HEADER TRANSFERASE 25-NOV-05 2F59 TITLE LUMAZINE SYNTHASE RIBH1 FROM BRUCELLA ABORTUS (GENE BRUAB1_0785, TITLE 2 SWISS-PROT ENTRY Q57DY1) COMPLEXED WITH INHIBITOR 5-NITRO-6-(D- TITLE 3 RIBITYLAMINO)-2,4(1H,3H) PYRIMIDINEDIONE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE 1; COMPND 3 CHAIN: A, B, C, D, E; COMPND 4 SYNONYM: DMRL SYNTHASE 1, LUMAZINE SYNTHASE 1, RIBOFLAVIN SYNTHASE 1 COMPND 5 BETA 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: RIBH1, RIBH, RIBH-1; 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: PT7-7 KEYWDS ENZYME-SUBSTRATE ANALOGUE, INHIBITOR COMPLEX, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.KLINKE,V.ZYLBERMAN,H.R.BONOMI,I.HAASE,B.G.GUIMARAES,B.C.BRADEN, AUTHOR 2 A.BACHER,M.FISCHER,F.A.GOLDBAUM REVDAT 8 23-AUG-23 2F59 1 REMARK LINK REVDAT 7 16-JAN-13 2F59 1 COMPND REVDAT 6 13-JUL-11 2F59 1 VERSN REVDAT 5 24-FEB-09 2F59 1 VERSN REVDAT 4 09-OCT-07 2F59 1 JRNL REVDAT 3 02-OCT-07 2F59 1 JRNL REVDAT 2 14-AUG-07 2F59 1 JRNL AUTHOR REVDAT 1 28-NOV-06 2F59 0 JRNL AUTH S.KLINKE,V.ZYLBERMAN,H.R.BONOMI,I.HAASE,B.G.GUIMARAES, JRNL AUTH 2 B.C.BRADEN,A.BACHER,M.FISCHER,F.A.GOLDBAUM JRNL TITL STRUCTURAL AND KINETIC PROPERTIES OF LUMAZINE SYNTHASE JRNL TITL 2 ISOENZYMES IN THE ORDER RHIZOBIALES JRNL REF J.MOL.BIOL. V. 373 664 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17854827 JRNL DOI 10.1016/J.JMB.2007.08.021 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 40562 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 SET) : 0.217 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2011 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 : 5463 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 111 REMARK 3 SOLVENT ATOMS : 219 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.07 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) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.210 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 2F59 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-DEC-05. REMARK 100 THE DEPOSITION ID IS D_1000035468. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUN-05 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.60 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) : 1.438 REMARK 200 MONOCHROMATOR : SI SINGLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40642 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 33.