HEADER TRANSFERASE 06-FEB-02 1KYY TITLE LUMAZINE SYNTHASE FROM S.POMBE BOUND TO NITROPYRIMIDINEDIONE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE; COMPND 3 CHAIN: A, B, C, D, E; COMPND 4 EC: 2.5.1.78; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SCHIZOSACCHAROMYCES POMBE; SOURCE 3 ORGANISM_COMMON: FISSION YEAST; SOURCE 4 ORGANISM_TAXID: 4896; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PNCO113 KEYWDS RIBOFLAVIN BIOSYNTHESIS, LUMAZINE SYNTHASE, SCHIZOSACCHAROMYCES KEYWDS 2 POMBE, LIGAND BINDING, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.GERHARDT,I.HAASE,S.STEINBACHER,J.T.KAISER,M.CUSHMAN,A.BACHER, AUTHOR 2 R.HUBER,M.FISCHER REVDAT 5 13-MAR-24 1KYY 1 REMARK REVDAT 4 23-JAN-13 1KYY 1 COMPND VERSN REVDAT 3 24-FEB-09 1KYY 1 VERSN REVDAT 2 04-DEC-02 1KYY 1 REMARK REVDAT 1 24-JUL-02 1KYY 0 JRNL AUTH S.GERHARDT,I.HAASE,S.STEINBACHER,J.T.KAISER,M.CUSHMAN, JRNL AUTH 2 A.BACHER,R.HUBER,M.FISCHER JRNL TITL THE STRUCTURAL BASIS OF RIBOFLAVIN BINDING TO JRNL TITL 2 SCHIZOSACCHAROMYCES POMBE 6,7-DIMETHYL-8-RIBITYLLUMAZINE JRNL TITL 3 SYNTHASE. JRNL REF J.MOL.BIOL. V. 318 1317 2002 JRNL REFN ISSN 0022-2836 JRNL PMID 12083520 JRNL DOI 10.1016/S0022-2836(02)00116-X REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.58 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) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 39590 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) : 0.183 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 3981 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 : 5659 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 130 REMARK 3 SOLVENT ATOMS : 127 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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) : 1.432 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL 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 : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1KYY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-FEB-02. REMARK 100 THE DEPOSITION ID IS D_1000015485. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-APR-01 REMARK 200 TEMPERATURE (KELVIN) : 295 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 : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39590 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 15.579 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL 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) : 2.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT 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 (%): 58.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CITRATE, AMMONIUM DIHYDROGEN REMARK 280 PHOSPHATE, PH 5.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 295K 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 63.93000 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 63.93000 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 55.63050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 72.52200 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 55.63050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 72.52200 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 63.93000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 55.63050 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 72.52200 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 63.93000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 55.63050 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 72.52200 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 A PENTAMER IN THE 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: 16430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -121.0 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: 35870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 49920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -249.0 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 111.26100 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 63.93000 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 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 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 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 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 TYR E 159 REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 ASP D 12 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 CD OE1 OE2 REMARK 480 ARG A 19 CD NE CZ NH1 NH2 REMARK 480 LYS A 37 CE NZ REMARK 480 LYS A 50 CE NZ REMARK 480 GLU A 57 CD OE1 OE2 REMARK 480 ARG A 75 NE CZ NH1 NH2 REMARK 480 GLU A 127 CD OE1 OE2 REMARK 480 ASP B 12 CB CG OD1 OD2 REMARK 480 GLN B 30 CD OE1 NE2 REMARK 480 LYS B 37 CD CE NZ REMARK 480 LYS B 46 CE NZ REMARK 480 GLU B 52 OE1 OE2 REMARK 480 GLU B 57 OE1 OE2 REMARK 480 GLU B 128 CG CD OE1 OE2 REMARK 480 SER C 11 CB OG REMARK 480 LYS C 14 CD CE NZ REMARK 480 GLN C 30 CD OE1 NE2 REMARK 480 LYS C 50 CD CE NZ REMARK 480 GLU C 128 CG CD OE1 OE2 REMARK 480 LYS D 14 NZ REMARK 480 GLU D 17 CB CG CD OE1 OE2 REMARK 480 ARG D 19 CD NE CZ NH1 NH2 REMARK 480 GLN D 30 CG CD OE1 NE2 REMARK 480 LYS D 37 CD CE NZ REMARK 480 LYS D 46 CD CE NZ REMARK 480 ARG D 75 CZ NH1 NH2 