HEADER LUMINESCENT PROTEIN 09-JUN-09 3A35 TITLE CRYSTAL STRUCTURE OF LUMP COMPLEXED WITH RIBOFLAVIN CAVEAT 3A35 CHIRALITY ERRORS AT CB CENTER OF THR B 112 AND ILE B 154 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LUMAZINE PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: LUMP; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHOTOBACTERIUM KISHITANII; SOURCE 3 ORGANISM_TAXID: 318456; SOURCE 4 GENE: LUMINOUS BACTERIA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET23A KEYWDS LUMINOUS BACTERIA, LUMAZINE PROTEIN, HOMOLOGUE OF RIBOFLAVIN KEYWDS 2 SYNTHASE, LUMINESCENT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.SATO REVDAT 4 01-NOV-23 3A35 1 REMARK REVDAT 3 13-JUL-11 3A35 1 VERSN REVDAT 2 22-DEC-09 3A35 1 HETNAM JRNL REVDAT 1 10-NOV-09 3A35 0 JRNL AUTH Y.SATO,S.SHIMIZU,A.OHTAKI,K.NOGUCHI,H.MIYATAKE,N.DOHMAE, JRNL AUTH 2 S.SASAKI,M.ODAKA,M.YOHDA JRNL TITL CRYSTAL STRUCTURES OF THE LUMAZINE PROTEIN FROM JRNL TITL 2 PHOTOBACTERIUM KISHITANII IN COMPLEXES WITH THE AUTHENTIC JRNL TITL 3 CHROMOPHORE, 6,7-DIMETHYL-8-(1'-D-RIBITYL) LUMAZINE AND ITS JRNL TITL 4 ANALOGUES, RIBOFLAVIN AND FMN, AT HIGH RESOLUTION JRNL REF J.BACTERIOL. V. 192 127 2009 JRNL REFN ISSN 0021-9193 JRNL PMID 19854891 JRNL DOI 10.1128/JB.01015-09 REMARK 2 REMARK 2 RESOLUTION. 1.42 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.42 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.15 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 58164 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) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 6533 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.42 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4176 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.10 REMARK 3 BIN R VALUE (WORKING SET) : 0.2280 REMARK 3 BIN FREE R VALUE SET COUNT : 440 REMARK 3 BIN FREE R VALUE : 0.2960 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2832 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 54 REMARK 3 SOLVENT ATOMS : 405 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.28 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.078 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.083 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.047 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.145 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.933 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2958 ; 0.033 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4008 ; 2.896 ; 1.994 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 373 ; 9.927 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 126 ;38.332 ;26.349 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 552 ;16.539 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;21.234 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 482 ; 0.353 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2159 ; 0.015 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1400 ; 0.242 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2048 ; 0.327 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 327 ; 0.160 ; 0.200 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): 86 ; 0.308 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 41 ; 0.204 ; 0.200 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): 1900 ; 1.991 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3001 ; 2.967 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1193 ; 4.015 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1007 ; 5.998 ; 4.500 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 : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3A35 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1000028752. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-AUG-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 58164 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.421 REMARK 200 RESOLUTION RANGE LOW (A) : 25.559 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 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: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 3DDY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% (W/V) PEG 4000, 0.2M MGCL2, 100MM REMARK 280 HEPES PH6.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 23.14400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 80.52650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.29100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 80.52650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.14400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.29100 REMARK 290 SMTRY3 4 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 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 VAL A 185 REMARK 465 SER A 186 REMARK 465 ASN A 187 REMARK 465 GLU A 188 REMARK 465 TRP A 189 REMARK 465 ASP A 190 REMARK 465 VAL B 185 REMARK 465 SER B 186 REMARK 465 ASN B 187 REMARK 465 GLU B 188 REMARK 465 TRP B 189 REMARK 465 ASP B 190 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 OD1 ASN A 162 O HOH A 657 1.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 608 O HOH B 293 4455 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 34 CG GLU A 34 CD 0.095 REMARK 500 GLU A 37 CB GLU A 37 CG -0.146 REMARK 500 GLU A 181 CG GLU A 181 CD -0.110 REMARK 500 SER B 164 CB SER B 164 OG 0.131 REMARK 500 VAL B 180 CB VAL B 180 CG2 -0.179 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 LYS A 38 CD - CE - NZ ANGL. DEV. = -15.7 DEGREES REMARK 500 ARG A 53 NE - CZ - NH2 ANGL. DEV. = -5.0 DEGREES REMARK 500 TYR A 60 CE1 - CZ - CE2 ANGL. DEV. = 10.2 DEGREES REMARK 500 ASP A 64 CB - CG - OD1 ANGL. DEV. = 8.3 DEGREES REMARK 500 LEU A 92 N - CA - C ANGL. DEV. = -18.3 DEGREES REMARK 500 LEU A 93 N - CA - C ANGL. DEV. = 19.6 DEGREES REMARK 500 GLY A 94 N - CA - C ANGL. DEV. = -16.5 DEGREES REMARK 500 ILE A 129 N - CA - C ANGL. DEV. = -16.6 DEGREES REMARK 500 ILE A 154 CG1 - CB - CG2 ANGL. DEV. = 15.6 DEGREES REMARK 500 LEU A 172 CB - CG - CD1 ANGL. DEV. = -10.4 DEGREES REMARK 500 PHE B 28 CB - CG - CD2 ANGL. DEV. = -4.2 DEGREES REMARK 500 LYS B 38 CD - CE - NZ ANGL. DEV. = -15.8 DEGREES REMARK 500 GLU B 88 N - CA - C ANGL. DEV. = 17.5 DEGREES REMARK 500 ASP B 116 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 ARG B 117 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG B 117 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 ILE B 150 CG1 - CB - CG2 ANGL. DEV. = 13.5 DEGREES REMARK 500 LEU B 183 CB - CG - CD2 ANGL. DEV. = 10.9 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 ASP A 19 -79.53 66.62 REMARK 500 ASP A 64 -73.10 -139.25 REMARK 500 LYS A 95 70.04 -168.66 REMARK 500 ASP A 127 30.69 -94.31 REMARK 500 ILE A 129 -59.24 171.85 REMARK 500 ASN A 131 -121.49 80.33 REMARK 500 ASP A 152 -119.87 54.49 REMARK 500 LEU A 183 58.74 -142.72 REMARK 500 ASN B 18 93.83 164.58 REMARK 500 ASP B 19 -80.05 -125.99 REMARK 500 ASP B 20 37.88 -88.57 REMARK 500 ASP B 64 -67.49 -140.29 REMARK 500 PHE B 89 -142.73 -121.31 REMARK 500 GLU B 135 -9.12 69.74 REMARK 500 ASP B 152 -122.69 62.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LEU A 92 LEU A 93 108.07 REMARK 500 GLU B 88 PHE B 89 51.10 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 RBF A 191 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RBF B 191 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3A3B RELATED DB: PDB REMARK 900 LUMP COMPLEXED WITH FLAVIN MONONUCLEOTIDE REMARK 900 RELATED ID: 3A3G RELATED DB: PDB REMARK 900 LUMP COMPLEXED WITH 6,7-DIMETHYL-8-(1'-D-RIBITYL) LUMAZINE REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE EXTERNAL REGION OF LUMP GENE FROM P. KISHITANII IS NOT CLEAR, REMARK 999 THEREFORE, DEPOSITORS DESIGNED