HEADER TRANSFERASE 13-JUL-15 5A89 TITLE CRYSTAL STRUCTURE OF THE RIBOFLAVIN KINASE MODULE OF FAD SYNTHETASE TITLE 2 FROM CORYNEBACTERIUM AMMONIAGENES IN COMPLEX WITH FMN AND ADP(P 21 21 TITLE 3 21) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBF; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RIBOFLAVIN KINASE DOMAIN, RESIDUES 183-338; COMPND 5 EC: 2.7.1.26; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: KINASE DOMAIN OF FAD SYNTHETASE (A BIFUNCTIONAL COMPND 8 ENZYME) SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CORYNEBACTERIUM AMMONIAGENES; SOURCE 3 ORGANISM_TAXID: 1697; SOURCE 4 ATCC: 6872; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS TRANSFERASE, RIBOFLAVIN KINASE DOMAIN, ATP-BINDING, NUCLEOTIDE- KEYWDS 2 BINDING EXPDTA X-RAY DIFFRACTION AUTHOR B.HERGUEDAS,M.MARTINEZ-JULVEZ,J.A.HERMOSO,M.MEDINA REVDAT 3 10-JAN-24 5A89 1 REMARK LINK REVDAT 2 16-DEC-15 5A89 1 JRNL REVDAT 1 09-DEC-15 5A89 0 JRNL AUTH B.HERGUEDAS,I.LANS,M.SEBASTIAN,J.A.HERMOSO, JRNL AUTH 2 M.MARTINEZ-JULVEZ,M.MEDINA JRNL TITL STRUCTURAL INSIGHTS INTO THE SYNTHESIS OF FMN IN PROKARYOTIC JRNL TITL 2 ORGANISMS. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 71 2526 2015 JRNL REFN ISSN 0907-4449 JRNL PMID 26627660 JRNL DOI 10.1107/S1399004715019641 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0103 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 57.62 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 33438 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) : 0.146 REMARK 3 R VALUE (WORKING SET) : 0.143 REMARK 3 FREE R VALUE : 0.176 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2560 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1762 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 70.54 REMARK 3 BIN R VALUE (WORKING SET) : 0.1690 REMARK 3 BIN FREE R VALUE SET COUNT : 173 REMARK 3 BIN FREE R VALUE : 0.2200 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2354 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 142 REMARK 3 SOLVENT ATOMS : 382 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.15 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.54000 REMARK 3 B22 (A**2) : -0.39000 REMARK 3 B33 (A**2) : -0.15000 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): 0.090 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.089 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.051 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.535 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): 2570 ; 0.015 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2317 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3517 ; 1.772 ; 2.009 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5336 ; 0.960 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 308 ; 6.566 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 118 ;32.369 ;24.492 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 372 ;11.004 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ; 7.494 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 382 ; 0.104 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2878 