HEADER TRANSFERASE 15-APR-04 1T13 TITLE CRYSTAL STRUCTURE OF LUMAZINE SYNTHASE FROM BRUCELLA ABORTUS BOUND TO TITLE 2 5-NITRO-6-(D-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 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BRUCELLA ABORTUS; SOURCE 3 ORGANISM_TAXID: 235; SOURCE 4 GENE: RIBH, BMEII0589, BRA0695; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET11B KEYWDS TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.KLINKE,V.ZYLBERMAN,D.R.VEGA,B.G.GUIMARAES,B.C.BRADEN,F.A.GOLDBAUM REVDAT 7 14-AUG-19 1T13 1 REMARK REVDAT 6 24-JUL-19 1T13 1 REMARK REVDAT 5 16-JAN-13 1T13 1 COMPND REVDAT 4 13-JUL-11 1T13 1 VERSN REVDAT 3 24-FEB-09 1T13 1 VERSN REVDAT 2 27-SEP-05 1T13 1 JRNL REVDAT 1 19-APR-05 1T13 0 JRNL AUTH S.KLINKE,V.ZYLBERMAN,D.R.VEGA,B.G.GUIMARAES,B.C.BRADEN, JRNL AUTH 2 F.A.GOLDBAUM JRNL TITL CRYSTALLOGRAPHIC STUDIES ON DECAMERIC BRUCELLA SPP. LUMAZINE JRNL TITL 2 SYNTHASE: A NOVEL QUATERNARY ARRANGEMENT EVOLVED FOR A NEW JRNL TITL 3 FUNCTION? JRNL REF J.MOL.BIOL. V. 353 124 2005 JRNL REFN ISSN 0022-2836 JRNL PMID 16165152 JRNL DOI 10.1016/J.JMB.2005.08.017 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 52.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 34200 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1706 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 REFLECTION IN BIN (WORKING SET) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE SET COUNT : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5739 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 130 REMARK 3 SOLVENT ATOMS : 89 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 63.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.50 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : NULL REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; NULL ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : NULL REMARK 3 ION PROBE RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE ELECTRONIC DENSITY: REMARK 3 CHAIN A: MET3, ASN4, GLN5, SER6, CYS7, PRO8, ASN9, VAL157. REMARK 3 CHAIN B: MET3, ASN4, GLN5, SER6, CYS7, PRO8, ASN9, LYS10, THR11, REMARK 3 LEU156, VAL157. REMARK 3 CHAIN C: MET3, ASN4, GLN5, SER6, CYS7, PRO8, ASN9, LYS10, THR11, REMARK 3 LEU156, VAL157. REMARK 3 CHAIN D: MET3, ASN4, GLN5, SER6, CYS7, PRO8, ASN9, LYS10, LEU156, REMARK 3 VAL157. REMARK 3 CHAIN E: MET3, ASN4, GLN5, SER6, CYS7, PRO8, ASN9, LYS10, LEU156, REMARK 3 VAL157. REMARK 3 THE FOLLOWING RESIDUES PRESENT POOR OR MISSING SIDE-CHAIN REMARK 3 ELECTRONIC DENSITY AND WERE MODELED AS ALANINE: CHAIN A: ARG152. REMARK 3 CHAIN B: GLU121. CHAIN D: THR11. CHAIN E: THR11. REMARK 4 REMARK 4 1T13 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-APR-04. REMARK 100 THE DEPOSITION ID IS D_1000022180. