HEADER TRANSFERASE 30-JUN-05 2A59 TITLE STRUCTURE OF 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE FROM TITLE 2 SCHIZOSACCHAROMYCES POMBE MUTANT W27Y WITH BOUND LIGAND 5-NITROSO-6- TITLE 3 RIBITYLAMINO-2,4(1H,3H)-PYRIMIDINEDIONE 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, SCHIZOSACCHAROMYCES POMBE, KEYWDS 2 MUTANT W27Y, LUSY, 5-NITROSO-6-RIBITYLAMINO-2, 4(1H, 3H)- KEYWDS 3 PYRIMIDINEDIONE, 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 14-FEB-24 2A59 1 REMARK REVDAT 5 20-OCT-21 2A59 1 REMARK SEQADV REVDAT 4 24-JUL-19 2A59 1 REMARK REVDAT 3 16-JAN-13 2A59 1 COMPND VERSN REVDAT 2 24-FEB-09 2A59 1 VERSN REVDAT 1 19-JUL-05 2A59 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. 2.70 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 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) (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 28599 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) : 0.191 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1393 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 : 125 REMARK 3 SOLVENT ATOMS : 58 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.03800 REMARK 3 B22 (A**2) : 1.39500 REMARK 3 B33 (A**2) : -4.43200 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) : 1.420 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 : 32.82 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 : NO.PAR REMARK 3 PARAMETER FILE 3 : CNS_TOPPAR:ION.PARAM REMARK 3 PARAMETER FILE 4 : CNS_TOPPAR:WATER_REP.PARAM REMARK 3 PARAMETER FILE 5 : 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 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2A59 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JUL-05. REMARK 100 THE DEPOSITION ID IS D_1000033504. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-OCT-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 : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28707 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.10900 REMARK 200 R SYM (I) : 0.10900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.48200 REMARK 200 R SYM FOR SHELL (I) : 0.02600 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 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 63.89000 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 63.89000 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 55.57500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 72.40500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 55.57500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 72.40500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 63.89000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 55.57500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 72.40500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 63.89000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 55.57500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 72.40500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 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: 15740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -90.0 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 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 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 C 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 A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LMZ A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LMZ B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LMZ C 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LMZ D 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LMZ E 304 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KYY RELATED DB: PDB REMARK 900 STRUCTURE OF 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE FROM REMARK 900 SCHIZOSACCHAROMYCES POMBE WITH BOUND LIGAND 5-NITRO-6-(D- REMARK 900 RIBITYLAMINO)-2,4(1H,3H)-PYRIMIDINEDIONE REMARK 900 RELATED ID: 2A57 RELATED DB: PDB REMARK 900 STRUCTURE OF 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE FROM REMARK 900 SCHIZOSACCHAROMYCES POMBE MUTANT W27Y WITH BOUND LIGAND 6- REMARK 900 CARBOXYETHYL-7-OXO-8-RIBITYLLUMAZINE REMARK 900 RELATED ID: 2A58 RELATED DB: PDB REMARK 900 STRUCTURE OF 