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 580 ; 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): 1221 ; 0.785 ; 0.979 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1219 ; 0.782 ; 0.976 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1523 ; 1.343 ; 1.460 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1349 ; 1.083 ; 1.153 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 : 2 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 186 A 337 REMARK 3 ORIGIN FOR THE GROUP (A): 14.2070 -24.9390 -13.8070 REMARK 3 T TENSOR REMARK 3 T11: 0.0358 T22: 0.0162 REMARK 3 T33: 0.0193 T12: -0.0188 REMARK 3 T13: 0.0197 T23: -0.0159 REMARK 3 L TENSOR REMARK 3 L11: 1.1668 L22: 2.1705 REMARK 3 L33: 1.4962 L12: -0.1136 REMARK 3 L13: 0.0485 L23: 0.2606 REMARK 3 S TENSOR REMARK 3 S11: 0.0209 S12: 0.0503 S13: -0.0316 REMARK 3 S21: 0.0707 S22: -0.0740 S23: 0.1290 REMARK 3 S31: 0.0901 S32: -0.0909 S33: 0.0532 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 187 B 338 REMARK 3 ORIGIN FOR THE GROUP (A): 18.9970 6.1590 -7.8350 REMARK 3 T TENSOR REMARK 3 T11: 0.0103 T22: 0.0036 REMARK 3 T33: 0.0317 T12: -0.0005 REMARK 3 T13: 0.0012 T23: -0.0011 REMARK 3 L TENSOR REMARK 3 L11: 0.5230 L22: 1.2080 REMARK 3 L33: 0.6499 L12: -0.0015 REMARK 3 L13: -0.1208 L23: 0.2694 REMARK 3 S TENSOR REMARK 3 S11: 0.0010 S12: 0.0294 S13: 0.0337 REMARK 3 S21: -0.0527 S22: -0.0252 S23: 0.0186 REMARK 3 S31: 0.0215 S32: -0.0401 S33: 0.0242 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. FINAL MODEL INCLUDES RESIDUES 186-336 IN CHAIN A AND REMARK 3 186- -338 IN CHAIN B REMARK 4 REMARK 4 5A89 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1290064321. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.933 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36054 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 35.240 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.16000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2X0K REMARK 200 REMARK 200 REMARK: ONLY RFK MODULE OF CAFDS-2X0K-AS SEARCHING MODEL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 26-30% PEG 4000, 200 MM LI2SO4 AND 100 REMARK 280 MM SODIUM ACETATE PH 5.0 AND 100 MM NAI REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 21.70000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.04000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.24000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.04000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.70000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.24000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 LEU A 183 REMARK 465 GLY A 184 REMARK 465 ARG A 185 REMARK 465 GLU A 337 REMARK 465 SER A 338 REMARK 465 LEU B 183 REMARK 465 GLY B 184 REMARK 465 ARG B 185 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 NZ LYS A 313 O HOH A 2149 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 265 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG B 199 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG B 199 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG B 265 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PHE A 187 126.89 -31.48 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 ZN A 343 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 186 NE2 REMARK 620 2 ASP A 321 OD1 122.2 REMARK 620 3 HIS A 325 NE2 109.0 103.3 REMARK 620 4 HOH A2004 O 109.2 105.0 107.