HEADER OXIDOREDUCTASE 01-NOV-20 7DE2 TITLE IRON AND ALPHA-KETOGLUTARATE-DEPENDENT ENDOPEROXIDASE NVFI COMPND MOL_ID: 1; COMPND 2 MOLECULE: NVFI; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ASPERGILLUS NOVOFUMIGATUS IBT 16806; SOURCE 3 ORGANISM_TAXID: 1392255; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NOVOFUMIGATONIN, ENDOPEROXIDASE, IRON AND ALPHA-KETOGLUTARATE- KEYWDS 2 DEPENDENT ENZYME, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR R.ZHAI,T.MORI,I.ABE REVDAT 3 29-MAY-24 7DE2 1 REMARK REVDAT 2 26-JAN-22 7DE2 1 JRNL REVDAT 1 14-JUL-21 7DE2 0 JRNL AUTH T.MORI,R.ZHAI,R.USHIMARU,Y.MATSUDA,I.ABE JRNL TITL MOLECULAR INSIGHTS INTO THE ENDOPEROXIDE FORMATION BY JRNL TITL 2 FE(II)/ ALPHA-KG-DEPENDENT OXYGENASE NVFI. JRNL REF NAT COMMUN V. 12 4417 2021 JRNL REFN ESSN 2041-1723 JRNL PMID 34285212 JRNL DOI 10.1038/S41467-021-24685-6 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 46668 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 2325 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 39.0800 - 4.8800 0.99 2709 129 0.1746 0.1889 REMARK 3 2 4.8800 - 3.8800 1.00 2647 157 0.1423 0.1521 REMARK 3 3 3.8800 - 3.3900 1.00 2638 129 0.1606 0.1557 REMARK 3 4 3.3900 - 3.0800 1.00 2600 153 0.1688 0.2075 REMARK 3 5 3.0800 - 2.8600 1.00 2612 134 0.1773 0.1782 REMARK 3 6 2.8600 - 2.6900 1.00 2594 156 0.1745 0.2135 REMARK 3 7 2.6900 - 2.5500 1.00 2571 158 0.1752 0.2019 REMARK 3 8 2.5500 - 2.4400 1.00 2629 129 0.1768 0.1968 REMARK 3 9 2.4400 - 2.3500 1.00 2582 125 0.1789 0.1934 REMARK 3 10 2.3500 - 2.2700 1.00 2601 145 0.1787 0.2168 REMARK 3 11 2.2700 - 2.2000 1.00 2586 128 0.1753 0.1958 REMARK 3 12 2.2000 - 2.1300 1.00 2617 140 0.1783 0.2376 REMARK 3 13 2.1300 - 2.0800 1.00 2591 138 0.1817 0.2303 REMARK 3 14 2.0800 - 2.0300 1.00 2579 119 0.1908 0.2245 REMARK 3 15 2.0300 - 1.9800 1.00 2577 152 0.1955 0.2060 REMARK 3 16 1.9800 - 1.9400 1.00 2590 115 0.1989 0.2602 REMARK 3 17 1.9400 - 1.9000 1.00 2620 118 0.2199 0.2704 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.46 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.47 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 : 0.009 4607 REMARK 3 ANGLE : 1.241 6286 REMARK 3 CHIRALITY : 0.072 665 REMARK 3 PLANARITY : 0.009 828 REMARK 3 DIHEDRAL : 21.457 1768 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 7DE2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-NOV-20. REMARK 100 THE DEPOSITION ID IS D_1300019227. