HEADER OXIDOREDUCTASE 17-MAY-12 4F8B TITLE CRYSTAL STRUCTURE OF THE COVALENT THIOIMIDE INTERMEDIATE OF UNIMODULAR TITLE 2 NITRILE REDUCTASE QUEF COMPND MOL_ID: 1; COMPND 2 MOLECULE: NADPH-DEPENDENT 7-CYANO-7-DEAZAGUANINE REDUCTASE; COMPND 3 CHAIN: A, B, C, D, E; COMPND 4 SYNONYM: QUEF, 7-CYANO-7-CARBAGUANINE REDUCTASE, NADPH-DEPENDENT COMPND 5 NITRILE OXIDOREDUCTASE, PREQ(0) REDUCTASE; COMPND 6 EC: 1.7.1.13; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS SUBSP. SUBTILIS; SOURCE 3 ORGANISM_TAXID: 224308; SOURCE 4 STRAIN: 168; SOURCE 5 GENE: BSU13750, QUEF, YKVM; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS BETA BARREL, PROTEIN THIOIMIDE COMPLEX, PTERIN BINDING FOLD, TUNNEL KEYWDS 2 FOLD, TRNA MODIFICATION ENZYME, 7-CYANO-7-DEAZAGUANINE, NADPH, KEYWDS 3 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR B.STEC,M.A.SWAIRJO REVDAT 6 06-NOV-24 4F8B 1 REMARK REVDAT 5 13-SEP-23 4F8B 1 REMARK LINK REVDAT 4 15-NOV-17 4F8B 1 REMARK REVDAT 3 19-SEP-12 4F8B 1 JRNL REVDAT 2 01-AUG-12 4F8B 1 JRNL REVDAT 1 11-JUL-12 4F8B 0 JRNL AUTH V.M.CHIKWANA,B.STEC,B.W.LEE,V.DE CRECY-LAGARD,D.IWATA-REUYL, JRNL AUTH 2 M.A.SWAIRJO JRNL TITL STRUCTURAL BASIS OF BIOLOGICAL NITRILE REDUCTION. JRNL REF J.BIOL.CHEM. V. 287 30560 2012 JRNL REFN ISSN 0021-9258 JRNL PMID 22787148 JRNL DOI 10.1074/JBC.M112.388538 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.56 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 32475 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) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1720 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2153 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.10 REMARK 3 BIN R VALUE (WORKING SET) : 0.2750 REMARK 3 BIN FREE R VALUE SET COUNT : 96 REMARK 3 BIN FREE R VALUE : 0.3110 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6013 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 85 REMARK 3 SOLVENT ATOMS : 165 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 54.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.54 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.93000 REMARK 3 B22 (A**2) : 1.93000 REMARK 3 B33 (A**2) : -2.89000 REMARK 3 B12 (A**2) : 0.96000 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): 0.445 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.305 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.209 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.355 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.886 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6292 ; 0.024 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8508 ; 2.057 ; 1.977 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 714 ; 7.533 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 