HEADER HYDROLASE 27-JAN-21 7E06 TITLE TRANS-3/4-PROLINE-HYDROXYLASE H11 WITH AKG COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHYTANOYL-COA DIOXYGENASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: UNCULTURED BACTERIUM ESNAPD13; SOURCE 3 ORGANISM_TAXID: 1366593; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS L-PROLINE, TRANS, HYDROXYLASE, AKG, HYDROLASE, MUTANT EXPDTA X-RAY DIFFRACTION AUTHOR W.G.GONG,L.Y.YANG REVDAT 2 29-NOV-23 7E06 1 REMARK REVDAT 1 02-FEB-22 7E06 0 JRNL AUTH W.G.GONG,L.Y.YANG JRNL TITL TRANS-3/4-PROLINE-HYDROXYLASE H11 WITH AKG AND L-PROLINE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 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) : 1.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 85.76 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 55651 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) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2882 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) : 1.98 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.03 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3755 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.73 REMARK 3 BIN R VALUE (WORKING SET) : 0.2020 REMARK 3 BIN FREE R VALUE SET COUNT : 174 REMARK 3 BIN FREE R VALUE : 0.2270 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4057 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 471 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.03000 REMARK 3 B22 (A**2) : 0.03000 REMARK 3 B33 (A**2) : -0.05000 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): 0.119 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.118 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.075 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.616 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4208 ; 0.024 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3913 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5712 ; 2.132 ; 1.944 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8970 ; 1.146 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 509 ; 7.250 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 210 ;34.634 ;23.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 661 ;15.481 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 38 ;18.150 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 610 ; 0.147 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4799 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1031 ; 0.002 ; 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 7E06 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-JAN-21. REMARK 100 THE DEPOSITION ID IS D_1300020367. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-APR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55651 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.970 REMARK 200 RESOLUTION RANGE LOW (A) : 85.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 24.30 REMARK 200 R MERGE (I) : 0.13100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 238.