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUN-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46701 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 46.130 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : 0.14100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.84300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM TRIS-HCL PH 7.0, 20% PEG3350, 20 REMARK 280 MM ALPHA-KETOGLUTARATE, 200 MM NASCN, AND 2 MM DTT, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 283K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 78.64300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.16850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 78.64300 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.16850 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 MET B -19 REMARK 465 GLY B -18 REMARK 465 SER B -17 REMARK 465 SER B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 SER B -9 REMARK 465 SER B -8 REMARK 465 GLY B -7 REMARK 465 LEU B -6 REMARK 465 VAL B -5 REMARK 465 PRO B -4 REMARK 465 ARG B -3 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 VAL B 2 REMARK 465 GLY B 3 REMARK 465 ASP B 18 REMARK 465 ALA B 19 REMARK 465 GLY B 20 REMARK 465 THR B 21 REMARK 465 LYS B 22 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 LYS A 22 CG CD CE NZ REMARK 470 GLU A 23 CG CD OE1 OE2 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 512 O HOH A 535 2.01 REMARK 500 O HOH A 431 O HOH A 537 2.01 REMARK 500 O HOH A 528 O HOH A 530 2.05 REMARK 500 O HOH A 491 O HOH A 568 2.07 REMARK 500 O HOH A 535 O HOH A 559 2.12 REMARK 500 O HOH B 572 O HOH B 603 2.12 REMARK 500 O HOH B 560 O HOH B 615 2.12 REMARK 500 O HOH B 629 O HOH B 630 2.13 REMARK 500 O HOH A 503 O HOH A 568 2.13 REMARK 500 O HOH A 475 O HOH A 542 2.17 REMARK 500 O HOH B 527 O HOH B 585 2.17 REMARK 500 O HOH B 478 O HOH B 609 2.19 REMARK 500 O HOH B 511 O HOH B 618 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 B 468 O HOH B 601 4455 2.11 REMARK 500 O HOH A 559 O HOH B 515 3545 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 132 CA - CB - CG ANGL. DEV. = -16.6 DEGREES REMARK 500 ARG A 132 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG A 278 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 278 NE - CZ - NH2 ANGL. DEV. = -6.1 DEGREES REMARK 500 ARG B 265 CG - CD - NE ANGL. DEV. = 17.2 DEGREES REMARK 500 ARG B 265 CD - NE - CZ ANGL. DEV. = 10.7 DEGREES REMARK 500 ARG B 265 NE - CZ - NH1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ARG B 265 NE - CZ - NH2 ANGL. DEV. = -5.