HEADER TRANSFERASE 30-JUN-05 2A57 TITLE STRUCTURE OF 6,7-DIMTHYL-8-RIBITYLLUMAZINE SYNTHASE FROM TITLE 2 SCHIZOSACCHAROMYCES POMBE MUTANT W27Y WITH BOUND LIGAND 6- TITLE 3 CARBOXYETHYL-7-OXO-8-RIBITYLLUMAZINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE; COMPND 3 CHAIN: A, B, C, D, E; COMPND 4 SYNONYM: DMRL SYNTHASE, LUMAZINE SYNTHASE, RIBOFLAVIN SYNTHASE BETA COMPND 5 CHAIN; COMPND 6 EC: 2.5.1.78; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SCHIZOSACCHAROMYCES POMBE; SOURCE 3 ORGANISM_COMMON: FISSION YEAST; SOURCE 4 ORGANISM_TAXID: 4896; SOURCE 5 GENE: RIB4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS 6, 7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE, RIBOFLAVIN, RIBOFLAVIN KEYWDS 2 BIOSYNTHESIS, LUSY, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.KOCH,C.BREITHAUPT,S.GERHARDT,I.HAASE,S.WEBER,M.CUSHMAN,R.HUBER, AUTHOR 2 A.BACHER,M.FISCHER REVDAT 6 23-AUG-23 2A57 1 REMARK REVDAT 5 20-OCT-21 2A57 1 REMARK SEQADV REVDAT 4 24-JUL-19 2A57 1 REMARK REVDAT 3 16-JAN-13 2A57 1 COMPND VERSN REVDAT 2 24-FEB-09 2A57 1 VERSN REVDAT 1 19-JUL-05 2A57 0 JRNL AUTH M.KOCH,C.BREITHAUPT,S.GERHARDT,I.HAASE,S.WEBER,M.CUSHMAN, JRNL AUTH 2 R.HUBER,A.BACHER,M.FISCHER JRNL TITL STRUCTURAL BASIS OF CHARGE TRANSFER COMPLEX FORMATION BY JRNL TITL 2 RIBOFLAVIN BOUND TO 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE JRNL REF EUR.J.BIOCHEM. V. 271 3208 2004 JRNL REFN ISSN 0014-2956 JRNL PMID 15265040 JRNL DOI 10.1111/J.1432-1033.2004.04253.X REMARK 2 REMARK 2 RESOLUTION. 2.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 26937 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1313 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5545 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 140 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 61.23 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 7.80700 REMARK 3 B22 (A**2) : 6.85300 REMARK 3 B33 (A**2) : -14.66100 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 58.75 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : CNS_TOPPAR:PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : CRBREDUCED.PARAM REMARK 3 PARAMETER FILE 3 : CNS_TOPPAR:ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2A57 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUL-05. REMARK 100 THE DEPOSITION ID IS D_1000033502. