HEADER OXIDOREDUCTASE 17-JAN-19 6NPB TITLE X-RAY CRYSTAL STRUCTURE OF TMPA, 2-TRIMETHYLAMINOETHYLPHOSPHONATE TITLE 2 HYDROXYLASE, WITH FE AND 2OG COMPND MOL_ID: 1; COMPND 2 MOLECULE: TMPA, 2-TRIMETHYLAMINOETHYLPHOSPHONATE HYDROXYLASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 1.-.-.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEISINGERA CAERULEA; SOURCE 3 ORGANISM_TAXID: 506591; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET-28A(+) KEYWDS ORGANOPHOSPHONATE, IRON OXYGENASE, HD-DOMAIN, GENE ANNOTATION, KEYWDS 2 ENZYME, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR L.J.RAJAKOVICH,A.J.MITCHELL,A.K.BOAL REVDAT 4 11-OCT-23 6NPB 1 LINK REVDAT 3 27-NOV-19 6NPB 1 REMARK REVDAT 2 10-APR-19 6NPB 1 JRNL REVDAT 1 06-MAR-19 6NPB 0 JRNL AUTH L.J.RAJAKOVICH,M.E.PANDELIA,A.J.MITCHELL,W.C.CHANG,B.ZHANG, JRNL AUTH 2 A.K.BOAL,C.KREBS,J.M.BOLLINGER JR. JRNL TITL A NEW MICROBIAL PATHWAY FOR ORGANOPHOSPHONATE DEGRADATION JRNL TITL 2 CATALYZED BY TWO PREVIOUSLY MISANNOTATED NON-HEME-IRON JRNL TITL 3 OXYGENASES. JRNL REF BIOCHEMISTRY V. 58 1627 2019 JRNL REFN ISSN 1520-4995 JRNL PMID 30789718 JRNL DOI 10.1021/ACS.BIOCHEM.9B00044 REMARK 2 REMARK 2 RESOLUTION. 1.73 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.73 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 83209 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4424 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.73 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.78 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5619 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.71 REMARK 3 BIN R VALUE (WORKING SET) : 0.2430 REMARK 3 BIN FREE R VALUE SET COUNT : 288 REMARK 3 BIN FREE R VALUE : 0.2560 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5886 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 464 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.114 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.104 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.073 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.274 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6055 ; 0.005 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5513 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8222 ; 1.022 ; 1.957 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12689 ; 0.694 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 753 ; 5.461 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 302 ;35.866 ;23.510 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 936 ;11.243 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 54 ;15.134 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 872 ; 0.062 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6983 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1435 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6NPB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JAN-19. REMARK 100 THE DEPOSITION ID IS D_1000228531. