HEADER TRANSFERASE 16-SEP-07 2VBV TITLE RIBOFLAVIN KINASE MJ0056 FROM METHANOCALDOCOCCUS JANNASCHII IN COMPLEX TITLE 2 WITH CDP AND FMN COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOFLAVIN KINASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: UNCHARACTERIZED PROTEIN MJ0056; COMPND 5 EC: 2.7.1.161; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCOCCUS JANNASCHII; SOURCE 3 ORGANISM_TAXID: 2190; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSFERASE, CRADLE-LOOP BARREL, CTP-DEPENDENT KINASE, FMN EXPDTA X-RAY DIFFRACTION AUTHOR M.D.HARTMANN,M.AMMELBURG,S.DJURANOVIC,J.MARTIN,A.N.LUPAS,K.ZETH REVDAT 5 13-DEC-23 2VBV 1 LINK REVDAT 4 24-FEB-09 2VBV 1 VERSN REVDAT 3 03-JUN-08 2VBV 1 COMPND REMARK REVDAT 2 25-DEC-07 2VBV 1 JRNL REVDAT 1 20-NOV-07 2VBV 0 JRNL AUTH M.AMMELBURG,M.D.HARTMANN,S.DJURANOVIC,V.ALVA,K.K.KORETKE, JRNL AUTH 2 J.MARTIN,G.SAUER,V.TRUFFAULT,K.ZETH,A.N.LUPAS,M.COLES JRNL TITL A CTP-DEPENDENT ARCHAEAL RIBOFLAVIN KINASE FORMS A BRIDGE IN JRNL TITL 2 THE EVOLUTION OF CRADLE-LOOP BARRELS. JRNL REF STRUCTURE V. 15 1577 2007 JRNL REFN ISSN 0969-2126 JRNL PMID 18073108 JRNL DOI 10.1016/J.STR.2007.09.027 REMARK 2 REMARK 2 RESOLUTION. 2.40 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 12202 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) : 0.232 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.323 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 644 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 857 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3170 REMARK 3 BIN FREE R VALUE SET COUNT : 46 REMARK 3 BIN FREE R VALUE : 0.4400 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2178 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 85 REMARK 3 SOLVENT ATOMS : 73 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.84000 REMARK 3 B22 (A**2) : 2.41000 REMARK 3 B33 (A**2) : -3.25000 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): 0.501 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.345 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.876 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2305 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1638 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3105 ; 1.700 ; 2.045 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4022 ; 4.036 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 268 ; 8.057 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 92 ;38.186 ;24.783 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 447 ;20.516 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;14.065 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 341 ; 0.088 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2409 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 444 ; 0.007 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 485 ; 0.225 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1656 ; 0.230 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1067 ; 0.196 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1207 ; 0.114 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 115 ; 0.223 ; 0.200 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): 12 ; 0.184 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 29 ; 0.209 