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 24.00 REMARK 200 R MERGE FOR SHELL (I) : 0.51200 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: 6LNS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.7M SODIUM CITRATE TRIBASIC REMARK 280 DIHYDRATE, 0.1M BIS-TRIS PROPANE (PH 7.0), VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 289.15K 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 72.00500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 53.38150 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 53.38150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 36.00250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 53.38150 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 53.38150 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 108.00750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 53.38150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 53.38150 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 36.00250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 53.38150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 53.38150 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 108.00750 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 72.00500 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 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 ASN A 55 REMARK 465 THR A 56 REMARK 465 ASP A 161 REMARK 465 ALA A 162 REMARK 465 ASP A 163 REMARK 465 VAL A 164 REMARK 465 LYS A 165 REMARK 465 GLY A 166 REMARK 465 GLU A 167 REMARK 465 GLY A 168 REMARK 465 TRP A 169 REMARK 465 ALA A 170 REMARK 465 ASN A 171 REMARK 465 THR A 172 REMARK 465 LEU A 173 REMARK 465 THR A 174 REMARK 465 ALA A 175 REMARK 465 GLU B 53 REMARK 465 GLN B 54 REMARK 465 ASN B 55 REMARK 465 THR B 56 REMARK 465 GLY B 57 REMARK 465 LYS B 165 REMARK 465 GLY B 168 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 53 CG CD OE1 OE2 REMARK 470 GLN A 54 CG CD OE1 NE2 REMARK 470 ILE A 58 CG1 CG2 CD1 REMARK 470 VAL A 183 CG1 CG2 REMARK 470 LYS B 107 CG CD CE NZ REMARK 470 ASP B 163 CG OD1 OD2 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 749 O HOH A 753 1.88 REMARK 500 O HOH A 667 O HOH A 669 2.08 REMARK 500 O HOH A 608 O HOH A 792 2.09 REMARK 500 O HOH A 753 O HOH A 818 2.09 REMARK 500 O HOH B 768 O HOH B 799 2.19 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 16 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 36 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG B 16 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG B 80 CB - CG - CD ANGL. DEV. = 19.7 DEGREES REMARK 500 ARG B 80 CG - CD - NE ANGL. DEV. = -18.2 DEGREES REMARK 500 ARG B 80 CD - NE - CZ ANGL. DEV. = 13.2 DEGREES REMARK 500 ARG B 80 NE - CZ - NH1 ANGL. DEV. = -9.7 DEGREES REMARK 500 ARG B 80 NE - CZ - NH2 ANGL. DEV. = 8.5 DEGREES REMARK 500 ARG B 225 NE - CZ - NH1 ANGL. DEV. = 5.3 DEGREES REMARK 500 ARG B 225 NE - CZ - NH2 ANGL. DEV. = -4.3 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 VAL A 59 108.90 -46.28 REMARK 500 LYS A 107 -168.65 -124.52 REMARK 500 PRO A 129 45.36 -80.38 REMARK 500 ASP A 182 170.82 -57.67 REMARK 500 LYS B 103 70.38 38.49 REMARK 500 PHE B 106 15.73 55.36 REMARK 500 LYS B 107 -154.77 -135.84 REMARK 500 PRO B 129 45.93 -79.08 REMARK 500 SER B 157 20.15 -141.91 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 856 DISTANCE = 6.73 ANGSTROMS REMARK 525 HOH B 815 DISTANCE = 6.23 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 FE A 502 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 114 NE2 REMARK 620 2 ASP A 116 OD1 91.3 REMARK 620 3 HIS A 214 NE2 90.3 101.4 REMARK 620 4 AKG A 501 O1 96.2 92.9 164.2 REMARK 620 5 AKG A 501 O5 94.6 170.7 85.9 79.2 REMARK 620 6 HOH A 702 O 177.1 90.0 92.0 81.2 83.