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 341 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 208 OG1 REMARK 620 2 THR A 208 O 85.8 REMARK 620 3 ASN A 210 OD1 89.7 80.9 REMARK 620 4 FMN A 339 O1P 78.4 162.5 91.4 REMARK 620 5 ADP A 501 O1A 94.2 92.8 172.3 95.8 REMARK 620 6 ADP A 501 O3B 176.5 90.8 88.9 104.9 86.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 343 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 186 NE2 REMARK 620 2 ASP B 321 OD1 113.3 REMARK 620 3 HIS B 325 NE2 104.0 109.1 REMARK 620 4 HOH B2004 O 119.1 106.7 103.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 341 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR B 208 O REMARK 620 2 THR B 208 OG1 85.2 REMARK 620 3 ASN B 210 OD1 81.2 90.1 REMARK 620 4 FMN B 339 O2P 163.4 80.0 91.3 REMARK 620 5 ADP B 340 O1A 90.7 94.7 170.2 98.0 REMARK 620 6 ADP B 340 O3B 89.2 174.0 87.0 105.2 87.5 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 MG A 341 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 343 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN B 339 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP B 340 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 341 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 343 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN A 339 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 1337 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1339 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1340 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1341 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5A88 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE RFK MODULE OF FAD SYNTHETASE FROM REMARK 900 CORYNEBACTERIUM AMMONIAGENES IN COMPLEX WITH ADP REMARK 900 RELATED ID: 5A8A RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE RFK MODULE OF FAD SYNTHETASE FROM REMARK 900 CORYNEBACTERIUM AMMONIAGENES IN COMPLEX WITH FMN AND ADP (P3221) REMARK 999 REMARK 999 SEQUENCE REMARK 999 TRUNCATED SEQUENCE OF CAFADS (FROM 183 TO 338 RESIDUE). DBREF 5A89 A 183 338 UNP Q59263 RIBF_CORAM 183 338 DBREF 5A89 B 183 338 UNP Q59263 RIBF_CORAM 183 338 SEQRES 1 A 156 LEU GLY ARG HIS PHE TYR VAL THR GLY PRO VAL VAL ARG SEQRES 2 A 156 GLY ALA GLY ARG GLY GLY LYS GLU LEU GLY PHE PRO THR SEQRES 3 A 156 ALA ASN GLN TYR PHE HIS ASP THR VAL ALA LEU PRO ALA SEQRES 4 A 156 ASP GLY VAL TYR ALA GLY TRP LEU THR ILE LEU PRO THR SEQRES 5 A 156 GLU ALA PRO VAL SER GLY ASN MET GLU PRO GLU VAL ALA SEQRES 6 A 156 TYR ALA ALA ALA ILE SER VAL GLY THR ASN PRO THR PHE SEQRES 7 A 156 GLY ASP GLU GLN ARG SER VAL GLU SER PHE VAL LEU ASP SEQRES 8 A 156 ARG ASP ALA ASP LEU TYR GLY HIS ASP VAL LYS VAL GLU SEQRES 9 A 156 PHE VAL ASP HIS VAL ARG ALA MET GLU LYS PHE ASP SER SEQRES 10 A 156 VAL GLU GLN LEU LEU GLU VAL MET ALA LYS ASP VAL GLN