NHX 1 JRNL REVDAT 2 18-MAR-15 4NHX 1 JRNL REVDAT 1 19-NOV-14 4NHX 0 JRNL AUTH S.HORITA,J.S.SCOTTI,C.THINNES,Y.S.MOTTAGHI-TAROMSARI, JRNL AUTH 2 A.THALHAMMER,W.GE,W.AIK,C.LOENARZ,C.J.SCHOFIELD, JRNL AUTH 3 M.A.MCDONOUGH JRNL TITL STRUCTURE OF THE RIBOSOMAL OXYGENASE OGFOD1 PROVIDES JRNL TITL 2 INSIGHTS INTO THE REGIO- AND STEREOSELECTIVITY OF PROLYL JRNL TITL 3 HYDROXYLASES. JRNL REF STRUCTURE V. 23 639 2015 JRNL REFN ISSN 0969-2126 JRNL PMID 25728928 JRNL DOI 10.1016/J.STR.2015.01.014 REMARK 2 REMARK 2 RESOLUTION. 2.11 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.2_1309 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.24 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 33004 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.070 REMARK 3 FREE R VALUE TEST SET COUNT : 2004 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 2.1580 - 2.1053 0.85 0 119 0.2965 0.3383 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.370 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.70 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 : 0.006 NULL REMARK 3 ANGLE : 1.000 NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -8.1162 9.1731 57.5758 REMARK 3 T TENSOR REMARK 3 T11: 0.3728 T22: 0.2654 REMARK 3 T33: 0.1957 T12: 0.0500 REMARK 3 T13: -0.0177 T23: -0.0074 REMARK 3 L TENSOR REMARK 3 L11: 3.7739 L22: 2.9380 REMARK 3 L33: 1.0293 L12: 2.8039 REMARK 3 L13: -1.4561 L23: -1.2218 REMARK 3 S TENSOR REMARK 3 S11: -0.0329 S12: -0.1718 S13: -0.0735 REMARK 3 S21: -0.2621 S22: -0.1179 S23: -0.0032 REMARK 3 S31: 0.1248 S32: 0.1517 S33: 0.1652 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 4NHX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-NOV-13. REMARK 100 THE DEPOSITION ID IS D_1000083224. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-SEP-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.83440 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33097 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 16.20 REMARK 200 R MERGE (I) : 0.15300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.7 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.64800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 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: PDB ENTRY 3KT7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.7 MM MNCL2, 1.0 MM OGA, 25% (W/V) REMARK 280 PEG 1500, 100 MM MIB BUFFER AND 100 MM GLYCINE, PH 6.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-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 154.69400 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 77.34700 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 77.34700 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 154.69400 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 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 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ASN A 2 REMARK 465 GLY A 3 REMARK 465 LYS A 4 REMARK 465 ARG A 5 REMARK 465 PRO A 6 REMARK 465 ALA A 