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE B 502 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 114 NE2 REMARK 620 2 ASP B 116 OD1 92.8 REMARK 620 3 HIS B 214 NE2 97.2 116.9 REMARK 620 4 AKG B 501 O2 95.2 85.0 154.1 REMARK 620 5 AKG B 501 O5 96.3 166.1 72.3 83.8 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AKG A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AKG B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE B 502 DBREF 7E06 A 1 266 UNP S5TUM1 S5TUM1_9BACT 1 266 DBREF 7E06 B 1 266 UNP S5TUM1 S5TUM1_9BACT 1 266 SEQADV 7E06 GLN A -1 UNP S5TUM1 EXPRESSION TAG SEQADV 7E06 ILE A 0 UNP S5TUM1 EXPRESSION TAG SEQADV 7E06 GLN B -1 UNP S5TUM1 EXPRESSION TAG SEQADV 7E06 ILE B 0 UNP S5TUM1 EXPRESSION TAG SEQRES 1 A 268 GLN ILE MET GLU PRO HIS ASP THR LEU SER PRO ALA GLN SEQRES 2 A 268 VAL ASP GLU TYR ARG LYS ASN GLY PHE LEU VAL GLN GLU SEQRES 3 A 268 HIS VAL PHE ASP GLU GLU GLU ILE GLU LEU LEU ARG ALA SEQRES 4 A 268 GLU ALA ALA GLN GLU PHE ALA SER GLY GLY GLU ARG VAL SEQRES 5 A 268 THR VAL GLU GLN ASN THR GLY ILE VAL ARG GLY VAL HIS SEQRES 6 A 268 GLY CYS HIS LEU TYR SER GLU VAL PHE GLY ARG LEU VAL SEQRES 7 A 268 ARG SER PRO ARG LEU LEU PRO ILE ALA ARG GLN LEU LEU SEQRES 8 A 268 ARG ASP ASP VAL TYR VAL HIS GLN PHE LYS ILE ASN ALA SEQRES 9 A 268 LYS ARG ALA PHE LYS GLY GLU VAL TRP GLU TRP HIS GLN SEQRES 10 A 268 ASP TYR THR PHE TRP HIS HIS GLU ASP GLY MET PRO ALA SEQRES 11 A 268 PRO ARG ALA LEU SER ALA ALA ILE PHE LEU ASP GLU VAL SEQRES 12 A 268 THR GLU PHE ASN GLY PRO LEU THR PHE VAL PRO GLY GLY SEQRES 13 A 268 HIS GLY SER GLY MET ILE ASP ALA ASP VAL LYS GLY GLU SEQRES 14 A 268 GLY TRP ALA ASN THR LEU THR ALA SER LEU LYS TYR SER SEQRES 15 A 268 LEU ASP VAL GLU THR MET ARG GLY LEU ILE GLU ARG ASN SEQRES 16 A 268 GLY MET VAL ALA PRO LYS GLY PRO ARG GLY SER VAL LEU SEQRES 17 A 268 TRP PHE ASP ALA ASN ILE PRO HIS SER SER VAL PRO ASN SEQRES 18 A 268 ILE SER PRO PHE ASP ARG GLY LEU VAL LEU ILE THR TYR SEQRES 19 A 268 ASN SER VAL GLU ASN LYS THR ASP VAL THR ARG GLY THR SEQRES 20 A 268 ARG PRO GLU TRP LEU ALA ALA ARG ASP PHE THR PRO LEU SEQRES 21 A 268 THR ALA LEU GLN ALA THR SER PHE SEQRES 1 B 268 GLN ILE MET GLU PRO HIS ASP THR LEU SER PRO ALA GLN SEQRES 2 B 268 VAL ASP GLU TYR ARG LYS ASN GLY PHE LEU VAL GLN GLU SEQRES 3 B 268 HIS VAL PHE ASP GLU GLU GLU ILE GLU LEU LEU ARG ALA SEQRES 4 B 268 GLU ALA ALA GLN GLU PHE ALA SER GLY GLY GLU ARG VAL SEQRES 5 B 268 THR VAL GLU GLN ASN THR GLY ILE VAL ARG GLY VAL HIS SEQRES 6 B 268 GLY CYS HIS LEU TYR SER GLU VAL PHE GLY ARG LEU VAL SEQRES 7 B 268 ARG SER PRO ARG LEU LEU PRO ILE ALA ARG GLN LEU LEU SEQRES 8 B 268 ARG ASP ASP VAL TYR VAL HIS GLN PHE LYS ILE ASN ALA SEQRES 9 B 268 LYS ARG ALA PHE LYS GLY GLU VAL TRP GLU TRP HIS GLN SEQRES 10 B 268 ASP TYR THR PHE TRP HIS HIS GLU ASP GLY MET PRO ALA SEQRES 11 B 268 PRO ARG ALA LEU SER ALA ALA ILE PHE LEU ASP GLU VAL SEQRES 12 B 268 THR GLU PHE ASN GLY PRO LEU THR PHE VAL PRO GLY GLY SEQRES 13 B 268 HIS GLY SER GLY MET ILE ASP ALA ASP VAL LYS GLY GLU SEQRES 14 B 268 GLY TRP ALA ASN THR LEU THR ALA SER LEU LYS TYR SER SEQRES 15 B 268 LEU ASP VAL GLU THR MET ARG GLY LEU ILE GLU ARG ASN SEQRES 16 B 268 GLY MET VAL ALA PRO LYS GLY PRO