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUL-03 REMARK 200 TEMPERATURE (KELVIN) : 115 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LNLS REMARK 200 BEAMLINE : D03B-MX1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.431 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : SI SINGLE-CRYSTAL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34456 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 52.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.70 REMARK 200 R MERGE (I) : 0.09300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.60 REMARK 200 R MERGE FOR SHELL (I) : 0.30700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1DI0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 400, 0.1M NA MES PH=6.5, 0.1M REMARK 280 NA ACETATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K, PH REMARK 280 6.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.22300 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 110.44600 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 110.44600 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 55.22300 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 A DIMER OF PENTAMERS WHICH CAN REMARK 300 BE GENERATED APPLYING CRYSTALLOGRAPHIC SYMMETRY OPERATIONS TO THE REMARK 300 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: DECAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DECAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 36340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 45050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -293.0 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 -0.500000 -0.866025 0.000000 189.48150 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 109.39720 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 55.22300 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 3 REMARK 465 ASN A 4 REMARK 465 GLN A 5 REMARK 465 SER A 6 REMARK 465 CYS A 7 REMARK 465 PRO A 8 REMARK 465 ASN A 9 REMARK 465 VAL A 157 REMARK 465 MET B 3 REMARK 465 ASN B 4 REMARK 465 GLN B 5 REMARK 465 SER B 6 REMARK 465 CYS B 7 REMARK 465 PRO B 8 REMARK 465 ASN B 9 REMARK 465 LYS B 10 REMARK 465 THR B 11 REMARK 465 LEU B 156 REMARK 465 VAL B 157 REMARK 465 MET C 3 REMARK 465 ASN C 4 REMARK 465 GLN C 5 REMARK 465 SER C 6 REMARK 465 CYS C 7 REMARK 465 PRO C 8 REMARK 465 ASN C 9 REMARK 465 LYS C 10 REMARK 465 THR C 11 REMARK 465 LEU C 156 REMARK 465 VAL C 157 REMARK 465 MET D 3 REMARK 465 ASN D 4 REMARK 465 GLN D 5 REMARK 465 SER D 6 REMARK 465 CYS D 7 REMARK 465 PRO D 8 REMARK 465 ASN D 9 REMARK 465 LYS D 10 REMARK 465 LEU D 156 REMARK 465 VAL D 157 REMARK 465 MET E 3 REMARK 465 ASN E 4 REMARK 465 GLN E 5 REMARK 465 SER E 6 REMARK 465 CYS E 7 REMARK 465 PRO E 8 REMARK 465 ASN E 9 REMARK 465 LYS E 10 REMARK 465 LEU E 156 REMARK 465 VAL E 157 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 152 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 121B CG CD OE1 OE2 REMARK 470 THR D 11 OG1 CG2 REMARK 470 THR E 11 OG1 CG2 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 PRO A 54 -71.61 -47.82 REMARK 500 ILE A 86 -60.42 -125.72 REMARK 500 GLU A 108 19.19 51.92 REMARK 500 GLU A 121B 69.19 38.51 