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-OCT-15 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 : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : DIAMOND(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 88259 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.730 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 (%) : 98.8 REMARK 200 DATA REDUNDANCY : 8.200 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.73 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.90 REMARK 200 R MERGE FOR SHELL (I) : 0.87100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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 3O2G REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15 MG/ML TMPA, 1.0-1.4 M LITHIUM REMARK 280 SULFATE, 1.6-1.8 M AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 110.34800 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 43.52550 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 43.52550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 55.17400 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 43.52550 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 43.52550 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 165.52200 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 43.52550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 43.52550 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 55.17400 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 43.52550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 43.52550 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 165.52200 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 110.34800 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: 8710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -110.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 GLY A 376 REMARK 465 GLY A 377 REMARK 465 HIS B -5 REMARK 465 HIS B -4 REMARK 465 HIS B -3 REMARK 465 HIS B -2 REMARK 465 GLY B 377 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 ASP A 68 75.83 12.46 REMARK 500 TYR A 190 47.21 -94.37 REMARK 500 ASN A 218 51.16 -156.05 REMARK 500 LYS A 258 49.82 -143.71 REMARK 500 ASN A 286 105.53 -166.44 REMARK 500 ARG A 338 -58.00 -143.40 REMARK 500 ASP B 113 -157.69 -134.52 REMARK 500 ASP B 261 34.21 -96.07 REMARK 500 ASN B 286 108.16 -161.47 REMARK 500 ARG B 338 -55.02 -144.07 REMARK 500 ALA B 342 -165.99 -166.97 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 