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 9.500 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : 0.05600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.4900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.90 REMARK 200 R MERGE FOR SHELL (I) : 0.34000 REMARK 200 R SYM FOR SHELL (I) : 0.34000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200 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 1RVV, STARTING RESIDUE 49 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG 400, 0.1M MES, 0.2M CALCIUM REMARK 280 CHLORIDE, PH 6.60, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 114.49533 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 57.24767 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 57.24767 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 114.49533 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 12760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -103.0 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: 27660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 48310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -271.0 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 142.97550 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 -82.54694 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -171.74300 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 CA CA C 303 LIES ON A SPECIAL POSITION. 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 GLU A 2 REMARK 465 PHE A 3 REMARK 465 LEU A 4 REMARK 465 MET A 5 REMARK 465 SER A 6 REMARK 465 LYS A 7 REMARK 465 HIS A 8 REMARK 465 GLU A 9 REMARK 465 ALA A 10 REMARK 465 ASP A 11 REMARK 465 MET B 1 REMARK 465 GLU B 2 REMARK 465 PHE B 3 REMARK 465 LEU B 4 REMARK 465 MET B 5 REMARK 465 SER B 6 REMARK 465 LYS B 7 REMARK 465 HIS B 8 REMARK 465 GLU B 9 REMARK 465 ALA B 10 REMARK 465 ASP B 11 REMARK 465 MET C 1 REMARK 465 GLU C 2 REMARK 465 PHE C 3 REMARK 465 LEU C 4 REMARK 465 MET C 5 REMARK 465 SER C 6 REMARK 465 LYS C 7 REMARK 465 HIS C 8 REMARK 465 GLU C 9 REMARK 465 ALA C 10 REMARK 465 ASP C 11 REMARK 465 MET D 1 REMARK 465 GLU D 2 REMARK 465 PHE D 3 REMARK 465 LEU D 4 REMARK 465 MET D 5 REMARK 465 SER D 6 REMARK 465 LYS D 7 REMARK 465 HIS D 8 REMARK 465 GLU D 9 REMARK 465 ALA D 10 REMARK 465 MET E 1 REMARK 465 GLU E 2 REMARK 465 PHE E 3 REMARK 465 LEU E 4 REMARK 465 MET E 5 REMARK 465 SER E 6 REMARK 465 LYS E 7 REMARK 465 HIS E 8 REMARK 465 GLU E 9 REMARK 465 ALA E 10 REMARK 465 ASP E 11 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 LYS B 135 CG CD CE NZ REMARK 480 LYS C 135 CD CE NZ REMARK 480 ASP D 11 CG OD1 OD2 REMARK 480 LYS D 135 CE NZ REMARK 480 LYS E 135 CD CE NZ 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 PHE A 22 -60.43 -99.32 REMARK 500 HIS A 90 39.41 -89.26 REMARK 500 PHE A 91 -53.24 -127.78 REMARK 500 ASP A 134 -123.76 -115.59 REMARK 500 ASP B 68 3.24 -69.58 REMARK 500 ASP B 134 -127.65 -99.39 REMARK 500 ASP C 134 -122.13 -107.69 REMARK 500 GLU D 87 -34.47 -130.17 REMARK 500 ASP D 134 -123.12 -114.35 REMARK 500 GLU E 87 -45.66 -134.03 REMARK 500 ASP E 134 -130.69 -104.