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUL-02 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26937 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.750 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : 0.08000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.51700 REMARK 200 R SYM FOR SHELL (I) : 0.51700 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1KYV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CITRATE, AMMONIUM DIHYDROGEN REMARK 280 PHOSPHATE, PH 5.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 64.15500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 64.15500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 55.56500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 72.44500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 55.56500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 72.44500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 64.15500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 55.56500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 72.44500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 64.15500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 55.56500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 72.44500 REMARK 290 SMTRY3 8 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS THE PENTAMER FOUND IN THE REMARK 300 ASYMMETRIC UNIT 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: PENTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: PENTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 16290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -122.0 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DECAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 35220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 48320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -247.0 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 -1.000000 0.000000 0.000000 111.13000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 64.15500 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 1 REMARK 465 PHE A 2 REMARK 465 SER A 3 REMARK 465 GLY A 4 REMARK 465 ILE A 5 REMARK 465 LYS A 6 REMARK 465 GLY A 7 REMARK 465 PRO A 8 REMARK 465 ASN A 9 REMARK 465 PRO A 10 REMARK 465 SER A 11 REMARK 465 ASP A 12 REMARK 465 TYR A 159 REMARK 465 MET B 1 REMARK 465 PHE B 2 REMARK 465 SER B 3 REMARK 465 GLY B 4 REMARK 465 ILE B 5 REMARK 465 LYS B 6 REMARK 465 GLY B 7 REMARK 465 PRO B 8 REMARK 465 ASN B 9 REMARK 465 PRO B 10 REMARK 465 SER B 11 REMARK 465 ASP B 12 REMARK 465 TYR B 159 REMARK 465 MET C 1 REMARK 465 PHE C 2 REMARK 465 SER C 3 REMARK 465 GLY C 4 REMARK 465 ILE C 5 REMARK 465 LYS C 6 REMARK 465 GLY C 7 REMARK 465 PRO C 8 REMARK 465 ASN C 9 REMARK 465 PRO C 