B 741 DISTANCE = 5.94 ANGSTROMS REMARK 525 HOH B 742 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH B 743 DISTANCE = 6.32 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 FE2 A 401 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 198 NE2 REMARK 620 2 ASP A 200 OD1 92.4 REMARK 620 3 HIS A 341 NE2 90.9 91.7 REMARK 620 4 AKG A 402 O5 90.3 175.9 91.3 REMARK 620 5 AKG A 402 O1 161.9 99.9 101.9 76.7 REMARK 620 6 HOH A 527 O 84.7 93.3 173.5 84.0 81.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE2 B 401 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 198 NE2 REMARK 620 2 ASP B 200 OD1 88.1 REMARK 620 3 HIS B 341 NE2 96.0 93.5 REMARK 620 4 HOH B 535 O 178.7 92.6 85.0 REMARK 620 5 HOH B 621 O 87.8 92.6 172.8 91.1 REMARK 620 6 HOH B 692 O 91.1 179.0 87.2 88.2 86.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE2 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AKG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE2 B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 403 DBREF 6NPB A -5 377 PDB 6NPB 6NPB -5 377 DBREF 6NPB B -5 377 PDB 6NPB 6NPB -5 377 SEQRES 1 A 383 HIS HIS HIS HIS HIS HIS MET PRO ARG SER VAL THR ALA SEQRES 2 A 383 ASP ALA SER GLY SER PHE LEU THR LEU THR PHE GLU ASP SEQRES 3 A 383 GLY SER GLU SER ARG PHE HIS ALA ILE TRP LEU ARG ASP SEQRES 4 A 383 ASN ALA LEU ASP PRO GLU THR ARG SER PRO GLY ASN GLY SEQRES 5 A 383 GLN ARG LEU ILE THR ILE GLY ASP ILE PRO ALA ASP THR SEQRES 6 A 383 ARG ILE SER THR ALA LEU VAL ASP ASP GLY ALA LEU THR SEQRES 7 A 383 VAL THR PHE ALA PRO GLU GLY LYS THR VAL THR PHE PRO SEQRES 8 A 383 GLY LYS TRP LEU LYS SER ASN ALA TYR ASP THR ASP GLN SEQRES 9 A 383 SER SER GLU VAL GLY ARG THR SER PRO ASP VAL GLU THR SEQRES 10 A 383 TRP ASP SER SER GLN PRO ALA PRO ALA PHE ASP TRP ASN SEQRES 11 A 383 GLU VAL GLN SER ASP PRO LYS ALA LYS ARG ASP TRP LEU SEQRES 12 A 383 ASP ALA ILE ALA ARG LEU GLY PHE ALA LYS LEU VAL ASN SEQRES 13 A 383 GLY PRO VAL ARG GLU GLY ALA LEU ILE GLU CYS ALA SER SEQRES 14 A 383 MET PHE GLY PHE VAL ARG GLU THR ASN TYR GLY LYS TYR SEQRES 15 A 383 PHE GLU VAL ARG THR GLU VAL ASN PRO THR ASN LEU ALA SEQRES 16 A 383 TYR THR GLY LEU GLY LEU GLN ALA HIS THR ASP ASN PRO SEQRES 17 A 383 TYR ARG ASP PRO VAL PRO SER LEU GLN ILE LEU TYR CYS SEQRES 18 A 383 LEU GLU ASN SER ALA GLU GLY GLY ASP SER ILE VAL VAL SEQRES 19 A 383 ASP GLY PHE ARG ALA ALA GLU ARG LEU ARG ASP GLU ASP SEQRES 20 A 383 PRO GLU GLY PHE ALA LEU LEU ALA GLY ASN PRO ALA ARG SEQRES 21 A 383 PHE GLU TYR LYS GLY SER ASP GLY VAL HIS LEU ARG ALA SEQRES 22 A 383 ARG ARG PRO MET ILE GLU LEU SER PRO ASP GLY GLU MET SEQRES 23 A 383 ILE ALA ILE ARG PHE ASN ASN ARG SER SER ALA PRO PHE SEQRES 24 A 