HEADER OXIDOREDUCTASE 20-AUG-15 5DAV TITLE FE(II)/(ALPHA)KETOGLUTARATE-DEPENDENT DIOXYGENASE ASQJ IN COMPLEX WITH TITLE 2 4-METHOXYDEHYDROCYCLOPEPTIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHYTANOYL-COA DIOXYGENASE FAMILY PROTEIN (AFU_ORTHOLOGUE COMPND 3 AFUA_8G00230); COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: UNP RESIDUES 110-416; COMPND 6 SYNONYM: ASQJ; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ASPERGILLUS NIDULANS FGSC A4; SOURCE 3 ORGANISM_TAXID: 227321; SOURCE 4 GENE: AN9227.2, ANIA_09227; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28B(+) KEYWDS ANTIBIOTICS, BIOSYNTHESIS, ALKALOIDS, VIRIDICATIN, DESATURASE, KEYWDS 2 EPOXIDASE, FRAGMENTATION, 4-METHOXYDEHYDROCYCLOPEPTIN, KEYWDS 3 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR M.GROLL,A.BRAEUER REVDAT 3 10-JAN-24 5DAV 1 LINK REVDAT 2 27-JAN-16 5DAV 1 JRNL REVDAT 1 25-NOV-15 5DAV 0 JRNL AUTH A.BRAUER,P.BECK,L.HINTERMANN,M.GROLL JRNL TITL STRUCTURE OF THE DIOXYGENASE ASQJ: MECHANISTIC INSIGHTS INTO JRNL TITL 2 A ONE-POT MULTISTEP QUINOLONE ANTIBIOTIC BIOSYNTHESIS. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 55 422 2016 JRNL REFN ESSN 1521-3773 JRNL PMID 26553478 JRNL DOI 10.1002/ANIE.201507835 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 26218 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) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1380 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1858 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.80 REMARK 3 BIN R VALUE (WORKING SET) : 0.2840 REMARK 3 BIN FREE R VALUE SET COUNT : 97 REMARK 3 BIN FREE R VALUE : 0.3340 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2227 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 238 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.15 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.81000 REMARK 3 B22 (A**2) : 2.80000 REMARK 3 B33 (A**2) : -1.00000 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): 0.247 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.114 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.080 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.886 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2308 ; 0.004 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2258 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3150 ; 1.045 ; 1.985 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5194 ; 0.741 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 287 ; 5.287 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 91 ;35.361 ;23.736 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 385 ;12.962 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;15.038 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 371 ; 0.058 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2568 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 499 ; 0.006 ; 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): 1152 ; 1.003 ; 2.479 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1150 ; 0.999 ; 2.474 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1437 ; 1.340 ; 3.708 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1438 ; 1.339 ; 3.713 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1156 ; 1.197 ; 2.709 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1156 ; 1.193 ; 2.710 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1714 ; 1.373 ; 3.970 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2746 ; 2.406 ;20.481 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2645 ; 2.167 ;20.077 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 4566 ; 0.866 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 64 ;25.019 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 4694 ; 6.819 ; 5.000 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A -10 A 9999 REMARK 3 ORIGIN FOR THE GROUP (A): -20.8692 -18.3040 -13.0645 REMARK 3 T TENSOR REMARK 3 T11: 0.0068 T22: 0.0019 REMARK 3 T33: 0.0075 T12: 0.0018 REMARK 3 T13: 0.0013 T23: 0.0003 REMARK 3 L TENSOR REMARK 3 L11: 0.0676 L22: 0.0212 REMARK 3 L33: 0.0119 L12: 0.0173 REMARK 3 L13: 0.0136 L23: 0.0108 REMARK 3 S TENSOR REMARK 3 S11: -0.0051 S12: 0.0022 S13: -0.0005 REMARK 3 S21: 0.0009 S22: 0.0049 S23: -0.0060 REMARK 3 S31: -0.0006 S32: 0.0018 S33: 0.0002 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK 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 REMARK 4 REMARK 4 5DAV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000212940. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA 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 : LN2 COOLED FIXED-EXIT. SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27599 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.00660 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.54500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 5DAP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS/HCL, 1 M LIBR, 27% PEG REMARK 280 6000, PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.33000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.33000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 36.52500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 60.38500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 36.52500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 60.38500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 33.33000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 36.52500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 60.38500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 33.33000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 36.52500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 60.38500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -51.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 -73.05000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -33.33000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 644 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 654 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 715 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 716 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 727 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 729 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 736 LIES ON A SPECIAL POSITION. 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 SER A 1 REMARK 465 THR A 2 REMARK 465 SER A 3 REMARK 465 LYS A 4 REMARK 465 ASP A 5 REMARK 465 HIS A 6 REMARK 465 VAL A 7 REMARK 465 HIS A 296 REMARK 465 ASP A 297 REMARK 465 ASP A 298 REMARK 465 GLU A 299 REMARK 465 ALA A 300 REMARK 465 GLU A 301 REMARK 465 PRO A 302 REMARK 465 LEU A 303 REMARK 465 CYS A 304 REMARK 465 ARG A 305 REMARK 465 GLU A 306 REMARK 465 THR A 307 REMARK 465 ILE A 308 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 690 O HOH A 690 3454 2.05 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 MET A 137 -3.63 82.71 REMARK 500 SER A 140 -32.47 -139.57 REMARK 500 LEU A 184 44.62 -108.12 REMARK 500 TRP A 262 40.37 -103.56 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 A 736 DISTANCE = 6.23 ANGSTROMS REMARK 525 HOH A 737 DISTANCE = 6.91 ANGSTROMS REMARK 525 HOH A 738 DISTANCE = 7.87 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 NI A 401 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 134 NE2 REMARK 620 2 ASP A 136 OD1 91.6 REMARK 620 3 HIS A 211 NE2 99.7 91.3 REMARK 620 4 TRS A 403 O1 175.7 88.0 84.6 REMARK 620 5 TRS A 403 O3 93.9 173.7 90.7 86.3 REMARK 620 6 TRS A 403 N 100.9 100.7 155.8 75.0 75.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 406 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 607 O REMARK 620 2 HOH A 650 O 135.1 REMARK 620 3 HOH A 691 O 77.0 138.2 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 58J A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TRS A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BR A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BR A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 406 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5DAP RELATED DB: PDB REMARK 900 FE(II)/(ALPHA)KETOGLUTARATE-DEPENDENT DIOXYGENASE ASQJ DBREF 5DAV A 2 308 UNP Q5AR53 Q5AR53_EMENI 110 416 SEQADV 5DAV SER A 1 UNP