326 ;35.639 ;24.080 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1045 ;19.630 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 29 ;19.121 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 837 ; 0.129 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4933 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2963 ; 0.251 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4190 ; 0.329 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 309 ; 0.177 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 3 ; 0.238 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 92 ; 0.254 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 20 ; 0.178 ; 0.200 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): 3740 ; 1.339 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5898 ; 2.210 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3031 ; 2.923 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2610 ; 4.348 ; 4.500 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 : 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 4F8B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-MAY-12. REMARK 100 THE DEPOSITION ID IS D_1000072581. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-APR-06 REMARK 200 TEMPERATURE (KELVIN) : 200 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000003 REMARK 200 MONOCHROMATOR : SIDE-SCATTERING CUBEROOT I-BEAM REMARK 200 BENT SINGLE CRYSTAL, ASYMMETRIC REMARK 200 CUT 12.2 DEGREES REMARK 200 OPTICS : MIRRORS 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 : 34623 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.502 REMARK 200 RESOLUTION RANGE LOW (A) : 41.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 9.900 REMARK 200 R MERGE (I) : 0.10200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.57 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.29000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: PDB ENTRY 3BP1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16-20% PEG500 MME, 60 MM IMIDAZOLE, 40 REMARK 280 MM IMIDAZOLIUM CHLORIDE, PH 7.4, 30 MM CALCIUM CHLORIDE OR REMARK 280 MAGNESIUM CHLORIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 129.13067 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 64.56533 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 64.56533 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 129.13067 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: DECAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DECAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 41190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 48840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -187.