7 REMARK 465 GLU A 8 REMARK 465 PRO A 9 REMARK 465 GLY A 10 REMARK 465 PRO A 11 REMARK 465 ALA A 12 REMARK 465 ARG A 13 REMARK 465 VAL A 14 REMARK 465 GLY A 15 REMARK 465 LYS A 16 REMARK 465 LYS A 17 REMARK 465 GLY A 18 REMARK 465 LYS A 19 REMARK 465 LYS A 20 REMARK 465 GLU A 21 REMARK 465 VAL A 22 REMARK 465 MET A 23 REMARK 465 GLU A 372 REMARK 465 GLU A 373 REMARK 465 ASP A 374 REMARK 465 GLU A 375 REMARK 465 MET A 376 REMARK 465 ASN A 377 REMARK 465 ASP A 378 REMARK 465 LYS A 379 REMARK 465 LYS A 380 REMARK 465 GLU A 381 REMARK 465 ALA A 382 REMARK 465 GLU A 383 REMARK 465 THR A 384 REMARK 465 THR A 385 REMARK 465 ASP A 386 REMARK 465 ILE A 387 REMARK 465 THR A 388 REMARK 465 GLU A 389 REMARK 465 GLU A 390 REMARK 465 GLY A 391 REMARK 465 THR A 392 REMARK 465 SER A 393 REMARK 465 HIS A 394 REMARK 465 SER A 395 REMARK 465 PRO A 396 REMARK 465 PRO A 397 REMARK 465 GLU A 398 REMARK 465 PRO A 399 REMARK 465 GLU A 400 REMARK 465 ASN A 401 REMARK 465 ASN A 402 REMARK 465 GLN A 403 REMARK 465 MET A 404 REMARK 465 ALA A 405 REMARK 465 ILE A 406 REMARK 465 SER A 407 REMARK 465 ASN A 408 REMARK 465 ASN A 409 REMARK 465 SER A 410 REMARK 465 GLN A 411 REMARK 465 GLN A 412 REMARK 465 SER A 413 REMARK 465 ASN A 414 REMARK 465 GLU A 415 REMARK 465 GLN A 416 REMARK 465 THR A 417 REMARK 465 ASP A 418 REMARK 465 PRO A 419 REMARK 465 GLU A 420 REMARK 465 PRO A 421 REMARK 465 GLU A 422 REMARK 465 GLU A 423 REMARK 465 ASN A 424 REMARK 465 GLU A 425 REMARK 465 THR A 426 REMARK 465 LYS A 427 REMARK 465 LYS A 428 REMARK 465 GLU A 429 REMARK 465 ASP A 452 REMARK 465 HIS A 453 REMARK 465 SER A 454 REMARK 465 LYS A 455 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 GLU A 33 CD OE1 OE2 REMARK 470 GLU A 90 CG CD OE1 OE2 REMARK 470 LYS A 105 NZ REMARK 470 LYS A 106 CE NZ REMARK 470 LYS A 117 CD CE NZ REMARK 470 GLU A 160 CD OE1 OE2 REMARK 470 GLU A 189 CD OE1 OE2 REMARK 470 PHE A 191 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 227 CD OE1 OE2 REMARK 470 ASN A 247 CG OD1 ND2 REMARK 470 PHE A 249 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 264 CD OE1 OE2 REMARK 470 GLN A 282 CD OE1 NE2 REMARK 470 GLU A 285 CD OE1 OE2 REMARK 470 GLU A 289 CD OE1 OE2 REMARK 470 GLU A 302 CG CD OE1 OE2 REMARK 470 LYS A 306 CD CE NZ REMARK 470 SER A 430 N CB OG REMARK 470 LYS A 443 CE NZ REMARK 470 GLU A 488 CB CG CD OE1 OE2 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 877 O HOH A 888 5665 2.12 REMARK 500 O HOH A 826 O HOH A 878 5565 2.17 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 27 119.36 -38.33 REMARK 500 ASN A 93 -153.54 -163.48 REMARK 500 PHE A 98 -175.76 -172.06 REMARK 500 GLU A 121 -64.25 -120.93 REMARK 500 THR A 149 -10.91 86.81 REMARK 500 ASP A 157 -0.63 67.03 REMARK 500 LYS A 194 -64.64 -107.72 REMARK 500 LEU A 242 -161.97 -72.78 REMARK 500 ASP A 262 -76.79 -111.56 REMARK 500 LYS A 326 -39.91 -130.13 REMARK 500 HIS A 515 126.78 -37.97 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 MN A 601 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 155 NE2 REMARK 620 2 ASP A 157 OD1 84.6 REMARK 620 3 HIS A 218 NE2 90.0 97.2 REMARK 620 4 OGA A 603 O2 95.7 103.7 158.7 REMARK 620 5 OGA A 603 O2' 104.4 170.7 81.1 77.7 REMARK 620 6 HOH A 841 O 176.2 91.7 91.1 84.4 79.