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 67 O REMARK 620 2 GLU A 73 OE1 89.2 REMARK 620 3 ALA E 67 O 135.4 87.8 REMARK 620 4 GLU E 73 OE1 81.2 169.8 96.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 304 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 124 OE1 REMARK 620 2 GLU A 124 OE2 46.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 302 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA B 67 O REMARK 620 2 GLU B 73 OE1 95.4 REMARK 620 3 ALA D 67 O 149.8 82.4 REMARK 620 4 GLU D 73 OE1 92.8 171.7 89.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA C 303 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA C 67 O REMARK 620 2 ALA C 67 O 144.2 REMARK 620 3 GLU C 73 OE1 93.5 85.6 REMARK 620 4 GLU C 73 OE1 85.2 92.7 175.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA C 305 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU C 124 OE1 REMARK 620 2 GLU C 124 OE2 47.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA D 306 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP D 24 OD1 REMARK 620 2 ASP D 25 OD1 106.4 REMARK 620 3 ASP D 28 OD2 137.5 113.7 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA C 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA C 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA D 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE INI A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE INI B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE INI C 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE INI D 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 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: 1DI0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF LUMAZINE SYNTHASE FROM BRUCELLA ABORTUS REMARK 900 RELATED ID: 1XN1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE SAME PROTEIN AT A DIFFERENT PH REMARK 900 RELATED ID: 1T13 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE SAME PROTEIN BOUND TO 5-NITRO-6-(D- REMARK 900 RIBITYLAMINO)-2,4(1H,3H) PYRIMIDINEDIONE DBREF 2F59 A 1 157 UNP Q57DY1 RISB1_BRUAB 1 157 DBREF 2F59 B 1 157 UNP Q57DY1 RISB1_BRUAB 1 157 DBREF 2F59 C 1 157 UNP Q57DY1 RISB1_BRUAB 1 157 DBREF 2F59 D 1 157 UNP Q57DY1 RISB1_BRUAB 1 157 DBREF 2F59 E 1 157 UNP Q57DY1 RISB1_BRUAB 1 157 SEQRES 1 A 157 MET GLU PHE LEU MET SER LYS HIS GLU ALA ASP ALA PRO SEQRES 2 A 157 HIS LEU LEU ILE VAL GLU ALA ARG PHE TYR ASP ASP LEU SEQRES 3 A 157 ALA ASP ALA LEU LEU ASP GLY ALA LYS ALA ALA LEU ASP SEQRES 4 A 157 GLU ALA GLY ALA THR TYR ASP VAL VAL THR VAL PRO GLY SEQRES 5 A 157 ALA LEU GLU ILE PRO ALA THR ILE SER PHE ALA LEU ASP SEQRES 6 A 157 GLY ALA ASP ASN GLY GLY THR GLU TYR ASP GLY PHE VAL SEQRES 7 A 157 ALA LEU GLY THR VAL ILE ARG GLY GLU THR TYR HIS PHE SEQRES 8 A 157 ASP ILE VAL SER ASN GLU SER CYS ARG ALA LEU THR ASP SEQRES 9 A 157 LEU SER