SEQRES 11 A 156 LYS THR ARG THR LEU LEU ALA GLN ASP VAL GLN ALA HIS SEQRES 12 A 156 LYS MET ALA PRO GLU THR TYR PHE LEU GLN ALA GLU SER SEQRES 1 B 156 LEU GLY ARG HIS PHE TYR VAL THR GLY PRO VAL VAL ARG SEQRES 2 B 156 GLY ALA GLY ARG GLY GLY LYS GLU LEU GLY PHE PRO THR SEQRES 3 B 156 ALA ASN GLN TYR PHE HIS ASP THR VAL ALA LEU PRO ALA SEQRES 4 B 156 ASP GLY VAL TYR ALA GLY TRP LEU THR ILE LEU PRO THR SEQRES 5 B 156 GLU ALA PRO VAL SER GLY ASN MET GLU PRO GLU VAL ALA SEQRES 6 B 156 TYR ALA ALA ALA ILE SER VAL GLY THR ASN PRO THR PHE SEQRES 7 B 156 GLY ASP GLU GLN ARG SER VAL GLU SER PHE VAL LEU ASP SEQRES 8 B 156 ARG ASP ALA ASP LEU TYR GLY HIS ASP VAL LYS VAL GLU SEQRES 9 B 156 PHE VAL ASP HIS VAL ARG ALA MET GLU LYS PHE ASP SER SEQRES 10 B 156 VAL GLU GLN LEU LEU GLU VAL MET ALA LYS ASP VAL GLN SEQRES 11 B 156 LYS THR ARG THR LEU LEU ALA GLN ASP VAL GLN ALA HIS SEQRES 12 B 156 LYS MET ALA PRO GLU THR TYR PHE LEU GLN ALA GLU SER HET FMN A 339 31 HET MG A 341 1 HET ZN A 343 1 HET ADP A 501 27 HET ACY A1337 4 HET FMN B 339 31 HET ADP B 340 27 HET MG B 341 1 HET ZN B 343 1 HET GOL B1339 6 HET GOL B1340 6 HET GOL B1341 6 HETNAM FMN FLAVIN MONONUCLEOTIDE HETNAM MG MAGNESIUM ION HETNAM ZN ZINC ION HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM ACY ACETIC ACID HETNAM GOL GLYCEROL HETSYN FMN RIBOFLAVIN MONOPHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 FMN 2(C17 H21 N4 O9 P) FORMUL 4 MG 2(MG 2+) FORMUL 5 ZN 2(ZN 2+) FORMUL 6 ADP 2(C10 H15 N5 O10 P2) FORMUL 7 ACY C2 H4 O2 FORMUL 12 GOL 3(C3 H8 O3) FORMUL 15 HOH *382(H2 O) HELIX 1 1 ARG A 199 GLY A 205 1 7 HELIX 2 2 SER A 299 HIS A 325 1 27 HELIX 3 3 ALA A 328 GLU A 330 5 3 HELIX 4 4 ARG B 199 GLY B 205 1 7 HELIX 5 5 SER B 299 LYS B 326 1 28 HELIX 6 6 ALA B 328 GLU B 330 5 3 SHEET 1 AA 6 TYR A 188 PRO A 192 0 SHEET 2 AA 6 ASP A 282 ARG A 292 -1 O VAL A 283 N GLY A 191 SHEET 3 AA 6 GLY A 223 ILE A 231 -1 O VAL A 224 N VAL A 291 SHEET 4 AA 6 ALA A 247 GLY A 255 -1 O TYR A 248 N LEU A 229 SHEET 5 AA 6 SER A 266 VAL A 271 -1 O SER A 266 N GLY A 255 SHEET 6 AA 6 ALA A 209 TYR A 212 -1 O ALA A 209 N SER A 269 SHEET 1 AB 5 TYR A 188 PRO A 192 0 SHEET 2 AB 5 ASP A 282 ARG A 292 -1 O VAL A 283 N GLY A 191 SHEET 3 AB 5 GLY A 223 ILE A 231 -1 O VAL A 224 N VAL A 291 SHEET 4 AB 5 ALA A 247 GLY A 255 -1 O TYR A 248 N LEU A 229 SHEET 5 AB 5 TYR A 332 PHE A 333 -1 O PHE A 333 N ALA A 249 SHEET 1 BA 6 PHE B 187 PRO B 192 0 SHEET 2 BA 6 ASP B 282 ALA B 293 -1 O VAL B 283 N GLY B 191 SHEET 3 BA 6 GLY B 223 ILE B 231 -1 O VAL B 224 N VAL B 291 SHEET 4 BA 6 ALA B 247 GLY B 255 -1 O TYR B 248 N LEU B 229 SHEET 5 BA 6 SER B 266 VAL B 271 -1 O SER B 266 N GLY B 255 SHEET 6 BA 6 ALA B 209 GLN B 211 -1 O ALA B 209 N SER B 269 SHEET 1 BB 5 PHE B 187 PRO B 192 0 SHEET 2 BB 5 ASP B 282 ALA B 293 -1 O VAL B 283 N GLY B 191 SHEET 3 BB 5 GLY B 223 ILE B 231 -1 O VAL B 224 N VAL B 291 SHEET 4 BB 5 ALA B 247 GLY B 255 -1 O TYR B 248 N LEU B 229 SHEET 5 BB 5 TYR B 332 PHE B 333 -1 O PHE B 333 N ALA B 249 SHEET 1 BC 2 SER B 239 GLY B 240 0 SHEET 2 BC 2 ALA B 276 ASP B 277 -1 O ASP B 277 N SER B 239 LINK NE2 HIS A 186 ZN ZN A 343 