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE FROM REMARK 900 SCHIZOSACCHAROMYCES POMBE MUTANT W27Y WITH BOUND LIGAND RIBOFLAVIN REMARK 900 RELATED ID: 1KYV RELATED DB: PDB REMARK 900 STRUCTURE OF 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE FROM REMARK 900 SCHIZOSACCHAROMYCES POMBE WITH BOUND RIBOFLAVIN DBREF 2A59 A 1 159 UNP Q9UUB1 RIB4_SCHPO 1 159 DBREF 2A59 B 1 159 UNP Q9UUB1 RIB4_SCHPO 1 159 DBREF 2A59 C 1 159 UNP Q9UUB1 RIB4_SCHPO 1 159 DBREF 2A59 D 1 159 UNP Q9UUB1 RIB4_SCHPO 1 159 DBREF 2A59 E 1 159 UNP Q9UUB1 RIB4_SCHPO 1 159 SEQADV 2A59 TYR A 27 UNP Q9UUB1 TRP 27 ENGINEERED MUTATION SEQADV 2A59 TYR B 27 UNP Q9UUB1 TRP 27 ENGINEERED MUTATION SEQADV 2A59 TYR C 27 UNP Q9UUB1 TRP 27 ENGINEERED MUTATION SEQADV 2A59 TYR D 27 UNP Q9UUB1 TRP 27 ENGINEERED MUTATION SEQADV 2A59 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 PO4 A 504 5 HET LMZ A 300 20 HET PO4 B 500 5 HET LMZ B 301 20 HET PO4 C 501 5 HET LMZ C 302 20 HET PO4 D 502 5 HET LMZ D 303 20 HET PO4 E 503 5 HET LMZ E 304 20 HETNAM PO4 PHOSPHATE ION HETNAM LMZ 5-NITROSO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE FORMUL 6 PO4 5(O4 P 3-) FORMUL 7 LMZ 5(C9 H14 N4 O7) FORMUL 16 HOH *58(H2 O) 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 TRP A 63 ASN A 76 1 14 HELIX 4 4 MET A 93 GLY A 114 1 22 HELIX 5 5 ASN A 126 ALA A 134 1 9 HELIX 6 6 ASN A 141 LEU A 158 1 18 HELIX 7 7 ASN B 28 ASP B 48 1 21 HELIX 8 8 LYS B 50 GLU B 52 5 3 HELIX 9 9 TRP B 63 ASN B 76 1 14 HELIX 10 10 MET B 93 GLY B 114 1 22 HELIX 11 11 ASN B 126 ALA B 134 1 9 HELIX 12 12 ASN B 141 LEU B 158 1 18 HELIX 13 13 ASN C 28 ASP C 48 1 21 HELIX 14 14 LYS C 50 GLU C 52 5 3 HELIX 15 15 TRP C 63 ASN C 76 1 14 HELIX 16 16 MET C 93 GLY C 114 1 22 HELIX 17 17 ASN C 126 ALA C 134 1 9 HELIX 18 18 ASN C 141 LEU C 158 1 18 HELIX 19 19 ASN D 28 ASP D 48 1 21 HELIX 20 20 LYS D 50 GLU D 52 5 3 HELIX 21 21 GLY D 61 TRP D 63 5 3 HELIX 22 22 GLU D 64 ASN D 76 1 13 HELIX 23 23 MET D 93 GLY D 114 1 22 HELIX 24 24 ASN D 126 ALA D 134 1 9 HELIX 25 25 ASN D 141 LEU D 158 1 18 HELIX 26 26 ASN E 28 ASP E 48 1 21 HELIX 27 27 LYS E 50 GLU E 52 5 3 HELIX 28 28 TRP E 63 ASN E 76 1 14 HELIX 29 29 MET E 93 GLY E 114 1 22 HELIX 30 30 ASN E 126 ALA E 134 1 9 HELIX 31 31 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 22 O GLU A 57 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 ILE A 118 N VAL A 81 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 22 O GLU B 57 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 ILE B 118 N VAL B 81 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 22 O GLU C 57 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 22 O GLU D 57 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 22 O GLU E 57 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 ILE E 118 N VAL E 81 SITE 1 AC1 6 ARG A 133 GLY B 90 SER B 91 THR B 92 SITE 2 AC1 6 HOH B 501 HOH B 510 SITE 1 AC2 6 ARG B 133 GLY C 90 SER C 91 THR C 92 SITE 2 AC2 6 HOH C 502 HOH C 513 SITE 1 AC3 7 ARG C 133 GLY D 90 SER D 91 THR D 92 SITE 2 AC3 7 HOH D 504 HOH D 507 HOH D 510 SITE 1 AC4 6 ARG D 133 GLY E 90 SER E 91 THR E 92 SITE 2 AC4 6 HOH E 508 HOH E 510 SITE 1 AC5 5 GLY A 90 SER A 91 THR A 92 HOH A 505 SITE 2 AC5 5 ARG E 133 SITE 1 AC6 13 TYR A 27 ASN A 28 GLY A 61 SER A 62 SITE 2 AC6 13 TRP A 63 GLU A 64 VAL A 86 LEU A 87 SITE 3 AC6 13 ILE A 88 HIS A 94 HOH A 506 ILE E 118 SITE 4 AC6 13 LEU E 119 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 HOH B 503 SITE 1 AC8 13 ILE B 118 LEU B 119 TYR C 27 ASN C 28 SITE 2 AC8 13 GLY C 61 SER C 62 TRP C 63 GLU C 64 SITE 3 AC8 13 VAL C 86 LEU C 87 ILE C 88 HIS C 94 SITE 4 AC8 13 HOH C 504 SITE 1 AC9 14 ILE C 118 LEU C 119 TYR D 27 ASN D 28 SITE 2 AC9 14 GLY D 61 SER D 62 TRP D 63 GLU D 64 SITE 3 AC9 14 VAL D 86 LEU D 87 ILE D 88 HIS D 94 SITE 4 AC9 14 HOH D 506 HOH D 508 SITE 1 BC1 14 ILE D 118 LEU D 119 TYR E 27 ASN E 28 SITE 2 BC1 14 GLY E 61 SER E 62 TRP E 63 GLU E 64 SITE 3 BC1 14 VAL E 86 LEU E 87 ILE E 88 HIS E 94 SITE 4 BC1 14 HOH E 506 HOH E 509 CRYST1 111.150 144.810 127.780 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 0.008997 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006906 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007826 0.00000