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 10 -155.04 -155.53 REMARK 500 LYS A 22 -95.59 -92.81 REMARK 500 ASP A 71 102.46 -160.60 REMARK 500 SER A 122 -174.96 -64.91 REMARK 500 SER A 161 -160.59 -111.72 REMARK 500 SER A 248 -168.51 -110.70 REMARK 500 CYS A 251 160.03 179.13 REMARK 500 SER B 10 -159.20 -148.29 REMARK 500 TYR B 202 -130.70 59.54 REMARK 500 SER B 248 -166.30 -109.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 GLU A 153 0.11 SIDE CHAIN 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 303 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 135 NE2 REMARK 620 2 ASP A 137 OD1 92.0 REMARK 620 3 HIS A 250 NE2 91.0 91.3 REMARK 620 4 AKG A 301 O1 170.3 97.4 90.9 REMARK 620 5 AKG A 301 O5 93.7 172.0 94.2 76.7 REMARK 620 6 HOH A 462 O 94.9 91.7 173.3 82.7 82.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE B 302 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 135 NE2 REMARK 620 2 ASP B 137 OD1 92.9 REMARK 620 3 HIS B 250 NE2 89.1 91.3 REMARK 620 4 AKG B 301 O1 170.9 95.9 88.7 REMARK 620 5 AKG B 301 O5 91.8 174.7 91.3 79.4 REMARK 620 6 HOH B 504 O 93.7 91.1 176.2 88.1 86.1 REMARK 620 N 1 2 3 4 5 DBREF 7DE2 A -19 278 PDB 7DE2 7DE2 -19 278 DBREF 7DE2 B -19 278 PDB 7DE2 7DE2 -19 278 SEQRES 1 A 298 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 298 LEU VAL PRO ARG GLY SER HIS MET VAL GLY SER ARG THR SEQRES 3 A 298 TRP CYS GLU SER GLU MET LEU PHE VAL GLN PRO ASP ALA SEQRES 4 A 298 GLY THR LYS GLU GLU LEU TYR TYR ARG VAL THR PRO LYS SEQRES 5 A 298 PRO GLY GLN THR GLN ALA ASN PHE ASN TRP THR PRO HIS SEQRES 6 A 298 LYS VAL ARG PHE HIS ASP ALA ARG PRO GLN ARG ASP SER SEQRES 7 A 298 PHE ASP LEU ASN THR HIS GLY PHE THR PHE VAL GLU ASP SEQRES 8 A 298 ALA ILE SER PRO GLN LEU ILE GLU ARG ILE ARG ALA ASP SEQRES 9 A 298 ASP THR ALA ALA VAL GLU GLY ASP TYR PHE ALA SER VAL SEQRES 10 A 298 ALA ALA LEU VAL LYS ARG VAL THR GLY ALA ASP HIS VAL SEQRES 11 A 298 VAL CYS PHE SER PRO TYR THR ARG LYS GLU ASN SER GLU SEQRES 12 A 298 LYS GLY ILE PHE GLY GLN PRO ALA ARG THR VAL HIS CYS SEQRES 13 A 298 ASP HIS THR PRO ALA ALA ALA ILE GLU LEU THR HIS LYS SEQRES 14 A 298 LEU CYS GLY GLU ASP ALA VAL ARG LEU LEU GLN SER ARG SEQRES 15 A 298 PHE ARG ALA PHE SER VAL TRP ARG PRO LEU VAL GLU PRO SEQRES 16 A 298 VAL LEU ASP TRP PRO LEU ALA VAL VAL ASP GLY ARG THR SEQRES 17 A 298 ILE ALA PRO ASP ASP LEU HIS PRO VAL HIS TRP LEU ARG SEQRES 18 A 298 TYR GLU LYS LYS ASP THR GLU PRO PRO PHE GLN LEU SER SEQRES 19 A 298 PHE SER GLU THR GLN LYS TRP TYR TYR LEU SER ARG GLN SEQRES 20 A 298 ARG SER ASP GLU VAL SER ILE VAL LYS ASN TYR ASP SER SEQRES 21 A 298 GLU VAL VAL PRO SER PRO ARG SER ALA HIS CYS ALA PHE SEQRES 22 A 298 LYS HIS PRO PHE VAL PRO LYS ASP ALA PRO PRO ARG GLU SEQRES 23 A 298 SER ILE