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 602 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 506 OD2 REMARK 620 2 ASP A 506 OD1 42.7 REMARK 620 3 THR A 509 OG1 87.0 58.7 REMARK 620 4 HOH A 944 O 76.5 114.4 156.1 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 MN A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OGA A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 604 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4NHY RELATED DB: PDB REMARK 900 RELATED ID: 4NHN RELATED DB: PDB REMARK 900 RELATED ID: 4NHM RELATED DB: PDB REMARK 900 RELATED ID: 4NHL RELATED DB: PDB REMARK 900 RELATED ID: 4NHK RELATED DB: PDB DBREF 4NHX A 1 542 UNP Q8N543 OGFD1_HUMAN 1 542 SEQADV 4NHX MET A -19 UNP Q8N543 INITIATING METHIONINE SEQADV 4NHX GLY A -18 UNP Q8N543 EXPRESSION TAG SEQADV 4NHX SER A -17 UNP Q8N543 EXPRESSION TAG SEQADV 4NHX SER A -16 UNP Q8N543 EXPRESSION TAG SEQADV 4NHX HIS A -15 UNP Q8N543 EXPRESSION TAG SEQADV 4NHX HIS A -14 UNP Q8N543 EXPRESSION TAG SEQADV 4NHX HIS A -13 UNP Q8N543 EXPRESSION TAG SEQADV 4NHX HIS A -12 UNP Q8N543 EXPRESSION TAG SEQADV 4NHX HIS A -11 UNP Q8N543 EXPRESSION TAG SEQADV 4NHX HIS A -10 UNP Q8N543 EXPRESSION TAG SEQADV 4NHX SER A -9 UNP Q8N543 EXPRESSION TAG SEQADV 4NHX SER A -8 UNP Q8N543 EXPRESSION TAG SEQADV 4NHX GLY A -7 UNP Q8N543 EXPRESSION TAG SEQADV 4NHX LEU A -6 UNP Q8N543 EXPRESSION TAG SEQADV 4NHX VAL A -5 UNP Q8N543 EXPRESSION TAG SEQADV 4NHX PRO A -4 UNP Q8N543 EXPRESSION TAG SEQADV 4NHX ARG A -3 UNP Q8N543 EXPRESSION TAG SEQADV 4NHX GLY A -2 UNP Q8N543 EXPRESSION TAG SEQADV 4NHX SER A -1 UNP Q8N543 EXPRESSION TAG SEQADV 4NHX HIS A 0 UNP Q8N543 EXPRESSION TAG SEQRES 1 A 562 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 562 LEU VAL PRO ARG GLY SER HIS MET ASN GLY LYS ARG PRO SEQRES 3 A 562 ALA GLU PRO GLY PRO ALA ARG VAL GLY LYS LYS GLY LYS SEQRES 4 A 562 LYS GLU VAL MET ALA GLU PHE SER ASP ALA VAL THR GLU SEQRES 5 A 562 GLU THR LEU LYS LYS GLN VAL ALA GLU ALA TRP SER ARG SEQRES 6 A 562 ARG THR PRO PHE SER HIS GLU VAL ILE VAL MET ASP MET SEQRES 7 A 562 ASP PRO PHE LEU HIS CYS VAL ILE PRO ASN PHE ILE GLN SEQRES 8 A 562 SER GLN ASP PHE LEU GLU GLY LEU GLN LYS GLU LEU MET SEQRES 9 A 562 ASN LEU ASP PHE HIS GLU LYS TYR ASN ASP LEU TYR LYS SEQRES 10 A 562 PHE GLN GLN SER ASP ASP LEU LYS LYS ARG ARG GLU PRO SEQRES 11 A 562 HIS ILE SER THR LEU ARG LYS ILE LEU PHE GLU ASP PHE SEQRES 12 A 562 ARG SER TRP LEU SER ASP ILE SER LYS ILE ASP LEU GLU SEQRES 13 A 562 SER THR ILE ASP MET SER CYS ALA LYS TYR GLU PHE THR SEQRES 14 A 562 ASP ALA LEU LEU CYS HIS ASP ASP GLU LEU GLU GLY ARG SEQRES 15 A 562 ARG ILE ALA PHE ILE LEU TYR LEU VAL PRO PRO TRP ASP SEQRES 16 A 562 ARG SER MET GLY GLY THR LEU ASP LEU TYR