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 7 ; 0.102 ; 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): 1337 ; 0.757 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2171 ; 1.406 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 968 ; 1.814 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 934 ; 2.951 ; 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 : BABINET MODEL WITH 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 2VBV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-SEP-07. REMARK 100 THE DEPOSITION ID IS D_1290033826. 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 : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2141 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12903 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 38.580 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.13000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.6700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.62 REMARK 200 R MERGE FOR SHELL (I) : 0.69000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.250 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 2VBT REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% W/V PEG 8000, 200 MM SODIUM IODIDE 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 20.74100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.45350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.64950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.45350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.74100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.64950 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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: PQS 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 ASP A 135 REMARK 465 GLU A 136 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 MET A 1 CG SD CE REMARK 470 LYS A 28 CE NZ REMARK 470 LYS A 33 CD CE NZ REMARK 470 MET B 1 CG SD CE REMARK 470 LYS B 3 CD CE NZ REMARK 470 GLU B 66 CD OE1 OE2 REMARK 470 ASP B 133 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 OG SER A 102 OE2 GLU A 104 2.14 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 49 -30.51 -37.65 REMARK 500 LYS A 88 83.69 -161.16 REMARK 500 SER A 102 173.81 -40.23 REMARK 500 ASN B 68 60.32 35.60 REMARK 500 LYS B 70 -163.07 69.12 REMARK 500 PHE B 73 -151.20 -87.93 REMARK 500 ASP B 133 -143.98 175.02 REMARK 500 LYS B 134 -63.38 -121.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LYS B 70 ARG B 71 -134.44 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 A2004 DISTANCE = 6.42 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 MG A1136 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 43 OG1 REMARK 620 2 THR A 43 O 80.4 REMARK 620 3 ASN A 45 OD1 97.5 86.8 REMARK 620 4 CDP A1135 O2B 159.6 82.0 91.6 REMARK 620 5 CDP A1135 O1A 96.9 80.1 158.6 70.0 REMARK 620 6 FMN A1140 O1P 100.5 177.1 95.9 96.6 97.