383 VAL ASP ILE PRO PHE GLU LYS MET GLU ALA TYR TYR ALA SEQRES 25 A 383 ALA TYR ARG ARG LEU GLY GLU PHE ILE ASP ASP PRO GLU SEQRES 26 A 383 MET GLY VAL SER PHE LYS LEU GLU PRO GLY GLU SER PHE SEQRES 27 A 383 ILE VAL ASP ASN THR ARG VAL LEU HIS ALA ARG LEU GLY SEQRES 28 A 383 TYR SER GLY SER GLY SER ARG TRP LEU GLN GLY CYS TYR SEQRES 29 A 383 ALA ASP LYS ASP GLY LEU PHE SER THR LEU ASN VAL LEU SEQRES 30 A 383 ASN ALA GLN LEU GLY GLY SEQRES 1 B 383 HIS HIS HIS HIS HIS HIS MET PRO ARG SER VAL THR ALA SEQRES 2 B 383 ASP ALA SER GLY SER PHE LEU THR LEU THR PHE GLU ASP SEQRES 3 B 383 GLY SER GLU SER ARG PHE HIS ALA ILE TRP LEU ARG ASP SEQRES 4 B 383 ASN ALA LEU ASP PRO GLU THR ARG SER PRO GLY ASN GLY SEQRES 5 B 383 GLN ARG LEU ILE THR ILE GLY ASP ILE PRO ALA ASP THR SEQRES 6 B 383 ARG ILE SER THR ALA LEU VAL ASP ASP GLY ALA LEU THR SEQRES 7 B 383 VAL THR PHE ALA PRO GLU GLY LYS THR VAL THR PHE PRO SEQRES 8 B 383 GLY LYS TRP LEU LYS SER ASN ALA TYR ASP THR ASP GLN SEQRES 9 B 383 SER SER GLU VAL GLY ARG THR SER PRO ASP VAL GLU THR SEQRES 10 B 383 TRP ASP SER SER GLN PRO ALA PRO ALA PHE ASP TRP ASN SEQRES 11 B 383 GLU VAL GLN SER ASP PRO LYS ALA LYS ARG ASP TRP LEU SEQRES 12 B 383 ASP ALA ILE ALA ARG LEU GLY PHE ALA LYS LEU VAL ASN SEQRES 13 B 383 GLY PRO VAL ARG GLU GLY ALA LEU ILE GLU CYS ALA SER SEQRES 14 B 383 MET PHE GLY PHE VAL ARG GLU THR ASN TYR GLY LYS TYR SEQRES 15 B 383 PHE GLU VAL ARG THR GLU VAL ASN PRO THR ASN LEU ALA SEQRES 16 B 383 TYR THR GLY LEU GLY LEU GLN ALA HIS THR ASP ASN PRO SEQRES 17 B 383 TYR ARG ASP PRO VAL PRO SER LEU GLN ILE LEU TYR CYS SEQRES 18 B 383 LEU GLU ASN SER ALA GLU GLY GLY ASP SER ILE VAL VAL SEQRES 19 B 383 ASP GLY PHE ARG ALA ALA GLU ARG LEU ARG ASP GLU ASP SEQRES 20 B 383 PRO GLU GLY PHE ALA LEU LEU ALA GLY ASN PRO ALA ARG SEQRES 21 B 383 PHE GLU TYR LYS GLY SER ASP GLY VAL HIS LEU ARG ALA SEQRES 22 B 383 ARG ARG PRO MET ILE GLU LEU SER PRO ASP GLY GLU MET SEQRES 23 B 383 ILE ALA ILE ARG PHE ASN ASN ARG SER SER ALA PRO PHE SEQRES 24 B 383 VAL ASP ILE PRO PHE GLU LYS MET GLU ALA TYR TYR ALA SEQRES 25 B 383 ALA TYR ARG ARG LEU GLY GLU PHE ILE ASP ASP PRO GLU SEQRES 26 B 383 MET GLY VAL SER PHE LYS LEU GLU PRO GLY GLU SER PHE SEQRES 27 B 383 ILE VAL ASP ASN THR ARG VAL LEU HIS ALA ARG LEU GLY SEQRES 28 B 383 TYR SER GLY SER GLY SER ARG TRP LEU GLN GLY CYS TYR SEQRES 29 B 383 ALA ASP LYS ASP GLY LEU PHE SER THR LEU ASN VAL LEU SEQRES 30 B 383 ASN ALA GLN LEU GLY GLY HET FE2 A 401 1 HET AKG A 402 10 HET SO4 A 403 5 HET SO4 A 404 5 HET FE2 B 401 1 HET SO4 B 402 5 HET SO4 B 403 5 HETNAM FE2 FE (II) ION HETNAM AKG 2-OXOGLUTARIC ACID HETNAM SO4 SULFATE ION FORMUL 3 FE2 2(FE 2+) FORMUL 4 AKG C5 H6 O5 FORMUL 5 SO4 4(O4 