10 REMARK 465 SER C 11 REMARK 465 ASP C 12 REMARK 465 TYR C 159 REMARK 465 MET D 1 REMARK 465 PHE D 2 REMARK 465 SER D 3 REMARK 465 GLY D 4 REMARK 465 ILE D 5 REMARK 465 LYS D 6 REMARK 465 GLY D 7 REMARK 465 PRO D 8 REMARK 465 ASN D 9 REMARK 465 PRO D 10 REMARK 465 SER D 11 REMARK 465 ASP D 12 REMARK 465 TYR D 159 REMARK 465 MET E 1 REMARK 465 PHE E 2 REMARK 465 SER E 3 REMARK 465 GLY E 4 REMARK 465 ILE E 5 REMARK 465 LYS E 6 REMARK 465 GLY E 7 REMARK 465 PRO E 8 REMARK 465 ASN E 9 REMARK 465 PRO E 10 REMARK 465 SER E 11 REMARK 465 ASP E 12 REMARK 465 TYR E 159 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU A 17 CB CG CD OE1 OE2 REMARK 480 ARG A 19 CD NE CZ NH1 NH2 REMARK 480 LYS A 37 CD CE NZ REMARK 480 GLU A 41 CD OE1 OE2 REMARK 480 GLU A 45 CD OE1 OE2 REMARK 480 LYS A 46 CD CE NZ REMARK 480 GLU A 57 CD OE1 OE2 REMARK 480 ARG A 70 NE CZ NH1 NH2 REMARK 480 ARG A 75 NE CZ NH1 NH2 REMARK 480 GLU A 127 CD OE1 OE2 REMARK 480 GLU A 128 CG CD OE1 OE2 REMARK 480 GLU B 17 CB CG CD OE1 OE2 REMARK 480 ARG B 19 CD NE CZ NH1 NH2 REMARK 480 LYS B 37 CD CE NZ REMARK 480 GLU B 41 CD OE1 OE2 REMARK 480 GLU B 45 CD OE1 OE2 REMARK 480 LYS B 46 CD CE NZ REMARK 480 GLU B 57 CD OE1 OE2 REMARK 480 ARG B 70 NE CZ NH1 NH2 REMARK 480 ARG B 75 NE CZ NH1 NH2 REMARK 480 GLU B 127 CD OE1 OE2 REMARK 480 GLU B 128 CG CD OE1 OE2 REMARK 480 GLU C 17 CB CG CD OE1 OE2 REMARK 480 ARG C 19 CD NE CZ NH1 NH2 REMARK 480 LYS C 37 CD CE NZ REMARK 480 GLU C 41 CD OE1 OE2 REMARK 480 GLU C 45 CD OE1 OE2 REMARK 480 LYS C 46 CD CE NZ REMARK 480 GLU C 57 CD OE1 OE2 REMARK 480 ARG C 70 NE CZ NH1 NH2 REMARK 480 ARG C 75 NE CZ NH1 NH2 REMARK 480 GLU C 127 CD OE1 OE2 REMARK 480 GLU C 128 CG CD OE1 OE2 REMARK 480 GLU D 17 CB CG CD OE1 OE2 REMARK 480 ARG D 19 CD NE CZ NH1 NH2 REMARK 480 LYS D 37 CD CE NZ REMARK 480 GLU D 41 CD OE1 OE2 REMARK 480 GLU D 45 CD OE1 OE2 REMARK 480 LYS D 46 CD CE NZ REMARK 480 GLU D 57 CD OE1 OE2 REMARK 480 ARG D 70 NE CZ NH1 NH2 REMARK 480 ARG D 75 NE CZ NH1 NH2 REMARK 480 GLU D 127 CD OE1 OE2 REMARK 480 GLU D 128 CG CD OE1 OE2 REMARK 480 GLU E 17 CB CG CD OE1 OE2 REMARK 480 ARG E 19 CD NE CZ NH1 NH2 REMARK 480 LYS E 37 CD CE NZ REMARK 480 GLU E 41 CD OE1 OE2 REMARK 480 GLU E 45 CD OE1 OE2 REMARK 480 LYS E 46 CD CE NZ REMARK 480 GLU E 57 CD OE1 OE2 REMARK 480 ARG E 70 NE CZ NH1 NH2 REMARK 480 ARG E 75 NE CZ NH1 NH2 REMARK 480 GLU E 127 CD OE1 OE2 REMARK 480 GLU E 128 CG CD OE1 OE2 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 ILE A 44 -74.43 -67.25 REMARK 500 PRO A 60 -73.45 -54.15 REMARK 500 ASN