REMARK 500 ILE B 86 -63.25 -108.29 REMARK 500 PHE C 121 94.93 -170.42 REMARK 500 PRO D 54 -73.44 -42.31 REMARK 500 GLU D 106 -72.25 -79.20 REMARK 500 GLU D 108 27.22 49.19 REMARK 500 PRO E 54 -70.47 -44.25 REMARK 500 ILE E 86 -68.82 -105.59 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 190 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 191 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 C 192 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 D 193 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 E 194 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE INI E 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE INI C 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE INI A 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 B 205 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DI0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF LUMAZINE SYNTHASE FROM BRUCELLA ABORTUS DBREF 1T13 A 3 157 UNP Q44668 RISB_BRUME 1 158 DBREF 1T13 B 3 157 UNP Q44668 RISB_BRUME 1 158 DBREF 1T13 C 3 157 UNP Q44668 RISB_BRUME 1 158 DBREF 1T13 D 3 157 UNP Q44668 RISB_BRUME 1 158 DBREF 1T13 E 3 157 UNP Q44668 RISB_BRUME 1 158 SEQRES 1 A 158 MET ASN GLN SER CYS PRO ASN LYS THR SER PHE LYS ILE SEQRES 2 A 158 ALA PHE ILE GLN ALA ARG TRP HIS ALA ASP ILE VAL ASP SEQRES 3 A 158 GLU ALA ARG LYS SER PHE VAL ALA GLU LEU ALA ALA LYS SEQRES 4 A 158 THR GLY GLY SER VAL GLU VAL GLU ILE PHE ASP VAL PRO SEQRES 5 A 158 GLY ALA TYR GLU ILE PRO LEU HIS ALA LYS THR LEU ALA SEQRES 6 A 158 ARG THR GLY ARG TYR ALA ALA ILE VAL GLY ALA ALA PHE SEQRES 7 A 158 VAL ILE ASP GLY GLY ILE TYR ARG HIS ASP PHE VAL ALA SEQRES 8 A 158 THR ALA VAL ILE ASN GLY MET MET GLN VAL GLN LEU GLU SEQRES 9 A 158 THR GLU VAL PRO VAL LEU SER VAL VAL LEU THR PRO HIS SEQRES 10 A 158 HIS PHE HIS GLU SER LYS GLU HIS HIS ASP PHE PHE HIS SEQRES 11 A 158 ALA HIS PHE LYS VAL LYS GLY VAL GLU ALA ALA HIS ALA SEQRES 12 A 158 ALA LEU GLN ILE VAL SER GLU ARG SER ARG ILE ALA ALA SEQRES 13 A 158 LEU VAL SEQRES 1 B 158 MET ASN GLN SER CYS PRO ASN LYS THR SER PHE LYS ILE SEQRES 2 B 158 ALA PHE ILE GLN ALA ARG TRP HIS ALA ASP ILE VAL ASP SEQRES 3 B 158 GLU ALA ARG LYS SER PHE VAL ALA GLU LEU ALA ALA LYS SEQRES 4 B 158 THR GLY GLY SER VAL GLU VAL GLU ILE PHE ASP VAL PRO SEQRES 5 B 158 GLY ALA TYR GLU ILE PRO LEU HIS ALA LYS THR LEU ALA SEQRES 6 B 158 ARG THR GLY ARG TYR ALA ALA ILE VAL GLY ALA ALA PHE SEQRES 7 B 158 VAL ILE ASP GLY GLY ILE TYR ARG HIS ASP PHE VAL ALA SEQRES 8 B 158 THR ALA VAL ILE ASN GLY MET MET GLN VAL GLN LEU GLU SEQRES 9 B 158 THR GLU VAL PRO VAL LEU SER VAL VAL LEU THR PRO HIS SEQRES 10 B 158 HIS PHE HIS GLU SER LYS GLU HIS HIS ASP PHE PHE HIS SEQRES 11 B 158 ALA HIS PHE LYS VAL LYS GLY VAL GLU ALA ALA HIS ALA SEQRES 12 B 158 ALA LEU GLN ILE VAL SER GLU ARG SER ARG ILE ALA ALA SEQRES 13 B 158 LEU VAL SEQRES 1 C 158 MET ASN GLN SER CYS PRO ASN LYS THR SER PHE LYS ILE SEQRES 2 C 158 ALA PHE ILE GLN ALA ARG TRP HIS ALA ASP ILE VAL