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 8 23-AUG-23 1T13 1 REMARK 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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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