ASP VAL ARG CYS LEU VAL PHE GLY GLY ARG SEQRES 1 B 298 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 298 LEU VAL PRO ARG GLY SER HIS MET VAL GLY SER ARG THR SEQRES 3 B 298 TRP CYS GLU SER GLU MET LEU PHE VAL GLN PRO ASP ALA SEQRES 4 B 298 GLY THR LYS GLU GLU LEU TYR TYR ARG VAL THR PRO LYS SEQRES 5 B 298 PRO GLY GLN THR GLN ALA ASN PHE ASN TRP THR PRO HIS SEQRES 6 B 298 LYS VAL ARG PHE HIS ASP ALA ARG PRO GLN ARG ASP SER SEQRES 7 B 298 PHE ASP LEU ASN THR HIS GLY PHE THR PHE VAL GLU ASP SEQRES 8 B 298 ALA ILE SER PRO GLN LEU ILE GLU ARG ILE ARG ALA ASP SEQRES 9 B 298 ASP THR ALA ALA VAL GLU GLY ASP TYR PHE ALA SER VAL SEQRES 10 B 298 ALA ALA LEU VAL LYS ARG VAL THR GLY ALA ASP HIS VAL SEQRES 11 B 298 VAL CYS PHE SER PRO TYR THR ARG LYS GLU ASN SER GLU SEQRES 12 B 298 LYS GLY ILE PHE GLY GLN PRO ALA ARG THR VAL HIS CYS SEQRES 13 B 298 ASP HIS THR PRO ALA ALA ALA ILE GLU LEU THR HIS LYS SEQRES 14 B 298 LEU CYS GLY GLU ASP ALA VAL ARG LEU LEU GLN SER ARG SEQRES 15 B 298 PHE ARG ALA PHE SER VAL TRP ARG PRO LEU VAL GLU PRO SEQRES 16 B 298 VAL LEU ASP TRP PRO LEU ALA VAL VAL ASP GLY ARG THR SEQRES 17 B 298 ILE ALA PRO ASP ASP LEU HIS PRO VAL HIS TRP LEU ARG SEQRES 18 B 298 TYR GLU LYS LYS ASP THR GLU PRO PRO PHE GLN LEU SER SEQRES 19 B 298 PHE SER GLU THR GLN LYS TRP TYR TYR LEU SER ARG GLN SEQRES 20 B 298 ARG SER ASP GLU VAL SER ILE VAL LYS ASN TYR ASP SER SEQRES 21 B 298 GLU VAL VAL PRO SER PRO ARG SER ALA HIS CYS ALA PHE SEQRES 22 B 298 LYS HIS PRO PHE VAL PRO LYS ASP ALA PRO PRO ARG GLU SEQRES 23 B 298 SER ILE ASP VAL ARG CYS LEU VAL PHE GLY GLY ARG HET AKG A 301 10 HET H3X A 302 32 HET FE A 303 1 HET AKG B 301 10 HET FE B 302 1 HETNAM AKG 2-OXOGLUTARIC ACID HETNAM H3X METHYL (3'~{A}~{R},4'~{S},5'~{S},5~{A}~{S},6~{S},7~{S}, HETNAM 2 H3X 9~{A}~{R})-1,1,3'~{A},4',5~{A},7,7'-HEPTAMETHYL-3,6'- HETNAM 3 H3X BIS(OXIDANYLIDENE)SPIRO[4,5,7,8,9,9~{A}- HETNAM 4 H3X HEXAHYDROBENZO[C]OXEPINE-6,2'-4,5-DIHYDRO-3~{H}-1- HETNAM 5 H3X BENZOFURAN]-5'-CARBOXYLATE HETNAM FE FE (III) ION FORMUL 3 AKG 2(C5 H6 O5) FORMUL 4 H3X C26 H38 O6 FORMUL 5 FE 2(FE 3+) FORMUL 8 HOH *421(H2 O) HELIX 1 AA1 ARG A 53 PHE A 59 5 7 HELIX 2 AA2 SER A 74 ALA A 83 1 10 HELIX 3 AA3 ASP A 85 GLY A 91 1 7 HELIX 4 AA4 GLY A 91 GLY A 106 1 16 HELIX 5 AA5 GLY A 125 GLN A 129 5 5 HELIX 6 AA6 THR A 139 GLY A 152 1 14 HELIX 7 AA7 ASP A 154 LEU A 159 1 6 HELIX 8 AA8 GLY A 186 ILE A 189 5 4 HELIX 9 AA9 ALA A 190 ASP A 192 5 3 HELIX 10 AB1 ARG B 53 PHE B 59 5 7 HELIX 11 AB2 SER B 74 ALA B 83 1 10 HELIX 12 AB3 ASP B 85 GLY B 91 1 7 HELIX 13 AB4 GLY B 91 GLY B 106 1 16 HELIX 14 