1555 1555 2.11 LINK OG1 THR A 208 MG MG A 341 1555 1555 2.15 LINK O THR A 208 MG MG A 341 1555 1555 2.06 LINK OD1 ASN A 210 MG MG A 341 1555 1555 2.10 LINK OD1 ASP A 321 ZN ZN A 343 1555 1555 1.93 LINK NE2 HIS A 325 ZN ZN A 343 1555 1555 2.15 LINK O1P FMN A 339 MG MG A 341 1555 1555 1.92 LINK MG MG A 341 O1A ADP A 501 1555 1555 2.12 LINK MG MG A 341 O3B ADP A 501 1555 1555 2.01 LINK ZN ZN A 343 O HOH A2004 1555 1555 2.01 LINK NE2 HIS B 186 ZN ZN B 343 1555 1555 2.13 LINK O THR B 208 MG MG B 341 1555 1555 2.12 LINK OG1 THR B 208 MG MG B 341 1555 1555 2.14 LINK OD1 ASN B 210 MG MG B 341 1555 1555 2.07 LINK OD1 ASP B 321 ZN ZN B 343 1555 1555 1.98 LINK NE2 HIS B 325 ZN ZN B 343 1555 1555 2.22 LINK O2P FMN B 339 MG MG B 341 1555 1555 2.01 LINK O1A ADP B 340 MG MG B 341 1555 1555 2.08 LINK O3B ADP B 340 MG MG B 341 1555 1555 2.01 LINK ZN ZN B 343 O HOH B2004 1555 1555 1.87 SITE 1 AC1 4 THR A 208 ASN A 210 FMN A 339 ADP A 501 SITE 1 AC2 4 HIS A 186 ASP A 321 HIS A 325 HOH A2004 SITE 1 AC3 26 VAL A 193 ARG A 195 GLY A 196 ALA A 197 SITE 2 AC3 26 GLY A 198 GLY A 200 GLY A 201 PRO A 207 SITE 3 AC3 26 THR A 208 ALA A 209 ASN A 210 SER A 269 SITE 4 AC3 26 VAL A 271 ARG A 274 ASP A 275 ALA A 276 SITE 5 AC3 26 LEU A 278 TYR A 279 FMN A 339 MG A 341 SITE 6 AC3 26 HOH A2016 HOH A2024 HOH A2030 HOH A2124 SITE 7 AC3 26 HOH A2131 HOH A2182 SITE 1 AC4 24 ALA B 197 GLY B 198 ARG B 199 GLY B 200 SITE 2 AC4 24 THR B 208 ASN B 210 VAL B 224 ALA B 251 SITE 3 AC4 24 SER B 253 ASN B 257 PRO B 258 THR B 259 SITE 4 AC4 24 PHE B 260 GLU B 268 ARG B 292 MET B 294 SITE 5 AC4 24 GLU B 295 PHE B 297 LEU B 303 ASP B 310 SITE 6 AC4 24 ADP B 340 MG B 341 HOH B2019 HOH B2029 SITE 1 AC5 26 VAL B 193 ARG B 195 GLY B 196 ALA B 197 SITE 2 AC5 26 GLY B 198 GLY B 200 GLY B 201 PRO B 207 SITE 3 AC5 26 THR B 208 ALA B 209 ASN B 210 SER B 269 SITE 4 AC5 26 VAL B 271 ARG B 274 ASP B 275 ALA B 276 SITE 5 AC5 26 ASP B 277 LEU B 278 TYR B 279 FMN B 339 SITE 6 AC5 26 MG B 341 HOH B2014 HOH B2017 HOH B2021 SITE 7 AC5 26 HOH B2118 HOH B2199 SITE 1 AC6 4 THR B 208 ASN B 210 FMN B 339 ADP B 340 SITE 1 AC7 4 HIS B 186 ASP B 321 HIS B 325 HOH B2004 SITE 1 AC8 26 GLY A 196 ALA A 197 GLY A 198 ARG A 199 SITE 2 AC8 26 GLY A 200 THR A 208 ASN A 210 VAL A 224 SITE 3 AC8 26 ALA A 251 SER A 253 ASN A 257 PRO A 258 SITE 4 AC8 26 THR A 259 PHE A 260 GLU A 268 ARG A 292 SITE 5 AC8 26 MET A 294 GLU A 295 PHE A 297 LEU A 303 SITE 6 AC8 26 MET A 307 ASP A 310 MG A 341 ADP A 501 SITE 7 AC8 26 HOH A2026 HOH A2034 SITE 1 AC9 4 ARG A 274 HOH A2082 HOH B2062 HOH B2064 SITE 1 BC1 10 HIS A 290 HOH A2056 HIS B 214 ASP B 215 SITE 2 BC1 10 VAL B 217 LEU B 219 GOL B1340 HOH B2035 SITE 3 BC1 10 HOH B2045 HOH B2200 SITE 1 BC2 6 HOH A2050 HOH A2052 ALA B 221 ASP B 222 SITE 2 BC2 6 ARG B 265 GOL B1339 SITE 1 BC3 7 LYS B 309 GLN B 312 TYR B 332 PHE B 333 SITE 2 BC3 7 LEU B 334 HOH B2171 HOH B2183 CRYST1 43.400 70.480 100.080 90.00 90.00 90.00 P 21 21 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 0.023041 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014188 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009992 0.00000