HEADER TRANSFERASE 13-JUL-15 5A8A TITLE CRYSTAL STRUCTURE OF THE RIBOFLAVIN KINASE MODULE OF FAD SYNTHETASE TITLE 2 FROM CORYNEBACTERIUM AMMONIAGENES IN COMPLEX WITH FMN AND ADP (P3 2 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 SYNONYM: FLAVOKINASE, FAD PYROPHOSPHORYLASE, FAD SYNTHASE, RFK COMPND 6 DOMAIN; COMPND 7 EC: 2.7.1.26; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: KINASE DOMAIN OF FAD SYNTHETASE (A BIFUNCTIONAL COMPND 10 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 5A8A 1 REMARK LINK REVDAT 2 16-DEC-15 5A8A 1 JRNL REVDAT 1 09-DEC-15 5A8A 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. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 63.81 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 40167 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) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.200 REMARK 3 FREE R VALUE TEST SET COUNT : 3101 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) : 2567 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.52 REMARK 3 BIN R VALUE (WORKING SET) : 0.2300 REMARK 3 BIN FREE R VALUE SET COUNT : 198 REMARK 3 BIN FREE R VALUE : 0.2630 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2378 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 136 REMARK 3 SOLVENT ATOMS : 321 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.91 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) : -0.10000 REMARK 3 B12 (A**2) : 0.02000 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): 0.102 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.101 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.065 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.525 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2621 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3597 ; 1.477 ; 2.009 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 321 ; 6.369 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 124 ;32.892 ;24.677 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 390 ;11.956 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ; 8.891 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 389 ; 0.107 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2017 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 1242 ; 0.842 ; 1.486 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1553 ; 1.467 ; 2.220 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1379 ; 1.062 ; 1.653 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 183 A 338 REMARK 3 ORIGIN FOR THE GROUP (A): 33.2160 -13.6430 -15.2490 REMARK 3 T TENSOR REMARK 3 T11: 0.0187 T22: 0.0102 REMARK 3 T33: 0.0223 T12: -0.0007 REMARK 3 T13: 0.0126 T23: 0.0068 REMARK 3 L TENSOR REMARK 3 L11: 1.0648 L22: 1.9937 REMARK 3 L33: 2.0030 L12: -0.3595 REMARK 3 L13: -0.2578 L23: 0.4955 REMARK 3 S TENSOR REMARK 3 S11: 0.0383 S12: 0.0080 S13: 0.0404 REMARK 3 S21: 0.0251 S22: -0.0214 S23: -0.0241 REMARK 3 S31: 0.0562 S32: -0.1291 S33: -0.0169 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 183 B 338 REMARK 3 ORIGIN FOR THE GROUP (A): 18.8610 14.5710 -11.8700 REMARK 3 T TENSOR REMARK 3 T11: 0.0976 T22: 0.1162 REMARK 3 T33: 0.1060 T12: 0.0390 REMARK 3 T13: 0.0121 T23: 0.0028 REMARK 3 L TENSOR REMARK 3 L11: 0.6161 L22: 1.2830 REMARK 3 L33: 1.2060 L12: -0.1987 REMARK 3 L13: -0.1568 L23: 0.1852 REMARK 3 S TENSOR REMARK 3 S11: 0.0044 S12: -0.0028 S13: -0.0289 REMARK 3 S21: -0.1140 S22: -0.0810 S23: 0.0478 REMARK 3 S31: -0.0014 S32: -0.0884 S33: 0.0767 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 184-337 IN CHAIN A AND REMARK 3 185- -338 IN CHAIN B REMARK 4 REMARK 4 5A8A 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_1290064322. 