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E 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 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 0 REMARK 465 THR A 1 REMARK 465 THR A 2 REMARK 465 ARG A 3 REMARK 465 LYS A 4 REMARK 465 GLU A 5 REMARK 465 SER A 6 REMARK 465 GLU A 7 REMARK 465 LEU A 8 REMARK 465 GLU A 9 REMARK 465 GLY A 10 REMARK 465 VAL A 11 REMARK 465 THR A 12 REMARK 465 LEU A 13 REMARK 465 LEU A 14 REMARK 465 GLY A 15 REMARK 465 ASN A 16 REMARK 465 GLN A 17 REMARK 465 GLY A 18 REMARK 465 THR A 19 REMARK 465 GLU A 159 REMARK 465 THR A 160 REMARK 465 ILE A 161 REMARK 465 ASP A 162 REMARK 465 ASN A 163 REMARK 465 ARG A 164 REMARK 465 MET B 0 REMARK 465 THR B 1 REMARK 465 THR B 2 REMARK 465 ARG B 3 REMARK 465 LYS B 4 REMARK 465 GLU B 5 REMARK 465 SER B 6 REMARK 465 GLU B 7 REMARK 465 LEU B 8 REMARK 465 GLU B 9 REMARK 465 GLY B 10 REMARK 465 VAL B 11 REMARK 465 THR B 12 REMARK 465 LEU B 13 REMARK 465 LEU B 14 REMARK 465 GLY B 15 REMARK 465 ASN B 16 REMARK 465 GLN B 17 REMARK 465 GLY B 18 REMARK 465 THR B 19 REMARK 465 MET C 0 REMARK 465 THR C 1 REMARK 465 THR C 2 REMARK 465 ARG C 3 REMARK 465 LYS C 4 REMARK 465 GLU C 5 REMARK 465 SER C 6 REMARK 465 GLU C 7 REMARK 465 LEU C 8 REMARK 465 GLU C 9 REMARK 465 GLY C 10 REMARK 465 VAL C 11 REMARK 465 THR C 12 REMARK 465 LEU C 13 REMARK 465 LEU C 14 REMARK 465 GLY C 15 REMARK 465 ASN C 16 REMARK 465 GLN C 17 REMARK 465 GLY C 18 REMARK 465 THR C 19 REMARK 465 MET D 0 REMARK 465 THR D 1 REMARK 465 THR D 2 REMARK 465 ARG D 3 REMARK 465 LYS D 4 REMARK 465 GLU D 5 REMARK 465 SER D 6 REMARK 465 GLU D 7 REMARK 465 LEU D 8 REMARK 465 GLU D 9 REMARK 465 GLY D 10 REMARK 465 VAL D 11 REMARK 465 THR D 12 REMARK 465 LEU D 13 REMARK 465 LEU D 14 REMARK 465 GLY D 15 REMARK 465 ASN D 16 REMARK 465 GLN D 17 REMARK 465 GLY D 18 REMARK 465 THR D 19 REMARK 465 MET E 0 REMARK 465 THR E 1 REMARK 465 THR E 2 REMARK 465 ARG E 3 REMARK 465 LYS E 4 REMARK 465 GLU E 5 REMARK 465 SER E 6 REMARK 465 GLU E 7 REMARK 465 LEU E 8 REMARK 465 GLU E 9 REMARK 465 GLY E 10 REMARK 465 VAL E 11 REMARK 465 THR E 12 REMARK 465 LEU E 13 REMARK 465 LEU E 14 REMARK 465 GLY E 15 REMARK 465 ASN E 16 REMARK 465 GLN E 17 REMARK 465 GLY E 18 REMARK 465 THR E 19 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 OE2 GLU D 78 N9 GD1 E 201 2.12 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 ASP A 73 -80.97 -100.59 REMARK 500 ASP B 73 -94.17 -93.71 REMARK 500 ALA C 26 76.50 -154.89 REMARK 500 ASP C 73 -81.24 -102.69 REMARK 500 ASP D 73 -91.47 -102.12 REMARK 500 ASP E 73 -97.26 -99.85 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 MG B 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 162 OD2 REMARK 620 2 ARG B 164 OXT 71.4 REMARK 620 3 HOH B 301 O 76.5 146.9 REMARK 620 4 HOH B 302 O 70.3 73.6 88.