SER ILE ASP SEQRES 17 A 562 GLU HIS PHE GLN PRO LYS GLN ILE VAL LYS SER LEU ILE SEQRES 18 A 562 PRO SER TRP ASN LYS LEU VAL PHE PHE GLU VAL SER PRO SEQRES 19 A 562 VAL SER PHE HIS GLN VAL SER GLU VAL LEU SER GLU GLU SEQRES 20 A 562 LYS SER ARG LEU SER ILE SER GLY TRP PHE HIS GLY PRO SEQRES 21 A 562 SER LEU THR ARG PRO PRO ASN TYR PHE GLU PRO PRO ILE SEQRES 22 A 562 PRO ARG SER PRO HIS ILE PRO GLN ASP HIS GLU ILE LEU SEQRES 23 A 562 TYR ASP TRP ILE ASN PRO THR TYR LEU ASP MET ASP TYR SEQRES 24 A 562 GLN VAL GLN ILE GLN GLU GLU PHE GLU GLU SER SER GLU SEQRES 25 A 562 ILE LEU LEU LYS GLU PHE LEU LYS PRO GLU LYS PHE THR SEQRES 26 A 562 LYS VAL CYS GLU ALA LEU GLU HIS GLY HIS VAL GLU TRP SEQRES 27 A 562 SER SER ARG GLY PRO PRO ASN LYS ARG PHE TYR GLU LYS SEQRES 28 A 562 ALA GLU GLU SER LYS LEU PRO GLU ILE LEU LYS GLU CYS SEQRES 29 A 562 MET LYS LEU PHE ARG SER GLU ALA LEU PHE LEU LEU LEU SEQRES 30 A 562 SER ASN PHE THR GLY LEU LYS LEU HIS PHE LEU ALA PRO SEQRES 31 A 562 SER GLU GLU ASP GLU MET ASN ASP LYS LYS GLU ALA GLU SEQRES 32 A 562 THR THR ASP ILE THR GLU GLU GLY THR SER HIS SER PRO SEQRES 33 A 562 PRO GLU PRO GLU ASN ASN GLN MET ALA ILE SER ASN ASN SEQRES 34 A 562 SER GLN GLN SER ASN GLU GLN THR ASP PRO GLU PRO GLU SEQRES 35 A 562 GLU ASN GLU THR LYS LYS GLU SER SER VAL PRO MET CYS SEQRES 36 A 562 GLN GLY GLU LEU ARG HIS TRP LYS THR GLY HIS TYR THR SEQRES 37 A 562 LEU ILE HIS ASP HIS SER LYS ALA GLU PHE ALA LEU ASP SEQRES 38 A 562 LEU ILE LEU TYR CYS GLY CYS GLU GLY TRP GLU PRO GLU SEQRES 39 A 562 TYR GLY GLY PHE THR SER TYR ILE ALA LYS GLY GLU ASP SEQRES 40 A 562 GLU GLU LEU LEU THR VAL ASN PRO GLU SER ASN SER LEU SEQRES 41 A 562 ALA LEU VAL TYR ARG ASP ARG GLU THR LEU LYS PHE VAL SEQRES 42 A 562 LYS HIS ILE ASN HIS ARG SER LEU GLU GLN LYS LYS THR SEQRES 43 A 562 PHE PRO ASN ARG THR GLY PHE TRP ASP PHE SER PHE ILE SEQRES 44 A 562 TYR TYR GLU HET MN A 601 1 HET NA A 602 1 HET OGA A 603 10 HET GOL A 604 6 HETNAM MN MANGANESE (II) ION HETNAM NA SODIUM ION HETNAM OGA N-OXALYLGLYCINE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 MN MN 2+ FORMUL 3 NA NA 1+ FORMUL 4 OGA C4 H5 N O5 FORMUL 5 GOL C3 H8 O3 FORMUL 6 HOH *175(H2 O) HELIX 1 1 SER A 27 THR A 31 5 5 HELIX 2 2 GLU A 32 ARG A 45 1 14 HELIX 3 3 SER A 72 ASN A 85 1 14 HELIX 4 4 GLU A 109 GLU A 121 1 13 HELIX 5 5 GLU A 121 LYS A 132 1 12 HELIX 6 6 ASP A 175 GLY A 179 5 5 HELIX 7 7 ILE A 265 ILE A 270 1 6 HELIX 8 8 ASN A 271 LEU A 275 5 5 HELIX 9 9 ASP A 276 SER A 291 1 16 HELIX 10 10 LYS A 300 GLY A 314 1 15 HELIX 11 11 GLU A 334 LEU A 337 5 4 HELIX 12 12 PRO A 338 SER A 350 1 13 HELIX 13 13 SER A 350 GLY A 362 1 13 HELIX 14 14 GLU A 472 GLY A 476 5 5 HELIX 15 15 ASN A 517 THR A 526 5 10 SHEET 1 A 9 PHE A 49 SER A 50 0 SHEET 2 A 9 VAL A 55 ASP A 57 -1 O MET A 56 N PHE A 49 SHEET 3 A 9 HIS A 63 ILE A 66 -1 O HIS A 63 N ASP A 57 SHEET 4 A 9 LEU A 207 GLU A 211 -1 O LEU A 207 N ILE A 66 SHEET 5 A 9 ARG A 162 TYR A 169 -1 N ALA A 165 O PHE A 210 SHEET 6 A 9 ARG A 230 