A 76 -164.75 -114.36 REMARK 500 ILE B 44 -76.09 -66.20 REMARK 500 PRO B 60 -74.15 -54.37 REMARK 500 ASN B 76 -166.30 -114.53 REMARK 500 ILE C 44 -76.63 -66.34 REMARK 500 PRO C 60 -73.95 -56.01 REMARK 500 ASN C 76 -165.86 -116.10 REMARK 500 ILE D 44 -76.45 -67.05 REMARK 500 PRO D 60 -73.29 -54.69 REMARK 500 ASN D 76 -164.84 -114.31 REMARK 500 ILE E 44 -77.29 -65.04 REMARK 500 PRO E 60 -74.70 -53.74 REMARK 500 ASN E 76 -164.66 -114.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 CRM A 300 REMARK 610 CRM B 301 REMARK 610 CRM C 302 REMARK 610 CRM D 303 REMARK 610 CRM E 304 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 D 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 E 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 E 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CRM A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CRM B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CRM C 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CRM D 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CRM E 304 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KYV RELATED DB: PDB REMARK 900 STRUCTURE OF 6,7-DIMTHYL-8-RIBITYLLUMAZINE SYNTHASE FROM REMARK 900 SCHIZOSACCHAROMYCES POMBE WITH BOUND RIBOFLAVIN REMARK 900 RELATED ID: 1KYX RELATED DB: PDB REMARK 900 STRUCTURE OF 6,7-DIMTHYL-8-RIBITYLLUMAZINE SYNTHASE FROM REMARK 900 SCHIZOSACCHAROMYCES POMBE WITH BOUND LIGAND 6-CARBOXYETHYL-7-OXO-8- REMARK 900 RIBITYLLUMAZINE DBREF 2A57 A 1 159 UNP Q9UUB1 RIB4_SCHPO 1 159 DBREF 2A57 B 1 159 UNP Q9UUB1 RIB4_SCHPO 1 159 DBREF 2A57 C 1 159 UNP Q9UUB1 RIB4_SCHPO 1 159 DBREF 2A57 D 1 159 UNP Q9UUB1 RIB4_SCHPO 1 159 DBREF 2A57 E 1 159 UNP Q9UUB1 RIB4_SCHPO 1 159 SEQADV 2A57 TYR A 27 UNP Q9UUB1 TRP 27 ENGINEERED MUTATION SEQADV 2A57 TYR B 27 UNP Q9UUB1 TRP 27 ENGINEERED MUTATION SEQADV 2A57 TYR C 27 UNP Q9UUB1 TRP 27 ENGINEERED MUTATION SEQADV 2A57 TYR D 27 UNP Q9UUB1 TRP 27 ENGINEERED MUTATION SEQADV 2A57 TYR E 27 UNP Q9UUB1 TRP 27 ENGINEERED MUTATION SEQRES 1 A 159 MET PHE SER GLY ILE LYS GLY PRO ASN PRO SER ASP LEU SEQRES 2 A 159 LYS GLY PRO GLU LEU ARG ILE LEU ILE VAL HIS ALA ARG SEQRES 3 A 159 TYR ASN LEU GLN ALA ILE GLU PRO LEU VAL LYS GLY ALA SEQRES 4 A 159 VAL GLU THR MET ILE GLU LYS HIS ASP VAL LYS LEU GLU SEQRES 5 A 159 ASN ILE ASP ILE GLU SER VAL PRO GLY SER TRP GLU LEU SEQRES 6 A 159 PRO GLN GLY ILE ARG ALA SER ILE ALA ARG ASN THR TYR SEQRES 7 A 159 ASP ALA VAL ILE GLY ILE GLY VAL LEU ILE LYS GLY SER SEQRES 8 A 159 THR MET HIS PHE GLU TYR ILE SER GLU ALA VAL VAL HIS SEQRES 