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP C 162 OD1 REMARK 620 2 ARG C 164 OXT 94.8 REMARK 620 3 HOH C 301 O 90.7 174.5 REMARK 620 4 HOH C 302 O 76.3 86.4 95.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG D 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP D 162 OD2 REMARK 620 2 ARG D 164 OXT 89.6 REMARK 620 3 HOH D 301 O 93.3 87.5 REMARK 620 4 HOH D 302 O 164.9 79.2 76.2 REMARK 620 5 HOH D 303 O 111.9 147.1 114.5 82.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG E 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP E 162 OD2 REMARK 620 2 ARG E 164 OXT 92.7 REMARK 620 3 HOH E 301 O 160.0 90.1 REMARK 620 4 HOH E 302 O 87.7 165.8 84.8 REMARK 620 5 HOH E 303 O 82.3 88.4 78.0 77.5 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 GD1 B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GD1 C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GD1 D 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PE4 D 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GD1 E 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG E 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4FGC RELATED DB: PDB DBREF 4F8B A 0 164 UNP O31678 QUEF_BACSU 1 165 DBREF 4F8B B 0 164 UNP O31678 QUEF_BACSU 1 165 DBREF 4F8B C 0 164 UNP O31678 QUEF_BACSU 1 165 DBREF 4F8B D 0 164 UNP O31678 QUEF_BACSU 1 165 DBREF 4F8B E 0 164 UNP O31678 QUEF_BACSU 1 165 SEQRES 1 A 165 MET THR THR ARG LYS GLU SER GLU LEU GLU GLY VAL THR SEQRES 2 A 165 LEU LEU GLY ASN GLN GLY THR ASN TYR LEU PHE GLU TYR SEQRES 3 A 165 ALA PRO ASP VAL LEU GLU SER PHE PRO ASN LYS HIS VAL SEQRES 4 A 165 ASN ARG ASP TYR PHE VAL LYS PHE ASN CYS PRO GLU PHE SEQRES 5 A 165 THR SER LEU CYS PRO LYS THR GLY GLN PRO ASP PHE ALA SEQRES 6 A 165 THR ILE TYR ILE SER TYR ILE PRO ASP GLU LYS MET VAL SEQRES 7 A 165 GLU SER LYS SER LEU LYS LEU TYR LEU PHE SER PHE ARG SEQRES 8 A 165 ASN HIS GLY ASP PHE HIS GLU ASP CYS MET ASN ILE ILE SEQRES 9 A 165 MET ASN ASP LEU ILE GLU LEU MET ASP PRO ARG TYR ILE SEQRES 10 A 165 GLU VAL TRP GLY LYS PHE THR PRO ARG GLY GLY ILE SER SEQRES 11 A 165 ILE ASP PRO TYR THR ASN TYR GLY LYS PRO GLY THR LYS SEQRES 12 A 165 TYR GLU LYS MET ALA GLU TYR ARG MET MET ASN HIS ASP SEQRES 13 A 165 LEU TYR PRO GLU THR ILE ASP ASN ARG SEQRES 1 B 165 MET THR THR ARG LYS GLU SER GLU LEU GLU GLY VAL THR SEQRES 2 B 165 LEU LEU GLY ASN GLN GLY THR ASN TYR LEU PHE GLU TYR SEQRES 3 B 165 ALA PRO ASP VAL LEU GLU SER PHE PRO ASN LYS HIS VAL SEQRES 4 B 165 ASN ARG ASP TYR PHE VAL LYS PHE ASN CYS PRO GLU PHE SEQRES 5 B 165 THR SER LEU CYS PRO LYS THR GLY GLN PRO ASP PHE ALA SEQRES 6 B 165 THR ILE TYR ILE SER TYR ILE PRO ASP GLU LYS MET VAL SEQRES 7 B 165 GLU SER LYS SER LEU LYS LEU TYR LEU PHE SER PHE ARG SEQRES 8 B 165 ASN HIS GLY ASP PHE HIS GLU ASP CYS MET ASN