ASP SEQRES 3 C 158 GLU ALA ARG LYS SER PHE VAL ALA GLU LEU ALA ALA LYS SEQRES 4 C 158 THR GLY GLY SER VAL GLU VAL GLU ILE PHE ASP VAL PRO SEQRES 5 C 158 GLY ALA TYR GLU ILE PRO LEU HIS ALA LYS THR LEU ALA SEQRES 6 C 158 ARG THR GLY ARG TYR ALA ALA ILE VAL GLY ALA ALA PHE SEQRES 7 C 158 VAL ILE ASP GLY GLY ILE TYR ARG HIS ASP PHE VAL ALA SEQRES 8 C 158 THR ALA VAL ILE ASN GLY MET MET GLN VAL GLN LEU GLU SEQRES 9 C 158 THR GLU VAL PRO VAL LEU SER VAL VAL LEU THR PRO HIS SEQRES 10 C 158 HIS PHE HIS GLU SER LYS GLU HIS HIS ASP PHE PHE HIS SEQRES 11 C 158 ALA HIS PHE LYS VAL LYS GLY VAL GLU ALA ALA HIS ALA SEQRES 12 C 158 ALA LEU GLN ILE VAL SER GLU ARG SER ARG ILE ALA ALA SEQRES 13 C 158 LEU VAL SEQRES 1 D 158 MET ASN GLN SER CYS PRO ASN LYS THR SER PHE LYS ILE SEQRES 2 D 158 ALA PHE ILE GLN ALA ARG TRP HIS ALA ASP ILE VAL ASP SEQRES 3 D 158 GLU ALA ARG LYS SER PHE VAL ALA GLU LEU ALA ALA LYS SEQRES 4 D 158 THR GLY GLY SER VAL GLU VAL GLU ILE PHE ASP VAL PRO SEQRES 5 D 158 GLY ALA TYR GLU ILE PRO LEU HIS ALA LYS THR LEU ALA SEQRES 6 D 158 ARG THR GLY ARG TYR ALA ALA ILE VAL GLY ALA ALA PHE SEQRES 7 D 158 VAL ILE ASP GLY GLY ILE TYR ARG HIS ASP PHE VAL ALA SEQRES 8 D 158 THR ALA VAL ILE ASN GLY MET MET GLN VAL GLN LEU GLU SEQRES 9 D 158 THR GLU VAL PRO VAL LEU SER VAL VAL LEU THR PRO HIS SEQRES 10 D 158 HIS PHE HIS GLU SER LYS GLU HIS HIS ASP PHE PHE HIS SEQRES 11 D 158 ALA HIS PHE LYS VAL LYS GLY VAL GLU ALA ALA HIS ALA SEQRES 12 D 158 ALA LEU GLN ILE VAL SER GLU ARG SER ARG ILE ALA ALA SEQRES 13 D 158 LEU VAL SEQRES 1 E 158 MET ASN GLN SER CYS PRO ASN LYS THR SER PHE LYS ILE SEQRES 2 E 158 ALA PHE ILE GLN ALA ARG TRP HIS ALA ASP ILE VAL ASP SEQRES 3 E 158 GLU ALA ARG LYS SER PHE VAL ALA GLU LEU ALA ALA LYS SEQRES 4 E 158 THR GLY GLY SER VAL GLU VAL GLU ILE PHE ASP VAL PRO SEQRES 5 E 158 GLY ALA TYR GLU ILE PRO LEU HIS ALA LYS THR LEU ALA SEQRES 6 E 158 ARG THR GLY ARG TYR ALA ALA ILE VAL GLY ALA ALA PHE SEQRES 7 E 158 VAL ILE ASP GLY GLY ILE TYR ARG HIS ASP PHE VAL ALA SEQRES 8 E 158 THR ALA VAL ILE ASN GLY MET MET GLN VAL GLN LEU GLU SEQRES 9 E 158 THR GLU VAL PRO VAL LEU SER VAL VAL LEU THR PRO HIS SEQRES 10 E 158 HIS PHE HIS GLU SER LYS GLU HIS HIS ASP PHE PHE HIS SEQRES 11 E 158 ALA HIS PHE LYS VAL LYS GLY VAL GLU ALA ALA HIS ALA SEQRES 12 E 158 ALA LEU GLN ILE VAL SER GLU ARG SER ARG ILE ALA ALA SEQRES 13 E 158 LEU VAL HET PO4 A 190 5 HET INI A 203 21 HET PO4 B 191 5 HET INI B 205 21 HET PO4 C 192 5 HET INI C 202 21 HET PO4 D 193 5 HET INI D 204 21 HET PO4 E 194 5 HET INI E 201 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 *89(H2 O) HELIX 1 1 HIS A 23 THR A 42 1 20 HELIX 2 2 GLY A 55 TYR A 57 5 3 HELIX 3 3 GLU A 58 THR A 69 1 12 HELIX 4 4 HIS A 89 GLU A 108 1 20 HELIX 5 5 SER A 121C ARG A 152 1 32 HELIX 6 6 HIS B 23 THR B 42 1 20 HELIX 7 7 GLY B 55 TYR B 57 5 3 HELIX 8 8 GLU B 58 ARG B 68 1 11 HELIX 9 9 HIS B 89 GLU B 108 1 20 HELIX 10 10 SER B 121C ALA B 155 1 35 HELIX 11 11 HIS C 23 GLY C 43 