ARG GLY SER VAL LEU SEQRES 17 B 268 TRP PHE ASP ALA ASN ILE PRO HIS SER SER VAL PRO ASN SEQRES 18 B 268 ILE SER PRO PHE ASP ARG GLY LEU VAL LEU ILE THR TYR SEQRES 19 B 268 ASN SER VAL GLU ASN LYS THR ASP VAL THR ARG GLY THR SEQRES 20 B 268 ARG PRO GLU TRP LEU ALA ALA ARG ASP PHE THR PRO LEU SEQRES 21 B 268 THR ALA LEU GLN ALA THR SER PHE HET AKG A 501 10 HET FE A 502 1 HET AKG B 501 10 HET FE B 502 1 HETNAM AKG 2-OXOGLUTARIC ACID HETNAM FE FE (III) ION FORMUL 3 AKG 2(C5 H6 O5) FORMUL 4 FE 2(FE 3+) FORMUL 7 HOH *471(H2 O) HELIX 1 AA1 SER A 8 GLY A 19 1 12 HELIX 2 AA2 ASP A 28 GLY A 46 1 19 HELIX 3 AA3 CYS A 65 TYR A 68 5 4 HELIX 4 AA4 SER A 69 VAL A 76 1 8 HELIX 5 AA5 LEU A 81 ARG A 90 1 10 HELIX 6 AA6 GLN A 115 GLY A 125 1 11 HELIX 7 AA7 ASP A 182 GLY A 194 1 13 HELIX 8 AA8 SER B 8 GLY B 19 1 12 HELIX 9 AA9 ASP B 28 GLY B 46 1 19 HELIX 10 AB1 CYS B 65 TYR B 68 5 4 HELIX 11 AB2 SER B 69 VAL B 76 1 8 HELIX 12 AB3 LEU B 81 ARG B 90 1 10 HELIX 13 AB4 ASP B 116 GLY B 125 1 10 HELIX 14 AB5 ASP B 182 GLY B 194 1 13 SHEET 1 AA1 7 PHE A 20 GLN A 23 0 SHEET 2 AA1 7 VAL A 205 ASP A 209 -1 O TRP A 207 N LEU A 21 SHEET 3 AA1 7 ALA A 131 PHE A 137 -1 N SER A 133 O PHE A 208 SHEET 4 AA1 7 ARG A 225 SER A 234 -1 O ILE A 230 N ALA A 134 SHEET 5 AA1 7 VAL A 93 LYS A 103 -1 N LYS A 99 O LEU A 229 SHEET 6 AA1 7 VAL A 59 HIS A 63 -1 N ARG A 60 O ALA A 102 SHEET 7 AA1 7 VAL A 50 VAL A 52 -1 N THR A 51 O GLY A 61 SHEET 1 AA2 3 TRP A 111 HIS A 114 0 SHEET 2 AA2 3 HIS A 214 SER A 216 -1 O SER A 216 N TRP A 111 SHEET 3 AA2 3 THR A 149 PHE A 150 -1 N THR A 149 O SER A 215 SHEET 1 AA3 7 PHE B 20 GLN B 23 0 SHEET 2 AA3 7 VAL B 205 ASP B 209 -1 O TRP B 207 N LEU B 21 SHEET 3 AA3 7 ALA B 131 PHE B 137 -1 N SER B 133 O PHE B 208 SHEET 4 AA3 7 LEU B 227 SER B 234 -1 O VAL B 228 N ILE B 136 SHEET 5 AA3 7 VAL B 93 ASN B 101 -1 N LYS B 99 O LEU B 229 SHEET 6 AA3 7 GLY B 61 HIS B 63 -1 N VAL B 62 O ILE B 100 SHEET 7 AA3 7 VAL B 50 THR B 51 -1 N THR B 51 O GLY B 61 SHEET 1 AA4 3 TRP B 111 GLN B 115 0 SHEET 2 AA4 3 PRO B 213 SER B 216 -1 O SER B 216 N TRP B 111 SHEET 3 AA4 3 THR B 149 PHE B 150 -1 N THR B 149 O SER B 215 LINK NE2 HIS A 114 FE FE A 502 1555 1555 2.26 LINK OD1 ASP A 116 FE FE A 502 1555 1555 2.18 LINK NE2 HIS A 214 FE FE A 502 1555 1555 2.01 LINK O1 AKG A 501 FE FE A 502 1555 1555 1.84 LINK O5 AKG A 501 FE FE A 502 1555 1555 2.09 LINK FE FE A 502 O HOH A 702 1555 1555 2.44 LINK NE2 HIS B 114 FE FE B 502 1555 1555 2.34 LINK OD1 ASP B 116 FE FE B 502 1555 1555 2.21 LINK NE2 HIS B 214 FE FE B 502 1555 1555 2.07 LINK O2 AKG B 501 FE FE B 502 1555 1555 1.89 LINK O5 AKG B 501 FE FE B 502 1555 1555 2.20 SITE 1 AC1 13 LYS A 99 ASN A 101 LYS A 103 TRP A 111 SITE 2 AC1 13 HIS A 114 ASP A 116 LEU A 148 HIS A 214 SITE 3 AC1 13 SER A 216 ARG A 225 FE A 502 HOH A 658 SITE 4 AC1 13 HOH A 702 SITE 1 AC2 5 HIS A 114 ASP A 116 HIS A 214 AKG A 501 SITE 2 AC2 5 HOH A 702 SITE 1 AC3 12 LYS B 99 ASN B 101 LYS B 103 TRP B 111 SITE 2 AC3 12 HIS B 114 ASP B 116 LEU B 148 THR B 172 SITE 3 AC3 12 HIS B 214 SER B 216 ARG B 225 FE B 502 SITE 1 AC4 4 HIS B 114 ASP B 116 HIS B 214 AKG B 501 CRYST1 106.763 106.763 144.010 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 0.009367 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009367 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006944 0.00000