VAL GLU GLU SER ILE ALA ILE GLY ASN GLY ILE SEQRES 10 A 157 LEU THR VAL GLU ASN GLU GLU GLN ALA TRP VAL HIS ALA SEQRES 11 A 157 ARG ARG GLU ASP LYS ASP LYS GLY GLY PHE ALA ALA ARG SEQRES 12 A 157 ALA ALA LEU THR MET ILE GLY LEU ARG LYS LYS PHE GLY SEQRES 13 A 157 ALA SEQRES 1 B 157 MET GLU PHE LEU MET SER LYS HIS GLU ALA ASP ALA PRO SEQRES 2 B 157 HIS LEU LEU ILE VAL GLU ALA ARG PHE TYR ASP ASP LEU SEQRES 3 B 157 ALA ASP ALA LEU LEU ASP GLY ALA LYS ALA ALA LEU ASP SEQRES 4 B 157 GLU ALA GLY ALA THR TYR ASP VAL VAL THR VAL PRO GLY SEQRES 5 B 157 ALA LEU GLU ILE PRO ALA THR ILE SER PHE ALA LEU ASP SEQRES 6 B 157 GLY ALA ASP ASN GLY GLY THR GLU TYR ASP GLY PHE VAL SEQRES 7 B 157 ALA LEU GLY THR VAL ILE ARG GLY GLU THR TYR HIS PHE SEQRES 8 B 157 ASP ILE VAL SER ASN GLU SER CYS ARG ALA LEU THR ASP SEQRES 9 B 157 LEU SER VAL GLU GLU SER ILE ALA ILE GLY ASN GLY ILE SEQRES 10 B 157 LEU THR VAL GLU ASN GLU GLU GLN ALA TRP VAL HIS ALA SEQRES 11 B 157 ARG ARG GLU ASP LYS ASP LYS GLY GLY PHE ALA ALA ARG SEQRES 12 B 157 ALA ALA LEU THR MET ILE GLY LEU ARG LYS LYS PHE GLY SEQRES 13 B 157 ALA SEQRES 1 C 157 MET GLU PHE LEU MET SER LYS HIS GLU ALA ASP ALA PRO SEQRES 2 C 157 HIS LEU LEU ILE VAL GLU ALA ARG PHE TYR ASP ASP LEU SEQRES 3 C 157 ALA ASP ALA LEU LEU ASP GLY ALA LYS ALA ALA LEU ASP SEQRES 4 C 157 GLU ALA GLY ALA THR TYR ASP VAL VAL THR VAL PRO GLY SEQRES 5 C 157 ALA LEU GLU ILE PRO ALA THR ILE SER PHE ALA LEU ASP SEQRES 6 C 157 GLY ALA ASP ASN GLY GLY THR GLU TYR ASP GLY PHE VAL SEQRES 7 C 157 ALA LEU GLY THR VAL ILE ARG GLY GLU THR TYR HIS PHE SEQRES 8 C 157 ASP ILE VAL SER ASN GLU SER CYS ARG ALA LEU THR ASP SEQRES 9 C 157 LEU SER VAL GLU GLU SER ILE ALA ILE GLY ASN GLY ILE SEQRES 10 C 157 LEU THR VAL GLU ASN GLU GLU GLN ALA TRP VAL HIS ALA SEQRES 11 C 157 ARG ARG GLU ASP LYS ASP LYS GLY GLY PHE ALA ALA ARG SEQRES 12 C 157 ALA ALA LEU THR MET ILE GLY LEU ARG LYS LYS PHE GLY SEQRES 13 C 157 ALA SEQRES 1 D 157 MET GLU PHE LEU MET SER LYS HIS GLU ALA ASP ALA PRO SEQRES 2 D 157 HIS LEU LEU ILE VAL GLU ALA ARG PHE TYR ASP ASP LEU SEQRES 3 D 157 ALA ASP ALA LEU LEU ASP GLY ALA LYS ALA ALA LEU ASP SEQRES 4 D 157 GLU ALA GLY ALA THR TYR ASP VAL VAL THR VAL PRO GLY SEQRES 5 D 157 ALA LEU GLU ILE PRO ALA THR ILE SER PHE ALA LEU ASP SEQRES 6 D 157 GLY ALA ASP ASN GLY GLY THR GLU TYR ASP GLY PHE VAL SEQRES 7 D 157 ALA LEU GLY THR VAL ILE ARG GLY GLU THR TYR HIS PHE SEQRES 8 D 157 ASP ILE VAL SER ASN GLU SER CYS ARG ALA LEU THR ASP SEQRES 9 D 157 LEU SER VAL GLU GLU SER ILE ALA ILE GLY ASN GLY ILE SEQRES 10 D 157 LEU THR VAL GLU ASN GLU GLU GLN ALA TRP VAL HIS ALA SEQRES 11 D 157 ARG ARG GLU ASP LYS ASP LYS GLY GLY PHE ALA ALA ARG SEQRES 12 D 157 ALA ALA LEU THR MET ILE GLY LEU ARG LYS LYS PHE GLY SEQRES 13 D 157 ALA SEQRES 1 E 157 