S 2-) FORMUL 10 HOH *464(H2 O) HELIX 1 AA1 ALA A 28 ASN A 34 1 7 HELIX 2 AA2 THR A 51 ILE A 55 5 5 HELIX 3 AA3 GLY A 86 ASN A 92 1 7 HELIX 4 AA4 TRP A 123 ASP A 129 1 7 HELIX 5 AA5 ASP A 129 GLY A 144 1 16 HELIX 6 AA6 GLY A 156 MET A 164 1 9 HELIX 7 AA7 ASN A 187 THR A 191 5 5 HELIX 8 AA8 GLY A 230 ASP A 241 1 12 HELIX 9 AA9 ASP A 241 ASN A 251 1 11 HELIX 10 AB1 PRO A 297 GLU A 299 5 3 HELIX 11 AB2 LYS A 300 ASP A 317 1 18 HELIX 12 AB3 ASP A 360 LEU A 375 1 16 HELIX 13 AB4 ALA B 28 ASN B 34 1 7 HELIX 14 AB5 THR B 51 ILE B 55 5 5 HELIX 15 AB6 GLY B 86 ASN B 92 1 7 HELIX 16 AB7 TRP B 123 ASP B 129 1 7 HELIX 17 AB8 ASP B 129 GLY B 144 1 16 HELIX 18 AB9 GLY B 156 MET B 164 1 9 HELIX 19 AC1 ASN B 187 GLY B 192 1 6 HELIX 20 AC2 GLY B 230 ASP B 241 1 12 HELIX 21 AC3 ASP B 241 ASN B 251 1 11 HELIX 22 AC4 PRO B 297 ASP B 317 1 21 HELIX 23 AC5 ASP B 360 GLY B 376 1 17 SHEET 1 AA1 3 PRO A 2 ALA A 7 0 SHEET 2 AA1 3 PHE A 13 PHE A 18 -1 O THR A 17 N ARG A 3 SHEET 3 AA1 3 GLU A 23 HIS A 27 -1 O SER A 24 N LEU A 16 SHEET 1 AA2 3 ARG A 60 ASP A 67 0 SHEET 2 AA2 3 ALA A 70 ALA A 76 -1 O THR A 72 N LEU A 65 SHEET 3 AA2 3 LYS A 80 PRO A 85 -1 O PHE A 84 N LEU A 71 SHEET 1 AA3 6 ALA A 120 ASP A 122 0 SHEET 2 AA3 6 PHE A 145 VAL A 149 1 O VAL A 149 N PHE A 121 SHEET 3 AA3 6 SER A 331 ASP A 335 -1 O SER A 331 N LEU A 148 SHEET 4 AA3 6 LEU A 210 ASN A 218 -1 N LEU A 213 O PHE A 332 SHEET 5 AA3 6 ARG A 352 ALA A 359 -1 O TRP A 353 N GLU A 217 SHEET 6 AA3 6 VAL A 168 ARG A 169 -1 N ARG A 169 O TYR A 358 SHEET 1 AA4 6 ALA A 120 ASP A 122 0 SHEET 2 AA4 6 PHE A 145 VAL A 149 1 O VAL A 149 N PHE A 121 SHEET 3 AA4 6 SER A 331 ASP A 335 -1 O SER A 331 N LEU A 148 SHEET 4 AA4 6 LEU A 210 ASN A 218 -1 N LEU A 213 O PHE A 332 SHEET 5 AA4 6 ARG A 352 ALA A 359 -1 O TRP A 353 N GLU A 217 SHEET 6 AA4 6 PHE A 177 VAL A 179 -1 N PHE A 177 O GLY A 356 SHEET 1 AA5 4 LEU A 195 HIS A 198 0 SHEET 2 AA5 4 VAL A 339 ARG A 343 -1 O ARG A 343 N LEU A 195 SHEET 3 AA5 4 SER A 225 ASP A 229 -1 N VAL A 228 O LEU A 340 SHEET 4 AA5 4 GLY A 321 PHE A 324 -1 O PHE A 324 N SER A 225 SHEET 1 AA6 2 GLU A 221 GLY A 222 0 SHEET 2 AA6 2 TYR A 346 SER A 347 -1 O SER A 347 N GLU A 221 SHEET 1 AA7 3 LEU A 265 ARG A 269 0 SHEET 2 AA7 3 ALA A 253 TYR A 257 -1 N TYR A 257 O LEU A 265 SHEET 3 AA7 3 SER A 290 ALA A 291 -1 O ALA A 291 N ARG A 254 SHEET 1 AA8 2 ILE A 272 LEU A 274 0 SHEET 2 AA8 2 MET A 280 ILE A 283 -1 O ALA A 282 N GLU A 273 SHEET 1 AA9 3 PRO B 2 ALA B 7 0 SHEET 2 AA9 3 PHE B 13 PHE B 18 -1 O THR B 17 N ARG B 3 SHEET 3 AA9 3 GLU B 23 HIS B 27 -1 O SER B 24 N LEU B 16 SHEET 1 AB1 3 ARG B 60 ASP B 67 0 SHEET 2 AB1 3 ALA B 70 ALA B 76 -1 O THR B 72 N LEU B 65 SHEET 3 AB1 3 THR B 81 PRO B 85 -1 O