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 : 43268 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 36.790 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.8000 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 (%) : 89.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.20000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.000 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 (%): 64.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.42 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 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 99.79333 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 49.89667 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 49.89667 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 99.79333 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 LEU B 183 REMARK 465 GLY B 184 REMARK 465 ARG B 185 REMARK 465 SER B 338 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 ZN ZN B 503 O HOH B 2001 1.68 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 A2150 DISTANCE = 6.34 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 ZN A 503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 186 NE2 REMARK 620 2 ASP A 321 OD1 123.9 REMARK 620 3 HIS A 325 NE2 105.9 100.7 REMARK 620 4 HOH A2004 O 98.6 105.8 124.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 208 OG1 REMARK 620 2 THR A 208 O 83.0 REMARK 620 3 ASN A 210 OD1 90.0 79.0 REMARK 620 4 FMN A 401 O1P 82.6 162.2 90.5 REMARK 620 5 ADP A 501 O3B 174.0 92.4 85.3 101.1 REMARK 620 6 ADP A 501 O1A 95.6 92.8 169.5 99.0 88.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 186 NE2 REMARK 620 2 ASP B 321 OD1 112.9 REMARK 620 3 HIS B 325 NE2 109.9 108.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR B 208 O REMARK 620 2 THR B 208 OG1 82.4 REMARK 620 3 FMN B 401 O1P 163.6 83.9 REMARK 620 4 ADP B 501 O3B 90.5 172.4 102.7 REMARK 620 5 ADP B 501 O1A 91.0 95.1 99.1 87.5 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 FMN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1339 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1338 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1340 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5A88 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE RIBOFLAVIN KINASE MODULE OF FAD SYNTHETASE REMARK 900 FROM CORYNEBACTERIUM AMMONIAGENES IN COMPLEX WITH ADP REMARK 900 RELATED ID: 5A89 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(P212121) REMARK 999 REMARK 999 SEQUENCE REMARK 999 TRUNCATED SEQUENCE OF CAFADS (FROM 183 TO 338 RESIDUE). DBREF 5A8A A 183 338 UNP Q59263 RIBF_CORAM 183 338 DBREF 5A8A 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 401 31 HET ADP A 501 27 HET MG A 502 1 HET ZN A 503 1 HET GOL A1339 6 HET SO4 A1340 5 HET FMN B 401 31 HET ADP B 501 27 HET MG B 502 1 HET ZN B 503 1 HET SO4 B1338 5 HETNAM FMN FLAVIN MONONUCLEOTIDE HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM ZN ZINC ION HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETSYN FMN RIBOFLAVIN MONOPHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 