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1136 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR B 43 OG1 REMARK 620 2 THR B 43 O 91.6 REMARK 620 3 ASN B 45 OD1 87.4 105.1 REMARK 620 4 CDP B1137 O2B 177.0 91.4 91.9 REMARK 620 5 CDP B1137 O1A 92.7 96.6 158.3 86.9 REMARK 620 6 HOH B2010 O 72.4 162.3 67.5 104.6 91.9 REMARK 620 N 1 2 3 4 5 REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 700 THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CDP A1135 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1136 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN A1140 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CDP B1137 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD A1138 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A1139 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B1136 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2P3M RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF MJ0056 REMARK 900 RELATED ID: 2VBS RELATED DB: PDB REMARK 900 RIBOFLAVIN KINASE MJ0056 FROM METHANOCALDOCOCCUS JANNASCHII IN REMARK 900 COMPLEX WITH PO4 REMARK 900 RELATED ID: 2VBT RELATED DB: PDB REMARK 900 RIBOFLAVIN KINASE MJ0056 FROM METHANOCALDOCOCCUS JANNASCHII IN REMARK 900 COMPLEX WITH CDP AND PO4 REMARK 900 RELATED ID: 2VBU RELATED DB: PDB REMARK 900 RIBOFLAVIN KINASE MJ0056 FROM METHANOCALDOCOCCUS JANNASCHII IN REMARK 900 COMPLEX WITH CDP DBREF 2VBV A 1 136 UNP Q60365 Y056_METJA 1 136 DBREF 2VBV B 1 136 UNP Q60365 Y056_METJA 1 136 SEQRES 1 A 136 MET VAL LYS LEU MET ILE ILE GLU GLY GLU VAL VAL SER SEQRES 2 A 136 GLY LEU GLY GLU GLY ARG TYR PHE LEU SER LEU PRO PRO SEQRES 3 A 136 TYR LYS GLU ILE PHE LYS LYS ILE LEU GLY PHE GLU PRO SEQRES 4 A 136 TYR GLU GLY THR LEU ASN LEU LYS LEU ASP ARG GLU PHE SEQRES 5 A 136 ASP ILE ASN LYS PHE LYS TYR ILE GLU THR GLU ASP PHE SEQRES 6 A 136 GLU PHE ASN GLY LYS ARG PHE PHE GLY VAL LYS VAL LEU SEQRES 7 A 136 PRO ILE LYS ILE LEU ILE GLY ASN LYS LYS ILE ASP GLY SEQRES 8 A 136 ALA ILE VAL VAL PRO LYS LYS THR TYR HIS SER SER GLU SEQRES 9 A 136 ILE ILE GLU ILE ILE ALA PRO MET LYS LEU ARG GLU GLN SEQRES 10 A 136 PHE ASN LEU LYS ASP GLY ASP VAL ILE LYS ILE LEU ILE SEQRES 11 A 136 LYS GLY ASP LYS ASP GLU SEQRES 1 B 136 MET VAL LYS LEU MET ILE ILE GLU GLY GLU VAL VAL SER SEQRES 2 B 136 GLY LEU GLY GLU GLY ARG TYR PHE LEU SER LEU PRO PRO SEQRES 3 B 136 TYR LYS GLU ILE PHE LYS LYS ILE LEU GLY PHE GLU PRO SEQRES 4 B 136 TYR GLU GLY THR LEU ASN LEU LYS LEU ASP ARG GLU PHE SEQRES 5 B 136 ASP ILE ASN LYS PHE LYS TYR ILE GLU THR GLU ASP PHE SEQRES 6 B 136 GLU PHE ASN GLY LYS ARG PHE PHE GLY VAL LYS VAL LEU SEQRES 7 B 136 PRO ILE LYS ILE LEU ILE GLY ASN LYS LYS ILE ASP GLY SEQRES 8 B 136 ALA ILE VAL VAL PRO LYS LYS THR TYR HIS SER SER GLU SEQRES 9 B 136 ILE ILE GLU ILE ILE ALA PRO MET LYS LEU ARG GLU GLN SEQRES 10 B 136 PHE ASN LEU LYS ASP GLY ASP VAL ILE LYS ILE LEU ILE SEQRES 11 B 136 LYS GLY ASP LYS ASP GLU HET CDP A1135 25 HET MG A1136 1 HET IOD A1138 1 HET CL A1139 1 HET FMN A1140 31 HET MG B1136 1 HET CDP B1137 25 HETNAM CDP CYTIDINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM IOD IODIDE ION HETNAM CL CHLORIDE ION HETNAM FMN FLAVIN MONONUCLEOTIDE HETSYN FMN RIBOFLAVIN MONOPHOSPHATE FORMUL 3 CDP 2(C9 H15 N3 O11 P2) FORMUL 4 MG 2(MG 2+) FORMUL 5 IOD I 1- FORMUL 6 CL CL 1- FORMUL 7 FMN C17 H21 N4 O9 P FORMUL 10 HOH *73(H2 O) HELIX 1 1 GLU A 17 LEU A 24 1 8 HELIX 2 2 LEU A 24 GLY A 36 1 13 HELIX 3 3 ASP A 53 PHE A 57 5 5 HELIX 4 4 LYS A 113 ASN A 119 1 7 HELIX 5 5 GLY B 16 LEU B 22 1 7 HELIX 6 6 LEU B 24 GLY B 36 1 13 HELIX 7 7 ASP B 53 PHE B 57 5 5 HELIX 8 8 LYS B 113 