VAL B 82 N VAL B 73 SHEET 1 AB2 6 ALA B 120 ASP B 122 0 SHEET 2 AB2 6 PHE B 145 VAL B 149 1 O VAL B 149 N PHE B 121 SHEET 3 AB2 6 SER B 331 ASP B 335 -1 O SER B 331 N LEU B 148 SHEET 4 AB2 6 LEU B 210 ASN B 218 -1 N LEU B 213 O PHE B 332 SHEET 5 AB2 6 GLY B 350 ALA B 359 -1 O TRP B 353 N LEU B 216 SHEET 6 AB2 6 VAL B 168 ARG B 169 -1 N ARG B 169 O TYR B 358 SHEET 1 AB3 6 ALA B 120 ASP B 122 0 SHEET 2 AB3 6 PHE B 145 VAL B 149 1 O VAL B 149 N PHE B 121 SHEET 3 AB3 6 SER B 331 ASP B 335 -1 O SER B 331 N LEU B 148 SHEET 4 AB3 6 LEU B 210 ASN B 218 -1 N LEU B 213 O PHE B 332 SHEET 5 AB3 6 GLY B 350 ALA B 359 -1 O TRP B 353 N LEU B 216 SHEET 6 AB3 6 PHE B 177 VAL B 183 -1 N VAL B 183 O GLY B 350 SHEET 1 AB4 3 GLY B 321 PHE B 324 0 SHEET 2 AB4 3 SER B 225 ASP B 229 -1 N VAL B 227 O VAL B 322 SHEET 3 AB4 3 VAL B 339 ARG B 343 -1 O LEU B 340 N VAL B 228 SHEET 1 AB5 2 ALA B 253 GLY B 259 0 SHEET 2 AB5 2 VAL B 263 ARG B 269 -1 O LEU B 265 N TYR B 257 SHEET 1 AB6 2 ILE B 272 LEU B 274 0 SHEET 2 AB6 2 MET B 280 ILE B 283 -1 O ALA B 282 N GLU B 273 LINK NE2 HIS A 198 FE FE2 A 401 1555 1555 2.24 LINK OD1 ASP A 200 FE FE2 A 401 1555 1555 2.03 LINK NE2 HIS A 341 FE FE2 A 401 1555 1555 2.21 LINK FE FE2 A 401 O5 AKG A 402 1555 1555 2.23 LINK FE FE2 A 401 O1 AKG A 402 1555 1555 2.08 LINK FE FE2 A 401 O HOH A 527 1555 1555 2.22 LINK NE2 HIS B 198 FE FE2 B 401 1555 1555 2.36 LINK OD1 ASP B 200 FE FE2 B 401 1555 1555 2.18 LINK NE2 HIS B 341 FE FE2 B 401 1555 1555 2.40 LINK FE FE2 B 401 O HOH B 535 1555 1555 2.06 LINK FE FE2 B 401 O HOH B 621 1555 1555 2.04 LINK FE FE2 B 401 O HOH B 692 1555 1555 2.16 CISPEP 1 ALA A 76 PRO A 77 0 9.47 CISPEP 2 ASP A 205 PRO A 206 0 10.37 CISPEP 3 ALA B 76 PRO B 77 0 9.15 CISPEP 4 ASP B 205 PRO B 206 0 6.05 SITE 1 AC1 5 HIS A 198 ASP A 200 HIS A 341 AKG A 402 SITE 2 AC1 5 HOH A 527 SITE 1 AC2 13 PHE A 177 VAL A 179 LEU A 195 HIS A 198 SITE 2 AC2 13 ASP A 200 GLN A 211 HIS A 341 ARG A 343 SITE 3 AC2 13 ARG A 352 LEU A 354 FE2 A 401 HOH A 508 SITE 4 AC2 13 HOH A 527 SITE 1 AC3 9 ASN A 187 HIS A 198 ASP A 200 ASN A 201 SITE 2 AC3 9 TYR A 203 ASN A 286 ARG A 288 HOH A 515 SITE 3 AC3 9 HOH A 527 SITE 1 AC4 5 LEU A 193 GLY A 194 GLY A 345 HOH A 598 SITE 2 AC4 5 HOH A 673 SITE 1 AC5 6 HIS B 198 ASP B 200 HIS B 341 HOH B 535 SITE 2 AC5 6 HOH B 621 HOH B 692 SITE 1 AC6 6 ASP B 200 ASN B 201 TYR B 203 ASN B 286 SITE 2 AC6 6 ARG B 288 HOH B 621 SITE 1 AC7 4 ASP A 108 HOH A 505 HOH A 607 ARG B 254 CRYST1 87.051 87.051 220.696 90.00 90.00 90.00 P 41 21 2 16 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 0.011488 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011488 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004531 0.00000