Q5AR53 EXPRESSION TAG SEQRES 1 A 308 SER THR SER LYS ASP HIS VAL LYS SER GLN ILE PRO ARG SEQRES 2 A 308 LEU SER ALA ILE ASN ASP LEU HIS LYS ILE TRP PRO THR SEQRES 3 A 308 VAL GLU GLU HIS GLY ALA ALA ILE ILE GLU SER PHE LEU SEQRES 4 A 308 SER LEU ASP ILE VAL ARG ARG LEU ASN GLU GLU VAL ASP SEQRES 5 A 308 PRO PHE VAL LYS ILE GLU PRO ILE PRO ALA ALA LYS THR SEQRES 6 A 308 LYS ASP HIS PRO ASN HIS VAL LEU SER THR THR THR ARG SEQRES 7 A 308 LEU VAL ASN VAL LEU ALA PRO ILE SER LYS ALA TYR ARG SEQRES 8 A 308 GLU ASP VAL LEU ASN SER LYS VAL LEU HIS ARG ILE CYS SEQRES 9 A 308 SER ASP ALA PHE HIS VAL TYR GLY ASP TYR TRP VAL LEU SEQRES 10 A 308 MET GLY ALA VAL MET GLU LEU ALA PRO SER ASN PRO ALA SEQRES 11 A 308 GLN PRO LEU HIS ARG ASP MET ARG PHE SER HIS PRO ILE SEQRES 12 A 308 VAL GLU TYR LEU LYS PRO ASP ALA PRO ALA THR SER ILE SEQRES 13 A 308 ASN PHE LEU VAL ALA LEU SER PRO PHE THR ALA GLU ASN SEQRES 14 A 308 GLY ALA THR HIS VAL ILE LEU GLY SER HIS LYS TRP GLN SEQRES 15 A 308 ASN LEU SER ASN VAL SER MET ASP ALA THR VAL ARG ALA SEQRES 16 A 308 LEU MET ASN PRO GLY ASP ALA LEU LEU ILE THR ASP SER SEQRES 17 A 308 THR ILE HIS CYS GLY GLY ALA GLU THR THR GLY THR GLU SEQRES 18 A 308 THR ARG ARG LEU LEU THR ILE THR MET GLY ILE SER GLN SEQRES 19 A 308 LEU THR PRO LEU GLU SER ASN LEU ALA VAL PRO ARG PRO SEQRES 20 A 308 VAL ILE GLU SER LEU THR PRO LEU ALA GLN ARG LEU LEU SEQRES 21 A 308 GLY TRP ALA SER GLN ARG SER ALA ALA PRO ARG ASP ILE SEQRES 22 A 308 GLY LEU LEU THR ILE ARG GLY ASN SER ILE GLU LYS THR SEQRES 23 A 308 MET ASN LEU LYS ALA GLU GLN PRO LEU HIS ASP ASP GLU SEQRES 24 A 308 ALA GLU PRO LEU CYS ARG GLU THR ILE HET NI A 401 1 HET 58J A 402 23 HET TRS A 403 8 HET BR A 404 1 HET BR A 405 1 HET K A 406 1 HETNAM NI NICKEL (II) ION HETNAM 58J 4-METHOXYDEHYDROCYCLOPEPTIN HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM BR BROMIDE ION HETNAM K POTASSIUM ION HETSYN TRS TRIS BUFFER FORMUL 2 NI NI 2+ FORMUL 3 58J C18 H16 N2 O3 FORMUL 4 TRS C4 H12 N O3 1+ FORMUL 5 BR 2(BR 1-) FORMUL 7 K K 1+ FORMUL 8 HOH *238(H2 O) HELIX 1 AA1 ASP A 19 HIS A 21 5 3 HELIX 2 AA2 LYS A 22 GLY A 31 1 10 HELIX 3 AA3 SER A 40 GLU A 58 1 19 HELIX 4 AA4 SER A 87 ASP A 93 1 7 HELIX 5 AA5 SER A 97 HIS A 109 1 13 HELIX 6 AA6 HIS A 141 LEU A 147 5 7 HELIX 7 AA7 GLY A 177 TRP A 181 5 5 HELIX 8 AA8 SER A 188 THR A 192 5 5 HELIX 9 AA9 PRO A 245 SER A 251 1 7 HELIX 10 AB1 THR A 253 LEU A 260 1 8 HELIX 11 AB2 SER A 282 MET A 287 1 6 SHEET 1 AA1 7 ARG A 13 SER A 15 0 SHEET 2 AA1 7 ALA A 32 GLU A 36 1 O ILE A 34 N LEU A 14 SHEET 3 AA1 7 ALA A 202 THR A 206 -1 O ALA A 202 N ILE A 35 SHEET 4 AA1 7 SER A 155 ALA A 161 -1 N LEU A 159 O LEU A 203 SHEET 5 AA1 7 ARG A 223 ILE A 232 -1 O MET A 230 N ILE A 156 SHEET 6 AA1 7 TYR A 114 LEU A 124 -1 N LEU A 124 O ARG A 223 SHEET 7 AA1 7 ARG A 78 ASN A 81 -1 N VAL A 80 O VAL A 121 SHEET 1 AA2 3 VAL A 193 ARG A 194 0 SHEET 2 AA2 3 HIS A 173 VAL A 174 -1 N VAL A 174 O VAL A 193 SHEET 3 AA2 3 HIS A 211 CYS A 212 -1 O CYS A 212 N HIS A 173 LINK NE2 HIS A 134 NI NI A 401 1555 1555 2.34 LINK OD1 ASP A 136 NI NI A 401 1555 1555 2.16 LINK NE2 HIS A 211 NI NI A 401 1555 1555 2.23 LINK NI NI A 401 O1 TRS A 403 1555 1555 2.36 LINK NI NI A 401 O3 TRS A 403 1555 1555 2.21 LINK NI NI A 401 N TRS A 403 1555 1555 2.35 LINK K K A 406 O HOH A 607 1555 1555 3.22 LINK K K A 406 O HOH A 650 1555 3454 3.09 LINK K K A 406 O HOH A 691 1555 1555 3.34 SITE 1 AC1 4 HIS A 134 ASP A 136 HIS A 211 TRS A 403 SITE 1 AC2 14 ASN A 70 VAL A 72 MET A 118 GLN A 131 SITE 2 AC2 14 PRO A 132 HIS A 134 ASP A 136 MET A 137 SITE 3 AC2 14 PHE A 139 TRS A 403 HOH A 538 HOH A 583 SITE 4 AC2 14 HOH A 609 HOH A 615 SITE 1 AC3 9 MET A 122 GLN A 131 HIS A 134 ASP A 136 SITE 2 AC3 9 ASN A 157 HIS A 211 NI A 401 58J A 402 SITE 3 AC3 9 HOH A 557 SITE 1 AC4 3 THR A 172 GLY A 213 ARG A 223 SITE 1 AC5 3 SER A 74 THR A 77 GLN A 131 SITE 1 AC6 1 HOH A 650 CRYST1 73.050 120.770 66.660 90.00 90.00 90.00 C 2 2 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.013689 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008280 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015002 0.00000