PHE B 118 1 6 SHEET 1 AA16 LEU A 4 VAL A 12 0 SHEET 2 AA16 VAL A 125 LYS A 131 -1 O ILE A 126 N GLY A 9 SHEET 3 AA16 VAL A 75 LEU A 83 -1 O LYS A 81 N LEU A 129 SHEET 4 AA16 ILE A 60 GLU A 61 -1 O ILE A 60 N VAL A 77 SHEET 5 AA16 LEU A 44 LEU A 48 0 SHEET 6 AA16 LEU A 4 VAL A 12 -1 O GLU A 10 N LYS A 47 SHEET 7 AA16 ILE A 60 GLU A 61 0 SHEET 8 AA16 VAL A 75 LEU A 83 -1 O VAL A 77 N ILE A 60 SHEET 9 AA16 VAL A 75 LEU A 83 0 SHEET 10 AA16 ILE A 60 GLU A 61 -1 O ILE A 60 N VAL A 77 SHEET 11 AA16 ILE A 89 PRO A 96 0 SHEET 12 AA16 VAL A 75 LEU A 83 1 O LYS A 76 N VAL A 95 SHEET 13 AA16 ILE A 105 ILE A 109 0 SHEET 14 AA16 LEU A 44 LEU A 48 -1 O LEU A 44 N ILE A 108 SHEET 15 AA16 VAL A 125 LYS A 131 0 SHEET 16 AA16 LEU A 4 VAL A 12 -1 O MET A 5 N ILE A 130 SHEET 1 AB 2 PHE A 65 PHE A 67 0 SHEET 2 AB 2 LYS A 70 PHE A 72 -1 O LYS A 70 N PHE A 67 SHEET 1 BA14 LEU B 4 VAL B 12 0 SHEET 2 BA14 VAL B 125 LYS B 131 -1 O ILE B 126 N GLY B 9 SHEET 3 BA14 LEU B 44 LYS B 47 0 SHEET 4 BA14 LEU B 4 VAL B 12 -1 O GLU B 10 N LYS B 47 SHEET 5 BA14 ILE B 60 GLU B 61 0 SHEET 6 BA14 LYS B 76 ILE B 84 -1 O VAL B 77 N ILE B 60 SHEET 7 BA14 LYS B 76 ILE B 84 1 N ILE B 84 O ILE B 82 SHEET 8 BA14 ILE B 60 GLU B 61 -1 O ILE B 60 N VAL B 77 SHEET 9 BA14 LYS B 87 VAL B 95 0 SHEET 10 BA14 LYS B 76 ILE B 84 -1 O LYS B 76 N VAL B 95 SHEET 11 BA14 ILE B 105 ILE B 109 0 SHEET 12 BA14 LEU B 44 LYS B 47 -1 O LEU B 44 N ILE B 108 SHEET 13 BA14 VAL B 125 LYS B 131 0 SHEET 14 BA14 LEU B 4 VAL B 12 -1 O MET B 5 N ILE B 130 SHEET 1 BB 2 PHE B 65 GLU B 66 0 SHEET 2 BB 2 ARG B 71 PHE B 72 -1 O PHE B 72 N PHE B 65 LINK OG1 THR A 43 MG MG A1136 1555 1555 2.19 LINK O THR A 43 MG MG A1136 1555 1555 2.01 LINK OD1 ASN A 45 MG MG A1136 1555 1555 2.02 LINK O2B CDP A1135 MG MG A1136 1555 1555 2.13 LINK O1A CDP A1135 MG MG A1136 1555 1555 2.00 LINK MG MG A1136 O1P FMN A1140 1555 1555 2.02 LINK OG1 THR B 43 MG MG B1136 1555 1555 2.24 LINK O THR B 43 MG MG B1136 1555 1555 2.20 LINK OD1 ASN B 45 MG MG B1136 1555 1555 2.01 LINK MG MG B1136 O2B CDP B1137 1555 1555 2.23 LINK MG MG B1136 O1A CDP B1137 1555 1555 2.00 LINK MG MG B1136 O HOH B2010 1555 1555 2.39 SITE 1 AC1 20 SER A 13 GLY A 14 LEU A 15 GLY A 16 SITE 2 AC1 20 GLY A 18 ARG A 19 TYR A 40 GLY A 42 SITE 3 AC1 20 THR A 43 LEU A 44 ASN A 45 MET A 112 SITE 4 AC1 20 LYS A 113 LEU A 114 ARG A 115 MG A1136 SITE 5 AC1 20 FMN A1140 HOH A2047 HOH A2048 HOH A2049 SITE 1 AC2 4 THR A 43 ASN A 45 CDP A1135 FMN A1140 SITE 1 AC3 17 GLY A 16 GLU A 17 GLY A 18 PHE A 21 SITE 2 AC3 17 THR A 43 ASN A 45 PHE A 72 PHE A 73 SITE 3 AC3 17 VAL A 75 PRO A 96 LYS A 98 THR A 99 SITE 4 AC3 17 TYR A 100 GLU A 107 CDP A1135 MG A1136 SITE 5 AC3 17 HOH A2050 SITE 1 AC4 18 GLY B 14 GLY B 16 GLU B 17 GLY B 18 SITE 2 AC4 18 ARG B 19 TYR B 40 GLY B 42 THR B 43 SITE 3 AC4 18 LEU B 44 ASN B 45 MET B 112 LYS B 113 SITE 4 AC4 18 LEU B 114 ARG B 115 MG B1136 HOH B2003 SITE 5 AC4 18 HOH B2004 HOH B2010 SITE 1 AC5 2 ASN A 68 HIS A 101 SITE 1 AC6 3 SER A 13 ASN A 68 GLY A 69 SITE 1 AC7 4 THR B 43 ASN B 45 CDP B1137 HOH B2010 CRYST1 41.482 73.299 104.907 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 0.024107 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013643 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009532 0.00000