ILE ILE SEQRES 9 B 165 MET ASN ASP LEU ILE GLU LEU MET ASP PRO ARG TYR ILE SEQRES 10 B 165 GLU VAL TRP GLY LYS PHE THR PRO ARG GLY GLY ILE SER SEQRES 11 B 165 ILE ASP PRO TYR THR ASN TYR GLY LYS PRO GLY THR LYS SEQRES 12 B 165 TYR GLU LYS MET ALA GLU TYR ARG MET MET ASN HIS ASP SEQRES 13 B 165 LEU TYR PRO GLU THR ILE ASP ASN ARG SEQRES 1 C 165 MET THR THR ARG LYS GLU SER GLU LEU GLU GLY VAL THR SEQRES 2 C 165 LEU LEU GLY ASN GLN GLY THR ASN TYR LEU PHE GLU TYR SEQRES 3 C 165 ALA PRO ASP VAL LEU GLU SER PHE PRO ASN LYS HIS VAL SEQRES 4 C 165 ASN ARG ASP TYR PHE VAL LYS PHE ASN CYS PRO GLU PHE SEQRES 5 C 165 THR SER LEU CYS PRO LYS THR GLY GLN PRO ASP PHE ALA SEQRES 6 C 165 THR ILE TYR ILE SER TYR ILE PRO ASP GLU LYS MET VAL SEQRES 7 C 165 GLU SER LYS SER LEU LYS LEU TYR LEU PHE SER PHE ARG SEQRES 8 C 165 ASN HIS GLY ASP PHE HIS GLU ASP CYS MET ASN ILE ILE SEQRES 9 C 165 MET ASN ASP LEU ILE GLU LEU MET ASP PRO ARG TYR ILE SEQRES 10 C 165 GLU VAL TRP GLY LYS PHE THR PRO ARG GLY GLY ILE SER SEQRES 11 C 165 ILE ASP PRO TYR THR ASN TYR GLY LYS PRO GLY THR LYS SEQRES 12 C 165 TYR GLU LYS MET ALA GLU TYR ARG MET MET ASN HIS ASP SEQRES 13 C 165 LEU TYR PRO GLU THR ILE ASP ASN ARG SEQRES 1 D 165 MET THR THR ARG LYS GLU SER GLU LEU GLU GLY VAL THR SEQRES 2 D 165 LEU LEU GLY ASN GLN GLY THR ASN TYR LEU PHE GLU TYR SEQRES 3 D 165 ALA PRO ASP VAL LEU GLU SER PHE PRO ASN LYS HIS VAL SEQRES 4 D 165 ASN ARG ASP TYR PHE VAL LYS PHE ASN CYS PRO GLU PHE SEQRES 5 D 165 THR SER LEU CYS PRO LYS THR GLY GLN PRO ASP PHE ALA SEQRES 6 D 165 THR ILE TYR ILE SER TYR ILE PRO ASP GLU LYS MET VAL SEQRES 7 D 165 GLU SER LYS SER LEU LYS LEU TYR LEU PHE SER PHE ARG SEQRES 8 D 165 ASN HIS GLY ASP PHE HIS GLU ASP CYS MET ASN ILE ILE SEQRES 9 D 165 MET ASN ASP LEU ILE GLU LEU MET ASP PRO ARG TYR ILE SEQRES 10 D 165 GLU VAL TRP GLY LYS PHE THR PRO ARG GLY GLY ILE SER SEQRES 11 D 165 ILE ASP PRO TYR THR ASN TYR GLY LYS PRO GLY THR LYS SEQRES 12 D 165 TYR GLU LYS MET ALA GLU TYR ARG MET MET ASN HIS ASP SEQRES 13 D 165 LEU TYR PRO GLU THR ILE ASP ASN ARG SEQRES 1 E 165 MET THR THR ARG LYS GLU SER GLU LEU GLU GLY VAL THR SEQRES 2 E 165 LEU LEU GLY ASN GLN GLY THR ASN TYR LEU PHE GLU TYR SEQRES 3 E 165 ALA PRO ASP VAL LEU GLU SER PHE PRO ASN LYS HIS VAL SEQRES 4 E 165 ASN ARG ASP TYR PHE VAL LYS PHE ASN CYS PRO GLU PHE SEQRES 5 E 165 THR SER LEU CYS PRO LYS THR GLY GLN PRO ASP PHE ALA SEQRES 6 E 165 THR ILE TYR ILE SER TYR ILE PRO ASP GLU LYS MET VAL SEQRES 7 E 165 GLU SER LYS SER LEU LYS LEU TYR LEU PHE SER PHE ARG SEQRES 8 E 165 ASN HIS GLY ASP PHE HIS GLU ASP CYS MET ASN ILE ILE SEQRES 9 E 165 MET ASN ASP LEU ILE GLU LEU MET ASP PRO ARG TYR ILE SEQRES 10 E 165 GLU VAL TRP GLY LYS PHE THR PRO ARG GLY GLY ILE SER SEQRES 11 E 165 ILE