9 A 159 GLY LEU MET ARG VAL GLY LEU ASP SER GLY VAL PRO VAL SEQRES 10 A 159 ILE LEU GLY LEU LEU THR VAL LEU ASN GLU GLU GLN ALA SEQRES 11 A 159 LEU TYR ARG ALA GLY LEU ASN GLY GLY HIS ASN HIS GLY SEQRES 12 A 159 ASN ASP TRP GLY SER ALA ALA VAL GLU MET GLY LEU LYS SEQRES 13 A 159 ALA LEU TYR SEQRES 1 B 159 MET PHE SER GLY ILE LYS GLY PRO ASN PRO SER ASP LEU SEQRES 2 B 159 LYS GLY PRO GLU LEU ARG ILE LEU ILE VAL HIS ALA ARG SEQRES 3 B 159 TYR ASN LEU GLN ALA ILE GLU PRO LEU VAL LYS GLY ALA SEQRES 4 B 159 VAL GLU THR MET ILE GLU LYS HIS ASP VAL LYS LEU GLU SEQRES 5 B 159 ASN ILE ASP ILE GLU SER VAL PRO GLY SER TRP GLU LEU SEQRES 6 B 159 PRO GLN GLY ILE ARG ALA SER ILE ALA ARG ASN THR TYR SEQRES 7 B 159 ASP ALA VAL ILE GLY ILE GLY VAL LEU ILE LYS GLY SER SEQRES 8 B 159 THR MET HIS PHE GLU TYR ILE SER GLU ALA VAL VAL HIS SEQRES 9 B 159 GLY LEU MET ARG VAL GLY LEU ASP SER GLY VAL PRO VAL SEQRES 10 B 159 ILE LEU GLY LEU LEU THR VAL LEU ASN GLU GLU GLN ALA SEQRES 11 B 159 LEU TYR ARG ALA GLY LEU ASN GLY GLY HIS ASN HIS GLY SEQRES 12 B 159 ASN ASP TRP GLY SER ALA ALA VAL GLU MET GLY LEU LYS SEQRES 13 B 159 ALA LEU TYR SEQRES 1 C 159 MET PHE SER GLY ILE LYS GLY PRO ASN PRO SER ASP LEU SEQRES 2 C 159 LYS GLY PRO GLU LEU ARG ILE LEU ILE VAL HIS ALA ARG SEQRES 3 C 159 TYR ASN LEU GLN ALA ILE GLU PRO LEU VAL LYS GLY ALA SEQRES 4 C 159 VAL GLU THR MET ILE GLU LYS HIS ASP VAL LYS LEU GLU SEQRES 5 C 159 ASN ILE ASP ILE GLU SER VAL PRO GLY SER TRP GLU LEU SEQRES 6 C 159 PRO GLN GLY ILE ARG ALA SER ILE ALA ARG ASN THR TYR SEQRES 7 C 159 ASP ALA VAL ILE GLY ILE GLY VAL LEU ILE LYS GLY SER SEQRES 8 C 159 THR MET HIS PHE GLU TYR ILE SER GLU ALA VAL VAL HIS SEQRES 9 C 159 GLY LEU MET ARG VAL GLY LEU ASP SER GLY VAL PRO VAL SEQRES 10 C 159 ILE LEU GLY LEU LEU THR VAL LEU ASN GLU GLU GLN ALA SEQRES 11 C 159 LEU TYR ARG ALA GLY LEU ASN GLY GLY HIS ASN HIS GLY SEQRES 12 C 159 ASN ASP TRP GLY SER ALA ALA VAL GLU MET GLY LEU LYS SEQRES 13 C 159 ALA LEU TYR SEQRES 1 D 159 MET PHE SER GLY ILE LYS GLY PRO ASN PRO SER ASP LEU SEQRES 2 D 159 LYS GLY PRO GLU LEU ARG ILE LEU ILE VAL HIS ALA ARG SEQRES 3 D 159 TYR ASN LEU GLN ALA ILE GLU PRO LEU VAL LYS GLY ALA SEQRES 4 D 159 VAL GLU THR MET ILE GLU LYS HIS ASP VAL LYS LEU GLU SEQRES 5 D 159 ASN ILE ASP ILE GLU SER VAL PRO GLY SER TRP GLU LEU SEQRES 6 D 159 PRO GLN GLY ILE ARG ALA SER ILE ALA ARG ASN THR TYR SEQRES 7 D 159 ASP ALA VAL ILE GLY ILE GLY VAL LEU ILE LYS GLY SER SEQRES 8 D 159 THR MET HIS PHE GLU TYR ILE SER GLU ALA VAL VAL HIS SEQRES 9 D 159 GLY LEU MET ARG