MET GLU PHE LEU MET SER LYS HIS GLU ALA ASP ALA PRO SEQRES 2 E 157 HIS LEU LEU ILE VAL GLU ALA ARG PHE TYR ASP ASP LEU SEQRES 3 E 157 ALA ASP ALA LEU LEU ASP GLY ALA LYS ALA ALA LEU ASP SEQRES 4 E 157 GLU ALA GLY ALA THR TYR ASP VAL VAL THR VAL PRO GLY SEQRES 5 E 157 ALA LEU GLU ILE PRO ALA THR ILE SER PHE ALA LEU ASP SEQRES 6 E 157 GLY ALA ASP ASN GLY GLY THR GLU TYR ASP GLY PHE VAL SEQRES 7 E 157 ALA LEU GLY THR VAL ILE ARG GLY GLU THR TYR HIS PHE SEQRES 8 E 157 ASP ILE VAL SER ASN GLU SER CYS ARG ALA LEU THR ASP SEQRES 9 E 157 LEU SER VAL GLU GLU SER ILE ALA ILE GLY ASN GLY ILE SEQRES 10 E 157 LEU THR VAL GLU ASN GLU GLU GLN ALA TRP VAL HIS ALA SEQRES 11 E 157 ARG ARG GLU ASP LYS ASP LYS GLY GLY PHE ALA ALA ARG SEQRES 12 E 157 ALA ALA LEU THR MET ILE GLY LEU ARG LYS LYS PHE GLY SEQRES 13 E 157 ALA HET CA A 301 1 HET CA A 304 1 HET INI A 201 21 HET CA B 302 1 HET INI B 202 21 HET CA C 303 1 HET CA C 305 1 HET INI C 203 21 HET CA D 306 1 HET INI D 204 21 HET INI E 205 21 HETNAM CA CALCIUM ION HETNAM INI 5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE FORMUL 6 CA 6(CA 2+) FORMUL 8 INI 5(C9 H14 N4 O8) FORMUL 17 HOH *219(H2 O) HELIX 1 1 TYR A 23 GLY A 42 1 20 HELIX 2 2 GLY A 52 LEU A 54 5 3 HELIX 3 3 GLU A 55 ASP A 68 1 14 HELIX 4 4 PHE A 91 GLU A 109 1 19 HELIX 5 5 ASN A 122 ARG A 131 1 10 HELIX 6 6 ASP A 136 GLY A 156 1 21 HELIX 7 7 TYR B 23 ALA B 41 1 19 HELIX 8 8 GLY B 52 LEU B 54 5 3 HELIX 9 9 GLU B 55 ASP B 68 1 14 HELIX 10 10 TYR B 89 SER B 110 1 22 HELIX 11 11 ASN B 122 ARG B 131 1 10 HELIX 12 12 ASP B 136 PHE B 155 1 20 HELIX 13 13 TYR C 23 GLY C 42 1 20 HELIX 14 14 GLY C 52 LEU C 54 5 3 HELIX 15 15 GLU C 55 ASN C 69 1 15 HELIX 16 16 TYR C 89 GLU C 109 1 21 HELIX 17 17 ASN C 122 ARG C 131 1 10 HELIX 18 18 ASP C 136 GLY C 156 1 21 HELIX 19 19 TYR D 23 GLY D 42 1 20 HELIX 20 20 GLY D 52 LEU D 54 5 3 HELIX 21 21 GLU D 55 ASN D 69 1 15 HELIX 22 22 TYR D 89 GLU D 109 1 21 HELIX 23 23 ASN D 122 ARG D 131 1 10 HELIX 24 24 ASP D 136 GLY D 156 1 21 HELIX 25 25 TYR E 23 ALA E 41 1 19 HELIX 26 26 GLY E 52 LEU E 54 5 3 HELIX 27 27 GLU E 55 ASP E 68 1 14 HELIX 28 28 TYR E 89 SER E 110 1 22 HELIX 29 29 ASN E 122 ARG E 131 1 10 HELIX 30 30 ASP E 136 PHE E 155 1 20 SHEET 1 A 4 THR A 44 VAL A 50 0 SHEET 2 A 4 HIS A 14 ALA A 20 1 N ILE A 17 O ASP A 46 SHEET 3 A 4 GLY A 76 ILE A 84 1 O LEU A 80 N ALA A 20 SHEET 4 A 4 ILE A 113 VAL A 120 1 O LEU A 118 N GLY A 81 SHEET 1 B 4 THR B 44 VAL B 50 0 SHEET 2 B 4 HIS B 14 ALA B 20 1 N ILE B 17 O ASP B 46 SHEET 3 B 4 GLY B 76 ILE B 84 1 O LEU B 80 N ALA B 20 SHEET 4 B 4 ALA B 112 VAL B 120 1 O LEU B 118 N GLY B 81 SHEET 1 C 4 THR C 44 VAL C 50 0 SHEET 2 C 4 HIS C 14 ALA C 20 1 N LEU C 15 O THR C 44 SHEET 3 C 4 GLY C 76 ILE C 84 1 O LEU C 80 N ALA C 20 SHEET 4 C 4 ILE C 113 VAL