1 21 HELIX 12 12 GLY C 55 TYR C 57 5 3 HELIX 13 13 GLU C 58 GLY C 70 1 13 HELIX 14 14 HIS C 89 GLU C 108 1 20 HELIX 15 15 SER C 121C ILE C 153 1 33 HELIX 16 16 HIS D 23 GLY D 43 1 21 HELIX 17 17 GLY D 55 TYR D 57 5 3 HELIX 18 18 GLU D 58 THR D 69 1 12 HELIX 19 19 HIS D 89 GLU D 108 1 20 HELIX 20 20 SER D 121C ALA D 154 1 34 HELIX 21 21 HIS E 23 GLY E 43 1 21 HELIX 22 22 GLY E 55 TYR E 57 5 3 HELIX 23 23 GLU E 58 THR E 69 1 12 HELIX 24 24 HIS E 89 GLU E 108 1 20 HELIX 25 25 SER E 121C ALA E 155 1 35 SHEET 1 A 4 VAL A 46 VAL A 53 0 SHEET 2 A 4 PHE A 13 ALA A 20 1 N PHE A 17 O GLU A 49 SHEET 3 A 4 ALA A 74 PHE A 80 1 O ALA A 78 N ALA A 20 SHEET 4 A 4 VAL A 111 LEU A 116 1 O VAL A 114 N GLY A 77 SHEET 1 B 4 GLU B 47 VAL B 53 0 SHEET 2 B 4 LYS B 14 ALA B 20 1 N ILE B 15 O GLU B 49 SHEET 3 B 4 ALA B 74 PHE B 80 1 O ALA B 78 N ALA B 20 SHEET 4 B 4 VAL B 111 LEU B 116 1 O VAL B 114 N GLY B 77 SHEET 1 C 4 GLU C 47 VAL C 53 0 SHEET 2 C 4 LYS C 14 ALA C 20 1 N PHE C 17 O GLU C 49 SHEET 3 C 4 ALA C 74 PHE C 80 1 O VAL C 76 N ALA C 16 SHEET 4 C 4 VAL C 111 LEU C 116 1 O VAL C 114 N GLY C 77 SHEET 1 D 4 VAL D 46 VAL D 53 0 SHEET 2 D 4 PHE D 13 ALA D 20 1 N GLN D 19 O PHE D 51 SHEET 3 D 4 ALA D 74 PHE D 80 1 O VAL D 76 N ILE D 18 SHEET 4 D 4 VAL D 111 LEU D 116 1 O VAL D 114 N GLY D 77 SHEET 1 E 4 GLU E 47 VAL E 53 0 SHEET 2 E 4 LYS E 14 ALA E 20 1 N PHE E 17 O PHE E 51 SHEET 3 E 4 ALA E 74 PHE E 80 1 O VAL E 76 N ALA E 16 SHEET 4 E 4 VAL E 111 LEU E 116 1 O VAL E 114 N GLY E 77 SITE 1 AC1 6 ILE A 82 ASP A 83 GLY A 84 GLY A 85 SITE 2 AC1 6 ILE A 86 TYR A 87 SITE 1 AC2 6 ILE B 82 ASP B 83 GLY B 84 GLY B 85 SITE 2 AC2 6 ILE B 86 TYR B 87 SITE 1 AC3 6 ASP C 83 GLY C 84 GLY C 85 ILE C 86 SITE 2 AC3 6 TYR C 87 INI C 202 SITE 1 AC4 5 ASP D 83 GLY D 84 GLY D 85 ILE D 86 SITE 2 AC4 5 TYR D 87 SITE 1 AC5 7 ILE E 82 ASP E 83 GLY E 84 GLY E 85 SITE 2 AC5 7 ILE E 86 TYR E 87 INI E 201 SITE 1 AC6 13 LEU D 112 SER D 113 ALA E 20 TRP E 22 SITE 2 AC6 13 GLY E 55 ALA E 56 TYR E 57 GLU E 58 SITE 3 AC6 13 PHE E 80 VAL E 81 ILE E 82 PO4 E 194 SITE 4 AC6 13 HOH E2110 SITE 1 AC7 12 LEU B 112 SER B 113 ALA C 20 TRP C 22 SITE 2 AC7 12 GLY C 55 ALA C 56 TYR C 57 GLU C 58 SITE 3 AC7 12 PHE C 80 VAL C 81 ILE C 82 PO4 C 192 SITE 1 AC8 12 ALA A 20 TRP A 22 GLY A 55 ALA A 56 SITE 2 AC8 12 TYR A 57 GLU A 58 PHE A 80 VAL A 81 SITE 3 AC8 12 ILE A 82 HOH A2023 LEU E 112 SER E 113 SITE 1 AC9 11 LEU C 112 SER C 113 ALA D 20 TRP D 22 SITE 2 AC9 11 GLY D 55 ALA D 56 TYR D 57 GLU D 58 SITE 3 AC9 11 PHE D 80 VAL D 81 ILE D 82 SITE 1 BC1 12 LEU A 112 SER A 113 ALA B 20 TRP B 22 SITE 2 BC1 12 GLY B 55 ALA B 56 TYR B 57 GLU B 58 SITE 3 BC1 12 PHE B 80 VAL B 81 ILE B 82 HOH B2052 CRYST1 126.321 126.321 165.669 90.00 90.00 120.00 P 31 2 1 30 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 0.007916 0.004571 0.000000 0.00000 SCALE2 0.000000 0.009141 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006036 0.00000 MASTER 406 0 10 25 20 0 26 6 0 0 0 65 END