VAL GLY LEU ASP SER GLY VAL PRO VAL SEQRES 10 D 159 ILE LEU GLY LEU LEU THR VAL LEU ASN GLU GLU GLN ALA SEQRES 11 D 159 LEU TYR ARG ALA GLY LEU ASN GLY GLY HIS ASN HIS GLY SEQRES 12 D 159 ASN ASP TRP GLY SER ALA ALA VAL GLU MET GLY LEU LYS SEQRES 13 D 159 ALA LEU TYR SEQRES 1 E 159 MET PHE SER GLY ILE LYS GLY PRO ASN PRO SER ASP LEU SEQRES 2 E 159 LYS GLY PRO GLU LEU ARG ILE LEU ILE VAL HIS ALA ARG SEQRES 3 E 159 TYR ASN LEU GLN ALA ILE GLU PRO LEU VAL LYS GLY ALA SEQRES 4 E 159 VAL GLU THR MET ILE GLU LYS HIS ASP VAL LYS LEU GLU SEQRES 5 E 159 ASN ILE ASP ILE GLU SER VAL PRO GLY SER TRP GLU LEU SEQRES 6 E 159 PRO GLN GLY ILE ARG ALA SER ILE ALA ARG ASN THR TYR SEQRES 7 E 159 ASP ALA VAL ILE GLY ILE GLY VAL LEU ILE LYS GLY SER SEQRES 8 E 159 THR MET HIS PHE GLU TYR ILE SER GLU ALA VAL VAL HIS SEQRES 9 E 159 GLY LEU MET ARG VAL GLY LEU ASP SER GLY VAL PRO VAL SEQRES 10 E 159 ILE LEU GLY LEU LEU THR VAL LEU ASN GLU GLU GLN ALA SEQRES 11 E 159 LEU TYR ARG ALA GLY LEU ASN GLY GLY HIS ASN HIS GLY SEQRES 12 E 159 ASN ASP TRP GLY SER ALA ALA VAL GLU MET GLY LEU LYS SEQRES 13 E 159 ALA LEU TYR HET CRM A 300 23 HET PO4 B 500 5 HET PO4 B 501 5 HET CRM B 301 23 HET CRM C 302 23 HET PO4 D 502 5 HET CRM D 303 23 HET PO4 E 503 5 HET PO4 E 504 5 HET CRM E 304 23 HETNAM CRM 3-[8-((2S,3S,4R)-2,3,4,5-TETRAHYDROXYPENTYL)-2,4,7- HETNAM 2 CRM TRIOXO-1,3,8-TRIHYDROPTERIDIN-6-YL]PROPANOIC ACID HETNAM PO4 PHOSPHATE ION HETSYN CRM CARBOXYETHYLLUMAZINE FORMUL 6 CRM 5(C14 H18 N4 O9) FORMUL 7 PO4 5(O4 P 3-) HELIX 1 1 ASN A 28 ASP A 48 1 21 HELIX 2 2 LYS A 50 GLU A 52 5 3 HELIX 3 3 GLY A 61 TRP A 63 5 3 HELIX 4 4 GLU A 64 ASN A 76 1 13 HELIX 5 5 MET A 93 GLY A 114 1 22 HELIX 6 6 ASN A 126 ALA A 134 1 9 HELIX 7 7 ASN A 141 LEU A 158 1 18 HELIX 8 8 ASN B 28 ASP B 48 1 21 HELIX 9 9 LYS B 50 GLU B 52 5 3 HELIX 10 10 GLY B 61 TRP B 63 5 3 HELIX 11 11 GLU B 64 ASN B 76 1 13 HELIX 12 12 MET B 93 GLY B 114 1 22 HELIX 13 13 ASN B 126 ALA B 134 1 9 HELIX 14 14 ASN B 141 LEU B 158 1 18 HELIX 15 15 ASN C 28 ASP C 48 1 21 HELIX 16 16 LYS C 50 GLU C 52 5 3 HELIX 17 17 GLY C 61 TRP C 63 5 3 HELIX 18 18 GLU C 64 ASN C 76 1 13 HELIX 19 19 MET C 93 GLY C 114 1 22 HELIX 20 20 ASN C 126 ALA C 134 1 9 HELIX 21 21 ASN C 141 LEU C 158 1 18 HELIX 22 22 ASN D 28 ASP D 48 1 21 HELIX 23 23 LYS D 50 GLU D 52 5 3 HELIX 24 24 GLY D 61 TRP D 63 5 3 HELIX 25 25 GLU D 64 ASN D 76 1 13 HELIX 26 26 MET D 93 GLY D 114 1 22 HELIX 27 27 ASN D 126 ALA D 134 1 9 HELIX 28 28 ASN D 141 LEU D 158 1 18 HELIX 29 29 ASN E 28 ASP E 48 1 21 HELIX 30 30 LYS E 50 GLU