HEADER TRANSFERASE 06-FEB-02 1KYX
TITLE LUMAZINE SYNTHASE FROM S.POMBE BOUND TO CARBOXYETHYLLUMAZINE
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 1KYX 1 REMARK
REVDAT 4 23-JAN-13 1KYX 1 COMPND VERSN
REVDAT 3 24-FEB-09 1KYX 1 VERSN
REVDAT 2 04-DEC-02 1KYX 1 REMARK
REVDAT 1 24-JUL-02 1KYX 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. 2.60 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) : 2.60
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.47
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 : 32116
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) : 0.175
REMARK 3 FREE R VALUE : 0.206
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : 3211
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 : 5646
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 160
REMARK 3 SOLVENT ATOMS : 45
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) : 1.437
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 1KYX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-FEB-02.
REMARK 100 THE DEPOSITION ID IS D_1000015484.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : NULL
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 : 32116
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600
REMARK 200 RESOLUTION RANGE LOW (A) : 15.467
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9
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) : 2.60
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.74
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
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 (%): 59.15
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.01
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 64.27700
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 64.27700
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 55.54350
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 72.58900
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 55.54350
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 72.58900
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 64.27700
REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 55.54350
REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 72.58900
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 64.27700
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 55.54350
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 72.58900
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 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: 17540 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 25770 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -135.0 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: 38000 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 48620 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -277.0 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 111.08700
REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 64.27700
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 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 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 ASP A 12 CB CG OD1 OD2
REMARK 480 ARG A 19 CD NE CZ NH1 NH2
REMARK 480 GLN A 30 CD OE1 NE2
REMARK 480 LYS A 37 CD CE NZ
REMARK 480 ARG B 19 NE CZ NH1 NH2
REMARK 480 GLN B 30 CD OE1 NE2
REMARK 480 LYS B 37 CD CE NZ
REMARK 480 GLU B 57 OE1
REMARK 480 ARG B 75 CD NE CZ NH1 NH2
REMARK 480 GLU B 128 CG CD OE1 OE2
REMARK 480 SER C 11 CB OG
REMARK 480 GLN C 30 CD OE1 NE2
REMARK 480 LYS C 46 CD CE NZ
REMARK 480 LYS C 50 CE NZ
REMARK 480 ARG C 75 CD NE CZ NH1 NH2
REMARK 480 LYS D 14 NZ
REMARK 480 ARG D 19 CD NE CZ NH1 NH2
REMARK 480 LEU D 125 CD1
REMARK 480 GLU E 17 CD OE1 OE2
REMARK 480 LYS E 37 CD CE NZ
REMARK 480 LYS E 50 NZ
REMARK 480 ASN E 76 OD1 ND2
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 A 152 NH2 ARG B 26 2.17
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 26 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES
REMARK 500 ARG B 70 NE - CZ - NH2 ANGL. DEV. = -3.3 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 THR B 92 -169.15 -102.88
REMARK 500 ASN E 9 67.76 -159.82
REMARK 500 LEU E 13 136.84 -10.47
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 A 1002
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 C 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 E 1005
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CRM A 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CRM B 502
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CRM C 503
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CRM D 504
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CRM E 505
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: 1KYY RELATED DB: PDB
REMARK 900 1KYY CONTAINS THE SAME PROTEIN COMPLEXED WITH NITROPYRIMIDINEDIONE.
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 1KYX A 1 159 UNP Q9UUB1 RIB4_SCHPO 1 159
DBREF 1KYX B 1 159 UNP Q9UUB1 RIB4_SCHPO 1 159
DBREF 1KYX C 1 159 UNP Q9UUB1 RIB4_SCHPO 1 159
DBREF 1KYX D 1 159 UNP Q9UUB1 RIB4_SCHPO 1 159
DBREF 1KYX 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 PO4 A1002 5
HET CRM A 501 27
HET CRM B 502 27
HET PO4 C1003 5
HET CRM C 503 27
HET PO4 D1004 5
HET CRM D 504 27
HET PO4 E1005 5
HET CRM E 505 27
HETNAM PO4 PHOSPHATE ION
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
HETSYN CRM CARBOXYETHYLLUMAZINE
FORMUL 6 PO4 5(O4 P 3-)
FORMUL 8 CRM 5(C14 H18 N4 O9)
FORMUL 16 HOH *45(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 ASN A 141 LYS A 156 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 ARG B 133 1 8
HELIX 14 14 ASN B 141 ALA B 157 1 17
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 ASN D 141 ALA D 157 1 17
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 SER A 91 THR A 92 CRM A 501 HOH A1009
SITE 2 AC1 6 HOH A1010 ARG E 133
SITE 1 AC2 6 ARG A 133 HOH A1006 HOH A1013 SER B 91
SITE 2 AC2 6 THR B 92 CRM B 502
SITE 1 AC3 7 ARG B 133 GLY C 90 SER C 91 THR C 92
SITE 2 AC3 7 CRM C 503 HOH C1004 HOH C1007
SITE 1 AC4 6 ARG C 133 SER D 91 THR D 92 CRM D 504
SITE 2 AC4 6 HOH D1005 HOH D1006
SITE 1 AC5 5 ARG D 133 SER E 91 THR E 92 CRM E 505
SITE 2 AC5 5 HOH E1006
SITE 1 AC6 17 TRP A 27 ASN A 28 GLY A 61 SER A 62
SITE 2 AC6 17 TRP A 63 GLU A 64 VAL A 86 LEU A 87
SITE 3 AC6 17 ILE A 88 HIS A 94 ILE A 98 PO4 A1001
SITE 4 AC6 17 HOH A1003 HOH A1011 ILE E 118 LEU E 119
SITE 5 AC6 17 TRP E 146
SITE 1 AC7 15 ILE A 118 LEU A 119 PO4 A1002 TRP B 27
SITE 2 AC7 15 GLY B 61 SER B 62 TRP B 63 GLU B 64
SITE 3 AC7 15 VAL B 86 LEU B 87 ILE B 88 HIS B 94
SITE 4 AC7 15 PHE B 95 ILE B 98 HOH B 503
SITE 1 AC8 16 ILE B 118 LEU B 119 TRP B 146 TRP C 27
SITE 2 AC8 16 ASN C 28 GLY C 61 SER C 62 TRP C 63
SITE 3 AC8 16 GLU C 64 VAL C 86 LEU C 87 ILE C 88
SITE 4 AC8 16 HIS C 94 ILE C 98 PO4 C1003 HOH C1006
SITE 1 AC9 17 ILE C 118 LEU C 119 TRP C 146 TRP D 27
SITE 2 AC9 17 ASN D 28 GLY D 61 SER D 62 TRP D 63
SITE 3 AC9 17 GLU D 64 VAL D 86 LEU D 87 ILE D 88
SITE 4 AC9 17 HIS D 94 ILE D 98 PO4 D1004 HOH D1005
SITE 5 AC9 17 HOH D1007
SITE 1 BC1 17 ILE D 118 LEU D 119 TRP D 146 HOH D1011
SITE 2 BC1 17 TRP E 27 ASN E 28 GLY E 61 SER E 62
SITE 3 BC1 17 TRP E 63 GLU E 64 VAL E 86 LEU E 87
SITE 4 BC1 17 ILE E 88 HIS E 94 ILE E 98 PO4 E1005
SITE 5 BC1 17 HOH E1009
CRYST1 111.087 145.178 128.554 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 0.009002 0.000000 0.000000 0.00000
SCALE2 0.000000 0.006888 0.000000 0.00000
SCALE3 0.000000 0.000000 0.007779 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