ASP PRO TYR THR ASN TYR GLY LYS PRO GLY THR LYS SEQRES 12 E 165 TYR GLU LYS MET ALA GLU TYR ARG MET MET ASN HIS ASP SEQRES 13 E 165 LEU TYR PRO GLU THR ILE ASP ASN ARG HET GD1 B 201 13 HET MG B 202 1 HET PO4 B 203 5 HET GD1 C 201 13 HET MG C 202 1 HET GD1 D 201 13 HET MG D 202 1 HET PE4 D 203 24 HET GD1 E 201 13 HET MG E 202 1 HETNAM GD1 2-AMINO-5-[(Z)-IMINOMETHYL]-3,7-DIHYDRO-4H-PYRROLO[2,3- HETNAM 2 GD1 D]PYRIMIDIN-4-ONE HETNAM MG MAGNESIUM ION HETNAM PO4 PHOSPHATE ION HETNAM PE4 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}- HETNAM 2 PE4 ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL HETSYN GD1 7-CYANO-7-DEAZAGUANINE, BOUND FORM HETSYN PE4 POLYETHYLENE GLYCOL PEG4000 FORMUL 6 GD1 4(C7 H7 N5 O) FORMUL 7 MG 4(MG 2+) FORMUL 8 PO4 O4 P 3- FORMUL 13 PE4 C16 H34 O8 FORMUL 16 HOH *165(H2 O) HELIX 1 1 ALA A 26 LEU A 30 5 5 HELIX 2 2 GLU A 78 SER A 88 1 11 HELIX 3 3 PHE A 95 ASP A 112 1 18 HELIX 4 4 THR A 141 TYR A 157 1 17 HELIX 5 5 ALA B 26 LEU B 30 5 5 HELIX 6 6 GLU B 78 SER B 88 1 11 HELIX 7 7 PHE B 95 ASP B 112 1 18 HELIX 8 8 THR B 141 ASN B 153 1 13 HELIX 9 9 ALA C 26 LEU C 30 5 5 HELIX 10 10 GLU C 78 SER C 88 1 11 HELIX 11 11 PHE C 95 ASP C 112 1 18 HELIX 12 12 THR C 141 ASN C 153 1 13 HELIX 13 13 ALA D 26 LEU D 30 5 5 HELIX 14 14 GLU D 78 SER D 88 1 11 HELIX 15 15 PHE D 95 ASP D 112 1 18 HELIX 16 16 THR D 141 ASN D 153 1 13 HELIX 17 17 ALA E 26 LEU E 30 5 5 HELIX 18 18 GLU E 78 SER E 88 1 11 HELIX 19 19 PHE E 95 ASP E 112 1 18 HELIX 20 20 THR E 141 ASN E 153 1 13 SHEET 1 A 2 SER A 32 PRO A 34 0 SHEET 2 A 2 LYS A 75 VAL A 77 -1 O MET A 76 N PHE A 33 SHEET 1 B21 ILE A 128 SER A 129 0 SHEET 2 B21 PHE E 43 LEU E 54 -1 O PHE E 43 N SER A 129 SHEET 3 B21 PRO E 61 ILE E 71 -1 O ILE E 68 N PHE E 46 SHEET 4 B21 TYR E 115 PHE E 122 -1 O TRP E 119 N TYR E 67 SHEET 5 B21 SER E 129 GLY E 137 -1 O PRO E 132 N GLY E 120 SHEET 6 B21 PHE D 43 LEU D 54 -1 N PHE D 43 O TYR E 133 SHEET 7 B21 PRO D 61 ILE D 71 -1 O ASP D 62 N SER D 53 SHEET 8 B21 TYR D 115 PHE D 122 -1 O TRP D 119 N TYR D 67 SHEET 9 B21 SER D 129 GLY D 137 -1 O THR D 134 N VAL D 118 SHEET 10 B21 TYR C 42 LEU C 54 -1 N PHE C 43 O TYR D 133 SHEET 11 B21 PRO C 61 ILE C 71 -1 O ASP C 62 N SER C 53 SHEET 12 B21 TYR C 115 PHE C 122 -1 O TRP C 119 N TYR C 67 SHEET 13 B21 SER C 129 GLY C 137 -1 O THR C 134 N VAL C 118 SHEET 14 B21 TYR B 42 LEU B 54 -1 N PHE B 43 O TYR C 133 SHEET 15 B21 PRO B 61 ILE B 71 -1 O ILE B 68 N PHE B 46 SHEET 16 B21 TYR B 115 PHE B 122 -1 O TRP B 119 N TYR B 67 SHEET 17 B21 SER B 129 GLY B 137 -1 O PRO B 132 N GLY B 120 SHEET 18 B21 PHE A 43 LEU A 54 -1 N PHE A 43 O TYR B 133 SHEET 19 B21 PRO A 61 ILE A 71 -1 O ILE A 68 N PHE A 46 SHEET 20 B21 TYR A 115 PHE A 122 -1 O LYS A 121 N THR A 65 SHEET 21 B21 TYR A 133 