E 52 5 3 HELIX 31 31 GLY E 61 TRP E 63 5 3 HELIX 32 32 GLU E 64 ASN E 76 1 13 HELIX 33 33 MET E 93 GLY E 114 1 22 HELIX 34 34 ASN E 126 ALA E 134 1 9 HELIX 35 35 ASN E 141 LEU E 158 1 18 SHEET 1 A 4 ILE A 54 VAL A 59 0 SHEET 2 A 4 ILE A 20 ALA A 25 1 N ILE A 20 O ASP A 55 SHEET 3 A 4 ALA A 80 ILE A 88 1 O ILE A 84 N VAL A 23 SHEET 4 A 4 VAL A 117 VAL A 124 1 O LEU A 122 N LEU A 87 SHEET 1 B 4 ILE B 54 VAL B 59 0 SHEET 2 B 4 ILE B 20 ALA B 25 1 N ILE B 20 O ASP B 55 SHEET 3 B 4 ALA B 80 ILE B 88 1 O ILE B 84 N VAL B 23 SHEET 4 B 4 VAL B 117 VAL B 124 1 O LEU B 122 N LEU B 87 SHEET 1 C 4 ILE C 54 VAL C 59 0 SHEET 2 C 4 ILE C 20 ALA C 25 1 N ILE C 20 O ASP C 55 SHEET 3 C 4 ALA C 80 ILE C 88 1 O ILE C 84 N VAL C 23 SHEET 4 C 4 VAL C 117 VAL C 124 1 O LEU C 122 N LEU C 87 SHEET 1 D 4 ILE D 54 VAL D 59 0 SHEET 2 D 4 ILE D 20 ALA D 25 1 N ILE D 20 O ASP D 55 SHEET 3 D 4 ALA D 80 ILE D 88 1 O ILE D 84 N VAL D 23 SHEET 4 D 4 VAL D 117 VAL D 124 1 O LEU D 122 N LEU D 87 SHEET 1 E 4 ILE E 54 VAL E 59 0 SHEET 2 E 4 ILE E 20 ALA E 25 1 N ILE E 20 O ASP E 55 SHEET 3 E 4 ALA E 80 ILE E 88 1 O ILE E 84 N VAL E 23 SHEET 4 E 4 VAL E 117 VAL E 124 1 O LEU E 122 N LEU E 87 SITE 1 AC1 4 ARG A 133 SER B 91 THR B 92 CRM B 301 SITE 1 AC2 4 ARG B 133 SER C 91 THR C 92 CRM C 302 SITE 1 AC3 4 ARG C 133 SER D 91 THR D 92 CRM D 303 SITE 1 AC4 4 ARG D 133 SER E 91 THR E 92 CRM E 304 SITE 1 AC5 4 SER A 91 THR A 92 CRM A 300 ARG E 133 SITE 1 AC6 12 TYR A 27 ASN A 28 GLY A 61 SER A 62 SITE 2 AC6 12 TRP A 63 GLU A 64 VAL A 86 LEU A 87 SITE 3 AC6 12 ILE A 88 ILE E 118 LEU E 119 PO4 E 504 SITE 1 AC7 13 ILE A 118 LEU A 119 TYR B 27 ASN B 28 SITE 2 AC7 13 GLY B 61 SER B 62 TRP B 63 GLU B 64 SITE 3 AC7 13 VAL B 86 LEU B 87 ILE B 88 HIS B 94 SITE 4 AC7 13 PO4 B 500 SITE 1 AC8 13 ILE B 118 LEU B 119 PO4 B 501 TYR C 27 SITE 2 AC8 13 ASN C 28 GLY C 61 SER C 62 TRP C 63 SITE 3 AC8 13 GLU C 64 VAL C 86 LEU C 87 ILE C 88 SITE 4 AC8 13 HIS C 94 SITE 1 AC9 13 ILE C 118 LEU C 119 TYR D 27 ASN D 28 SITE 2 AC9 13 GLY D 61 SER D 62 TRP D 63 GLU D 64 SITE 3 AC9 13 VAL D 86 LEU D 87 ILE D 88 HIS D 94 SITE 4 AC9 13 PO4 D 502 SITE 1 BC1 13 ILE D 118 LEU D 119 TYR E 27 ASN E 28 SITE 2 BC1 13 GLY E 61 SER E 62 TRP E 63 GLU E 64 SITE 3 BC1 13 VAL E 86 LEU E 87 ILE E 88 HIS E 94 SITE 4 BC1 13 PO4 E 503 CRYST1 111.130 144.890 128.310 90.00 90.00 90.00 C 2 2 21 40 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 0.008998 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006902 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007794 0.00000