C 120 1 O LEU C 118 N VAL C 83 SHEET 1 D 4 THR D 44 VAL D 50 0 SHEET 2 D 4 HIS D 14 ALA D 20 1 N ILE D 17 O ASP D 46 SHEET 3 D 4 GLY D 76 ILE D 84 1 O LEU D 80 N ALA D 20 SHEET 4 D 4 ILE D 113 VAL D 120 1 O LEU D 118 N GLY D 81 SHEET 1 E 4 THR E 44 VAL E 50 0 SHEET 2 E 4 HIS E 14 ALA E 20 1 N ILE E 17 O ASP E 46 SHEET 3 E 4 GLY E 76 ILE E 84 1 O LEU E 80 N ALA E 20 SHEET 4 E 4 ALA E 112 VAL E 120 1 O LEU E 118 N VAL E 83 LINK O ALA A 67 CA CA A 301 1555 1555 2.85 LINK OE1 GLU A 73 CA CA A 301 1555 1555 2.97 LINK OE1 GLU A 124 CA CA A 304 1555 1555 2.77 LINK OE2 GLU A 124 CA CA A 304 1555 1555 2.84 LINK CA CA A 301 O ALA E 67 1555 4644 2.89 LINK CA CA A 301 OE1 GLU E 73 1555 4644 3.00 LINK O ALA B 67 CA CA B 302 1555 1555 2.94 LINK OE1 GLU B 73 CA CA B 302 1555 1555 2.83 LINK CA CA B 302 O ALA D 67 1555 4644 2.87 LINK CA CA B 302 OE1 GLU D 73 1555 4644 2.86 LINK O ALA C 67 CA CA C 303 1555 1555 2.85 LINK O ALA C 67 CA CA C 303 4644 1555 2.86 LINK OE1 GLU C 73 CA CA C 303 1555 1555 2.91 LINK OE1 GLU C 73 CA CA C 303 4644 1555 2.94 LINK OE1 GLU C 124 CA CA C 305 1555 1555 2.74 LINK OE2 GLU C 124 CA CA C 305 1555 1555 2.72 LINK OD1 ASP D 24 CA CA D 306 6763 1555 2.94 LINK OD1 ASP D 25 CA CA D 306 1555 1555 3.09 LINK OD2 ASP D 28 CA CA D 306 1555 1555 2.55 SITE 1 AC1 4 ALA A 67 GLU A 73 ALA E 67 GLU E 73 SITE 1 AC2 1 GLU A 124 SITE 1 AC3 4 ALA B 67 GLU B 73 ALA D 67 GLU D 73 SITE 1 AC4 2 ALA C 67 GLU C 73 SITE 1 AC5 1 GLU C 124 SITE 1 AC6 3 ASP D 24 ASP D 25 ASP D 28 SITE 1 AC7 15 PHE A 22 PRO A 51 GLY A 52 ALA A 53 SITE 2 AC7 15 LEU A 54 GLU A 55 THR A 82 VAL A 83 SITE 3 AC7 15 HIS A 90 PHE A 91 VAL A 94 HOH A 306 SITE 4 AC7 15 ASN E 115 LYS E 137 PHE E 140 SITE 1 AC8 16 ASN A 115 LYS A 137 PHE A 140 HOH A 348 SITE 2 AC8 16 PHE B 22 PRO B 51 GLY B 52 ALA B 53 SITE 3 AC8 16 LEU B 54 GLU B 55 THR B 82 VAL B 83 SITE 4 AC8 16 HIS B 90 PHE B 91 VAL B 94 HOH B 303 SITE 1 AC9 17 ASN B 115 LYS B 137 PHE B 140 ALA B 144 SITE 2 AC9 17 HOH B 331 PHE C 22 PRO C 51 GLY C 52 SITE 3 AC9 17 ALA C 53 LEU C 54 GLU C 55 THR C 82 SITE 4 AC9 17 VAL C 83 HIS C 90 PHE C 91 VAL C 94 SITE 5 AC9 17 HOH C 309 SITE 1 BC1 14 ASN C 115 PHE C 140 PHE D 22 PRO D 51 SITE 2 BC1 14 GLY D 52 ALA D 53 LEU D 54 GLU D 55 SITE 3 BC1 14 THR D 82 VAL D 83 HIS D 90 PHE D 91 SITE 4 BC1 14 VAL D 94 HOH D 310 SITE 1 BC2 17 ASN D 115 LYS D 137 PHE D 140 ALA E 20 SITE 2 BC2 17 PHE E 22 TYR E 23 PRO E 51 GLY E 52 SITE 3 BC2 17 ALA E 53 LEU E 54 GLU E 55 THR E 82 SITE 4 BC2 17 VAL E 83 HIS E 90 PHE E 91 VAL E 94 SITE 5 BC2 17 HOH E 209 CRYST1 95.317 95.317 171.743 90.00 90.00 120.00 P 32 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 0.010491 0.006057 0.000000 0.00000 SCALE2 0.000000 0.012114 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005823 0.00000