REMARK 480 SER E 11 CB OG REMARK 480 GLU E 17 CD OE1 OE2 REMARK 480 ARG E 19 CG CD NE CZ NH1 NH2 REMARK 480 LYS E 37 CD CE NZ REMARK 480 LYS E 46 CD CE NZ REMARK 480 LYS E 50 NZ REMARK 480 GLU E 52 CG CD OE1 OE2 REMARK 480 ARG E 75 NE CZ NH1 NH2 REMARK 480 GLU E 128 CG CD OE1 OE2 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 OE2 GLU B 128 O HOH B 1021 2.01 REMARK 500 OE2 GLU E 128 O HOH E 1017 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG B 70 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 11 -96.21 -68.07 REMARK 500 THR A 92 -169.13 -113.83 REMARK 500 THR B 92 -165.05 -105.54 REMARK 500 THR C 92 -169.56 -113.76 REMARK 500 ILE D 44 -72.87 -64.91 REMARK 500 THR D 92 -165.33 -106.99 REMARK 500 LEU E 13 145.23 -34.59 REMARK 500 ILE E 44 -70.12 -66.30 REMARK 500 THR E 92 -169.25 -110.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 E 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 D 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 C 1005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE INI A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE INI B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE INI C 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE INI D 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE INI E 205 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KYV RELATED DB: PDB REMARK 900 1KYV CONTAINS THE SAME PROTEIN COMPLEXED WITH RIBOFLAVIN. REMARK 900 RELATED ID: 1KYX RELATED DB: PDB REMARK 900 1KYX CONTAINS THE SAME PROTEIN COMPLEXED WITH CARBOXYETHYLLUMAZINE. REMARK 900 RELATED ID: 1KZ1 RELATED DB: PDB REMARK 900 1KZ1 CONTAINS THE SAME PROTEIN, W27G MUTANT. REMARK 900 RELATED ID: 1KZ4 RELATED DB: PDB REMARK 900 1KZ4 CONTAINS THE SAME PROTEIN, W63Y MUTANT. REMARK 900 RELATED ID: 1KZ6 RELATED DB: PDB REMARK 900 1KZ6 CONTAINS THE SAME PROTEIN, W63Y/L119F MUTANT. REMARK 900 RELATED ID: 1KZ9 RELATED DB: PDB REMARK 900 1KZ9 CONTAINS THE SAME PROTEIN, L119F MUTANT. DBREF 1KYY A 1 159 UNP Q9UUB1 RIB4_SCHPO 1 159 DBREF 1KYY B 1 159 UNP Q9UUB1 RIB4_SCHPO 1 159 DBREF 1KYY C 1 159 UNP Q9UUB1 RIB4_SCHPO 1 159 DBREF 1KYY D 1 159 UNP Q9UUB1 RIB4_SCHPO 1 159 DBREF 1KYY E 1 159 UNP Q9UUB1 RIB4_SCHPO 1 159 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 TRP 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 TRP 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 TRP 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 TRP 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 TRP 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 A1001 5 HET INI A 201 21 HET PO4 B1002 5 HET INI B 202 21 HET PO4 C1005 5 HET INI C 203 21 HET PO4 D1004 5 HET INI D 204 21 HET PO4 E1003 5 HET INI E 205 21 HETNAM PO4 PHOSPHATE ION HETNAM INI 5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE FORMUL 6 PO4 5(O4 P 3-) FORMUL 7 INI 5(C9 H14 N4 O8) FORMUL 16 HOH *127(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 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 HIS A 142 ALA A 157 1 16 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 LYS B 156 1 16 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 TYR C 159 1 19 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 HIS D 142 ALA D 157 1 16 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 ALA E 157 1 17 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 ILE C 118 N VAL C 81 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 ILE D 118 N VAL D 81 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 GLY A 90 SER A 91 THR A 92 HOH A1002 SITE 2 AC1 6 HOH A1010 ARG E 133 SITE 1 AC2 7 ARG A 133 SER B 91 THR B 92 HOH B1004 SITE 2 AC2 7 HOH B1010 HOH B1016 HOH B1026 SITE 1 AC3 8 ARG D 133 GLY E 90 SER E 91 THR E 92 SITE 2 AC3 8 HIS E 94 HOH E1005 HOH E1007 HOH E1016 SITE 1 AC4 6 ARG C 133 SER D 91 THR D 92 HOH D1005 SITE 2 AC4 6 HOH D1008 HOH D1016 SITE 1 AC5 8 ARG B 133 GLY C 90 SER C 91 THR C 92 SITE 2 AC5 8 HOH C1006 HOH C1009 HOH C1016 HOH C1035 SITE 1 AC6 16 TRP A 27 GLY A 61 SER A 62 TRP A 63 SITE 2 AC6 16 GLU A 64 VAL A 86 LEU A 87 ILE A 88 SITE 3 AC6 16 HIS A 94 ILE A 98 HOH A1003 HOH A1005 SITE 4 AC6 16 HOH A1024 HOH A1027 ILE E 118 LEU E 119 SITE 1 AC7 16 ILE A 118 LEU A 119 TRP B 27 GLY B 61 SITE 2 AC7 16 SER B 62 TRP B 63 GLU B 64 VAL B 86 SITE 3 AC7 16 LEU B 87 ILE B 88 HIS B 94 ILE B 98 SITE 4 AC7 16 HOH B1003 HOH B1013 HOH B1025 HOH B1026 SITE 1 AC8 16 ILE B 118 LEU B 119 TRP C 27 GLY C 61 SITE 2 AC8 16 SER C 62 TRP C 63 GLU C 64 VAL C 86 SITE 3 AC8 16 LEU C 87 ILE C 88 HIS C 94 ILE C 98 SITE 4 AC8 16 HOH C1008 HOH C1015 HOH C1039 HOH C1040 SITE 1 AC9 16 ILE C 118 LEU C 119 TRP D 27 GLY D 61 SITE 2 AC9 16 SER D 62 TRP D 63 GLU D 64 VAL D 86 SITE 3 AC9 16 LEU D 87 ILE D 88 HIS D 94 ILE D 98 SITE 4 AC9 16 HOH D1006 HOH D1014 HOH D1015 HOH D1019 SITE 1 BC1 12 ILE D 118 LEU D 119 TRP E 27 GLY E 61 SITE 2 BC1 12 SER E 62 TRP E 63 GLU E 64 VAL E 86 SITE 3 BC1 12 LEU E 87 ILE E 88 HIS E 94 HOH E1004 CRYST1 111.261 145.044 127.860 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 0.008988 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006894 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007821 0.00000