FMN 2(C17 H21 N4 O9 P) FORMUL 4 ADP 2(C10 H15 N5 O10 P2) FORMUL 5 MG 2(MG 2+) FORMUL 6 ZN 2(ZN 2+) FORMUL 7 GOL C3 H8 O3 FORMUL 8 SO4 2(O4 S 2-) FORMUL 14 HOH *321(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 ASN B 257 GLY B 261 5 5 HELIX 6 6 SER B 299 LYS B 326 1 28 HELIX 7 7 ALA B 328 GLU B 330 5 3 SHEET 1 AA 6 PHE A 187 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 PHE A 187 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 AC 2 SER A 239 GLY A 240 0 SHEET 2 AC 2 ALA A 276 ASP A 277 -1 O ASP A 277 N SER A 239 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 LINK NE2 HIS A 186 ZN ZN A 503 1555 1555 2.06 LINK OG1 THR A 208 MG MG A 502 1555 1555 2.16 LINK O THR A 208 MG MG A 502 1555 1555 2.10 LINK OD1 ASN A 210 MG MG A 502 1555 1555 2.12 LINK OD1 ASP A 321 ZN ZN A 503 1555 1555 2.00 LINK NE2 HIS A 325 ZN ZN A 503 1555 1555 1.96 LINK O1P FMN A 401 MG MG A 502 1555 1555 2.01 LINK O3B ADP A 501 MG MG A 502 1555 1555 2.09 LINK O1A ADP A 501 MG MG A 502 1555 1555 2.05 LINK ZN ZN A 503 O HOH A2004 1555 1555 1.76 LINK NE2 HIS B 186 ZN ZN B 503 1555 1555 2.05 LINK O THR B 208 MG MG B 502 1555 1555 2.16 LINK OG1 THR B 208 MG MG B 502 1555 1555 2.23 LINK OD1 ASP B 321 ZN ZN B 503 1555 1555 1.98 LINK NE2 HIS B 325 ZN ZN B 503 1555 1555 1.96 LINK O1P FMN B 401 MG MG B 502 1555 1555 1.93 LINK O3B ADP B 501 MG MG B 502 1555 1555 2.04 LINK O1A ADP B 501 MG MG B 502 1555 1555 2.12 SITE 1 AC1 25 GLY A 196 ALA A 197 GLY A 198 ARG A 199 SITE 2 AC1 25 GLY A 200 THR A 208 ASN A 210 VAL A 224 SITE 3 AC1 25 SER A 253 ASN A 257 PRO A 258 THR A 259 SITE 4 AC1 25 PHE A 260 GLU A 268 ARG A 292 MET A 294 SITE 5 AC1 25 GLU A 295 PHE A 297 LEU A 303 MET A 307 SITE 6 AC1 25 ASP A 310 ADP A 501 MG A 502 HOH A2018 SITE 7 AC1 25 HOH A2027 SITE 1 AC2 25 VAL A 193 GLY A 196 ALA A 197 GLY A 198 SITE 2 AC2 25 GLY A 200 GLY A 201 PRO A 207 THR A 208 SITE 3 AC2 25 ALA A 209 ASN A 210 SER A 269 VAL A 271 SITE 4 AC2 25 ARG A 274 ASP A 275 ALA A 276 LEU A 278 SITE 5 AC2 25 TYR A 279 FMN A 401 MG A 502 HOH A2010 SITE 6 AC2 25 HOH A2016 HOH A2021 HOH A2117 HOH A2119 SITE 7 AC2 25 HOH A2180 SITE 1 AC3 4 THR A 208 ASN A 210 FMN A 401 ADP A 501 SITE 1 AC4 4 HIS A 186 ASP A 321 HIS A 325 HOH A2004 SITE 1 AC5 25 GLY B 196 ALA B 197 GLY B 198 ARG B 199 SITE 2 AC5 25 GLY B 200 THR B 208 ASN B 210 VAL B 224 SITE 3 AC5 25 SER B 253 ASN B 257 PRO B 258 THR B 259 SITE 4 AC5 25 PHE B 260 GLU B 268 ARG B 292 MET B 294 SITE 5 AC5 25 GLU B 295 PHE B 297 LEU B 303 MET B 307 SITE 6 AC5 25 ASP B 310 ADP B 501 MG B 502 HOH B2012 SITE 7 AC5 25 HOH B2021 SITE 1 AC6 25 VAL B 193 ARG B 195 GLY B 196 ALA B 197 SITE 2 AC6 25 GLY B 198 GLY B 200 GLY B 201 PRO B 207 SITE 3 AC6 25 THR B 208 ALA B 209 ASN B 210 SER B 269 SITE 4 AC6 25 VAL B 271 ARG B 274 ASP B 275 ALA B 276 SITE 5 AC6 25 LEU B 278 TYR B 279 FMN B 401 MG B 502 SITE 6 AC6 25 HOH B2007 HOH B2010 HOH B2014 HOH B2091 SITE 7 AC6 25 HOH B2144 SITE 1 AC7 4 THR B 208 ASN B 210 FMN B 401 ADP B 501 SITE 1 AC8 4 HIS B 186 ASP B 321 HIS B 325 HOH B2001 SITE 1 AC9 3 ALA A 247 GLU A 286 MET A 327 SITE 1 BC1 1 ARG B 274 SITE 1 BC2 3 ASN A 241 ARG A 274 HOH A2074 CRYST1 73.590 73.590 149.690 90.00 90.00 120.00 P 32 2 1 12 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 0.013589 0.007845 0.000000 0.00000 SCALE2 0.000000 0.015691 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006680 0.00000