HIS A 238 -1 O ILE A 233 N LEU A 168 SHEET 7 A 9 MET A 141 TYR A 146 -1 N TYR A 146 O ARG A 230 SHEET 8 A 9 TYR A 96 SER A 101 -1 N GLN A 99 O LYS A 145 SHEET 9 A 9 PHE A 88 TYR A 92 -1 N LYS A 91 O PHE A 98 SHEET 1 B12 PHE A 49 SER A 50 0 SHEET 2 B12 VAL A 55 ASP A 57 -1 O MET A 56 N PHE A 49 SHEET 3 B12 HIS A 63 ILE A 66 -1 O HIS A 63 N ASP A 57 SHEET 4 B12 LEU A 207 GLU A 211 -1 O LEU A 207 N ILE A 66 SHEET 5 B12 ARG A 162 TYR A 169 -1 N ALA A 165 O PHE A 210 SHEET 6 B12 ARG A 230 HIS A 238 -1 O ILE A 233 N LEU A 168 SHEET 7 B12 MET A 141 TYR A 146 -1 N TYR A 146 O ARG A 230 SHEET 8 B12 TYR A 96 SER A 101 -1 N GLN A 99 O LYS A 145 SHEET 9 B12 ALA A 151 HIS A 155 -1 O ALA A 151 N LYS A 97 SHEET 10 B12 HIS A 218 VAL A 220 -1 O VAL A 220 N LEU A 152 SHEET 11 B12 LEU A 182 ILE A 187 -1 N ASP A 183 O GLN A 219 SHEET 12 B12 PRO A 193 LEU A 200 -1 O LYS A 198 N LEU A 184 SHEET 1 C 7 GLU A 292 LEU A 295 0 SHEET 2 C 7 LEU A 500 ARG A 505 -1 O LEU A 500 N LEU A 295 SHEET 3 C 7 ALA A 459 CYS A 466 -1 N ALA A 459 O ARG A 505 SHEET 4 C 7 PHE A 533 TYR A 541 -1 O TRP A 534 N CYS A 466 SHEET 5 C 7 MET A 434 TRP A 442 -1 N TRP A 442 O PHE A 533 SHEET 6 C 7 ARG A 327 ALA A 332 -1 N ALA A 332 O LEU A 439 SHEET 7 C 7 TRP A 318 ARG A 321 -1 N ARG A 321 O TYR A 329 SHEET 1 D 7 GLU A 292 LEU A 295 0 SHEET 2 D 7 LEU A 500 ARG A 505 -1 O LEU A 500 N LEU A 295 SHEET 3 D 7 ALA A 459 CYS A 466 -1 N ALA A 459 O ARG A 505 SHEET 4 D 7 PHE A 533 TYR A 541 -1 O TRP A 534 N CYS A 466 SHEET 5 D 7 MET A 434 TRP A 442 -1 N TRP A 442 O PHE A 533 SHEET 6 D 7 ARG A 327 ALA A 332 -1 N ALA A 332 O LEU A 439 SHEET 7 D 7 TYR A 447 THR A 448 -1 O TYR A 447 N PHE A 328 SHEET 1 E 3 GLU A 489 VAL A 493 0 SHEET 2 E 3 THR A 479 ALA A 483 -1 N THR A 479 O VAL A 493 SHEET 3 E 3 THR A 509 VAL A 513 -1 O PHE A 512 N SER A 480 LINK NE2 HIS A 155 MN MN A 601 1555 1555 2.24 LINK OD1 ASP A 157 MN MN A 601 1555 1555 2.11 LINK NE2 HIS A 218 MN MN A 601 1555 1555 2.11 LINK OD2 ASP A 506 NA NA A 602 1555 1555 2.89 LINK OD1 ASP A 506 NA NA A 602 1555 1555 3.11 LINK OG1 THR A 509 NA NA A 602 1555 1555 2.36 LINK MN MN A 601 O2 OGA A 603 1555 1555 2.15 LINK MN MN A 601 O2' OGA A 603 1555 1555 2.20 LINK MN MN A 601 O HOH A 841 1555 1555 2.24 LINK NA NA A 602 O HOH A 944 1555 1555 2.36 CISPEP 1 ASP A 59 PRO A 60 0 2.37 CISPEP 2 ASP A 59 PRO A 60 0 1.96 CISPEP 3 GLY A 322 PRO A 323 0 0.18 SITE 1 AC1 5 HIS A 155 ASP A 157 HIS A 218 OGA A 603 SITE 2 AC1 5 HOH A 841 SITE 1 AC2 4 ARG A 108 ASP A 506 THR A 509 HOH A 944 SITE 1 AC3 13 LEU A 152 HIS A 155 ASP A 157 TYR A 169 SITE 2 AC3 13 HIS A 218 VAL A 220 ARG A 230 MN A 601 SITE 3 AC3 13 GOL A 604 HOH A 838 HOH A 841 HOH A 843 SITE 4 AC3 13 HOH A 844 SITE 1 AC4 4 HIS A 155 ARG A 162 TRP A 236 OGA A 603 CRYST1 64.401 64.401 232.041 90.00 90.00 120.00 P 32 2 1 6 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 0.015528 0.008965 0.000000 0.00000 SCALE2 0.000000 0.017930 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004310 0.00000