AB5 THR B 139 GLY B 152 1 14 HELIX 15 AB6 ASP B 154 LEU B 159 1 6 HELIX 16 AB7 GLY B 186 ILE B 189 5 4 HELIX 17 AB8 ALA B 190 ASP B 192 5 3 SHEET 1 AA1 6 GLY A 3 SER A 4 0 SHEET 2 AA1 6 TRP A 7 PHE A 14 -1 O TRP A 7 N SER A 4 SHEET 3 AA1 6 THR A 43 ASP A 51 -1 O PHE A 49 N CYS A 8 SHEET 4 AA1 6 TRP A 221 TYR A 223 1 O TRP A 221 N HIS A 50 SHEET 5 AA1 6 LEU A 181 VAL A 184 -1 N VAL A 183 O TYR A 222 SHEET 6 AA1 6 HIS A 250 ALA A 252 -1 O CYS A 251 N ALA A 182 SHEET 1 AA2 4 LEU A 25 ARG A 28 0 SHEET 2 AA2 4 LEU A 194 LEU A 200 1 O LEU A 200 N TYR A 27 SHEET 3 AA2 4 PHE A 211 LEU A 213 -1 O GLN A 212 N HIS A 195 SHEET 4 AA2 4 HIS A 135 CYS A 136 -1 N CYS A 136 O PHE A 211 SHEET 1 AA3 5 PHE A 66 GLU A 70 0 SHEET 2 AA3 5 GLU A 231 ASP A 239 -1 O VAL A 232 N VAL A 69 SHEET 3 AA3 5 PHE A 163 PRO A 171 -1 N TRP A 169 O SER A 233 SHEET 4 AA3 5 GLU A 266 PHE A 275 -1 O VAL A 274 N ARG A 164 SHEET 5 AA3 5 HIS A 109 LYS A 119 -1 N ARG A 118 O SER A 267 SHEET 1 AA4 5 TRP B 7 VAL B 15 0 SHEET 2 AA4 5 TRP B 42 ASP B 51 -1 O PHE B 49 N CYS B 8 SHEET 3 AA4 5 TRP B 221 TYR B 223 1 O TRP B 221 N HIS B 50 SHEET 4 AA4 5 LEU B 181 VAL B 184 -1 N VAL B 183 O TYR B 222 SHEET 5 AA4 5 HIS B 250 ALA B 252 -1 O CYS B 251 N ALA B 182 SHEET 1 AA5 4 LEU B 25 ARG B 28 0 SHEET 2 AA5 4 LEU B 194 LEU B 200 1 O HIS B 198 N TYR B 27 SHEET 3 AA5 4 PHE B 211 LEU B 213 -1 O GLN B 212 N HIS B 195 SHEET 4 AA5 4 HIS B 135 CYS B 136 -1 N CYS B 136 O PHE B 211 SHEET 1 AA6 5 PHE B 66 GLU B 70 0 SHEET 2 AA6 5 GLU B 231 ASP B 239 -1 O VAL B 232 N VAL B 69 SHEET 3 AA6 5 PHE B 163 PRO B 171 -1 N ALA B 165 O ASN B 237 SHEET 4 AA6 5 GLU B 266 PHE B 275 -1 O VAL B 274 N ARG B 164 SHEET 5 AA6 5 HIS B 109 LYS B 119 -1 N TYR B 116 O ASP B 269 LINK NE2 HIS A 135 FE FE A 303 1555 1555 2.11 LINK OD1 ASP A 137 FE FE A 303 1555 1555 2.16 LINK NE2 HIS A 250 FE FE A 303 1555 1555 2.03 LINK O1 AKG A 301 FE FE A 303 1555 1555 2.03 LINK O5 AKG A 301 FE FE A 303 1555 1555 2.03 LINK FE FE A 303 O HOH A 462 1555 1555 2.12 LINK NE2 HIS B 135 FE FE B 302 1555 1555 2.14 LINK OD1 ASP B 137 FE FE B 302 1555 1555 2.20 LINK NE2 HIS B 250 FE FE B 302 1555 1555 2.09 LINK O1 AKG B 301 FE FE B 302 1555 1555 2.02 LINK O5 AKG B 301 FE FE B 302 1555 1555 2.07 LINK FE FE B 302 O HOH B 504 1555 1555 2.17 CISPEP 1 GLU A 174 PRO A 175 0 -8.14 CISPEP 2 GLU B 174 PRO B 175 0 -8.45 CRYST1 157.286 48.337 79.638 90.00 101.04 90.00 C 1 2 1 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 0.006358 0.000000 0.001240 0.00000 SCALE2 0.000000 0.020688 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012794 0.00000