GLY A 137 -1 O THR A 134 N VAL A 118 SHEET 1 C 2 SER B 32 PRO B 34 0 SHEET 2 C 2 LYS B 75 VAL B 77 -1 O MET B 76 N PHE B 33 SHEET 1 D 2 SER C 32 PRO C 34 0 SHEET 2 D 2 LYS C 75 VAL C 77 -1 O MET C 76 N PHE C 33 SHEET 1 E 2 SER D 32 PRO D 34 0 SHEET 2 E 2 LYS D 75 VAL D 77 -1 O MET D 76 N PHE D 33 SHEET 1 F 2 SER E 32 PRO E 34 0 SHEET 2 F 2 LYS E 75 VAL E 77 -1 O MET E 76 N PHE E 33 LINK SG CYS B 55 C77 GD1 B 201 1555 1555 1.87 LINK SG CYS C 55 C77 GD1 C 201 1555 1555 1.89 LINK SG CYS D 55 C77 GD1 D 201 1555 1555 1.88 LINK SG CYS E 55 C77 GD1 E 201 1555 1555 1.91 LINK OD2 ASP B 162 MG MG B 202 1555 1555 2.99 LINK OXT ARG B 164 MG MG B 202 1555 1555 2.49 LINK MG MG B 202 O HOH B 301 1555 1555 2.21 LINK MG MG B 202 O HOH B 302 1555 1555 2.71 LINK OD1 ASP C 162 MG MG C 202 1555 1555 2.21 LINK OXT ARG C 164 MG MG C 202 1555 1555 2.47 LINK MG MG C 202 O HOH C 301 1555 1555 1.92 LINK MG MG C 202 O HOH C 302 1555 1555 1.88 LINK OD2 ASP D 162 MG MG D 202 1555 1555 2.22 LINK OXT ARG D 164 MG MG D 202 1555 1555 2.33 LINK MG MG D 202 O HOH D 301 1555 1555 2.21 LINK MG MG D 202 O HOH D 302 1555 1555 2.04 LINK MG MG D 202 O HOH D 303 1555 1555 2.17 LINK OD2 ASP E 162 MG MG E 202 1555 1555 2.21 LINK OXT ARG E 164 MG MG E 202 1555 1555 2.53 LINK MG MG E 202 O HOH E 301 1555 1555 2.16 LINK MG MG E 202 O HOH E 302 1555 1555 2.23 LINK MG MG E 202 O HOH E 303 1555 1555 2.10 SITE 1 AC1 10 PHE A 33 VAL A 77 GLU A 78 SER A 79 SITE 2 AC1 10 CYS B 55 ASP B 62 PHE B 95 HIS B 96 SITE 3 AC1 10 GLU B 97 ILE B 130 SITE 1 AC2 7 ASP B 162 ARG B 164 HOH B 301 HOH B 302 SITE 2 AC2 7 ARG E 164 MG E 202 HOH E 301 SITE 1 AC3 3 ASN B 39 HOH B 337 HOH B 340 SITE 1 AC4 9 VAL B 77 GLU B 78 SER B 79 CYS C 55 SITE 2 AC4 9 ASP C 62 PHE C 95 HIS C 96 GLU C 97 SITE 3 AC4 9 ILE C 130 SITE 1 AC5 7 ASP C 162 ARG C 164 HOH C 301 HOH C 302 SITE 2 AC5 7 ARG D 164 MG D 202 HOH D 302 SITE 1 AC6 11 PHE C 33 VAL C 77 GLU C 78 SER C 79 SITE 2 AC6 11 CYS D 55 PRO D 56 ASP D 62 PHE D 95 SITE 3 AC6 11 HIS D 96 GLU D 97 ILE D 130 SITE 1 AC7 7 ARG C 164 MG C 202 ASP D 162 ARG D 164 SITE 2 AC7 7 HOH D 301 HOH D 302 HOH D 303 SITE 1 AC8 11 TYR B 149 ASN B 153 TYR B 157 TYR C 149 SITE 2 AC8 11 ASN C 153 TYR C 157 ASN D 153 TYR D 157 SITE 3 AC8 11 HOH D 327 TYR E 149 TYR E 157 SITE 1 AC9 12 PHE D 33 VAL D 77 GLU D 78 SER D 79 SITE 2 AC9 12 CYS E 55 PRO E 56 LYS E 57 ASP E 62 SITE 3 AC9 12 PHE E 95 HIS E 96 GLU E 97 ILE E 130 SITE 1 BC1 7 ARG B 164 MG B 202 ASP E 162 ARG E 164 SITE 2 BC1 7 HOH E 301 HOH E 302 HOH E 303 CRYST1 93.507 93.507 193.696 90.00 90.00 120.00 P 32 2 1 30 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 0.010694 0.006174 0.000000 0.00000 SCALE2 0.000000 0.012349 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005163 0.00000