THESE PRIMER REGION TO AMPLIFY THE REMARK 999 GENE BASED ON INTERNAL REGION OF LUMP GENE FROM P. PHOSPHOREUM. REMARK 999 THIS SEQUENCE WAS COMPLETELY MATCH LUMP GENE FROM P. PHOSPHOREUM. DBREF 3A35 A 8 184 UNP C4TPG1 C4TPG1_9GAMM 1 177 DBREF 3A35 B 8 184 UNP C4TPG1 C4TPG1_9GAMM 1 177 SEQADV 3A35 MET A 1 UNP C4TPG1 SEE REMARK 999 SEQADV 3A35 PHE A 2 UNP C4TPG1 SEE REMARK 999 SEQADV 3A35 LYS A 3 UNP C4TPG1 SEE REMARK 999 SEQADV 3A35 GLY A 4 UNP C4TPG1 SEE REMARK 999 SEQADV 3A35 ILE A 5 UNP C4TPG1 SEE REMARK 999 SEQADV 3A35 VAL A 6 UNP C4TPG1 SEE REMARK 999 SEQADV 3A35 GLN A 7 UNP C4TPG1 SEE REMARK 999 SEQADV 3A35 VAL A 185 UNP C4TPG1 SEE REMARK 999 SEQADV 3A35 SER A 186 UNP C4TPG1 SEE REMARK 999 SEQADV 3A35 ASN A 187 UNP C4TPG1 SEE REMARK 999 SEQADV 3A35 GLU A 188 UNP C4TPG1 SEE REMARK 999 SEQADV 3A35 TRP A 189 UNP C4TPG1 SEE REMARK 999 SEQADV 3A35 ASP A 190 UNP C4TPG1 SEE REMARK 999 SEQADV 3A35 MET B 1 UNP C4TPG1 SEE REMARK 999 SEQADV 3A35 PHE B 2 UNP C4TPG1 SEE REMARK 999 SEQADV 3A35 LYS B 3 UNP C4TPG1 SEE REMARK 999 SEQADV 3A35 GLY B 4 UNP C4TPG1 SEE REMARK 999 SEQADV 3A35 ILE B 5 UNP C4TPG1 SEE REMARK 999 SEQADV 3A35 VAL B 6 UNP C4TPG1 SEE REMARK 999 SEQADV 3A35 GLN B 7 UNP C4TPG1 SEE REMARK 999 SEQADV 3A35 VAL B 185 UNP C4TPG1 SEE REMARK 999 SEQADV 3A35 SER B 186 UNP C4TPG1 SEE REMARK 999 SEQADV 3A35 ASN B 187 UNP C4TPG1 SEE REMARK 999 SEQADV 3A35 GLU B 188 UNP C4TPG1 SEE REMARK 999 SEQADV 3A35 TRP B 189 UNP C4TPG1 SEE REMARK 999 SEQADV 3A35 ASP B 190 UNP C4TPG1 SEE REMARK 999 SEQRES 1 A 190 MET PHE LYS GLY ILE VAL GLN GLY ALA GLY ILE ILE LYS SEQRES 2 A 190 LYS ILE SER LYS ASN ASP ASP THR GLN ARG HIS GLY ILE SEQRES 3 A 190 THR PHE PRO LYS ASP ILE LEU GLU SER VAL GLU LYS GLY SEQRES 4 A 190 THR VAL MET LEU VAL ASN GLY CYS SER LEU THR VAL VAL SEQRES 5 A 190 ARG ILE SER GLY ASP VAL VAL TYR PHE ASP ILE ASP GLN SEQRES 6 A 190 ALA ILE ASN THR THR THR PHE ARG GLU LEU GLU VAL GLY SEQRES 7 A 190 ASN LYS VAL ASN LEU GLU VAL ARG PRO GLU PHE GLY SER SEQRES 8 A 190 LEU LEU GLY LYS GLY ALA LEU THR GLY ASN ILE LYS GLY SEQRES 9 A 190 VAL ALA THR VAL ASP ASN ILE THR GLU GLU GLU ASP ARG SEQRES 10 A 190 LEU LYS VAL TYR ILE LYS ILE PRO LYS ASP LEU ILE GLU SEQRES 11 A 190 ASN ILE LEU SER GLU ASP HIS ILE GLY ILE ASN GLY VAL SEQRES 12 A 190 SER HIS SER ILE GLU GLU ILE SER ASP ASP ILE ILE PHE SEQRES 13 A 190 ILE ASN TYR PRO LYS ASN LEU SER ILE THR THR ASN LEU SEQRES 14 A 190 GLY THR LEU GLU LYS GLY SER ASP VAL ASN VAL GLU THR SEQRES 15 A 190 LEU ASN VAL SER ASN GLU TRP ASP SEQRES 1 B 190 MET PHE LYS GLY ILE VAL GLN GLY ALA GLY ILE ILE LYS SEQRES 2 B 190 LYS ILE SER LYS ASN ASP ASP THR GLN ARG HIS GLY ILE SEQRES 3 B 190 THR PHE PRO LYS ASP ILE LEU GLU SER VAL GLU LYS GLY SEQRES 4 B 190 THR VAL MET LEU VAL ASN GLY CYS SER LEU THR VAL VAL SEQRES 5 B 190 ARG ILE SER GLY ASP VAL VAL TYR PHE ASP ILE ASP GLN SEQRES 6 B 190 ALA ILE ASN THR THR THR PHE ARG GLU LEU GLU VAL GLY SEQRES 7 B 190 ASN LYS VAL ASN LEU GLU VAL ARG PRO GLU PHE GLY SER SEQRES 8 B 190 LEU LEU GLY LYS GLY ALA LEU THR GLY ASN ILE LYS GLY SEQRES 9 B 190 VAL ALA THR VAL ASP ASN ILE THR GLU GLU GLU ASP ARG SEQRES 10 B 190 LEU LYS VAL TYR ILE LYS ILE PRO LYS ASP LEU ILE GLU SEQRES 11 B 190 ASN ILE LEU SER GLU ASP HIS ILE GLY ILE ASN GLY VAL SEQRES 12 B 190 SER HIS SER ILE GLU GLU ILE SER ASP ASP ILE ILE PHE SEQRES 13 B 190 ILE ASN TYR PRO LYS ASN LEU SER ILE THR THR ASN LEU SEQRES 14 B 190 GLY THR LEU GLU LYS GLY SER ASP VAL ASN VAL GLU THR SEQRES 15 B 190 LEU ASN VAL SER ASN GLU TRP ASP HET RBF A 191 27 HET RBF B 191 27 HETNAM RBF RIBOFLAVIN HETSYN RBF RIBOFLAVINE; VITAMIN B2 FORMUL 3 RBF 2(C17 H20 N4 O6) FORMUL 5 HOH *405(H2 O) HELIX 1 1 PRO A 29 SER A 35 1 7 HELIX 2 2 THR A 71 LEU A 75 5 5 HELIX 3 3 ASN A 162 THR A 167 1 6 HELIX 4 4 ASN A 168 LEU A 172 5 5 HELIX 5 5 PRO B 29 SER B 35 1 7 HELIX 6 6 THR B 71 LEU B 75 5 5 HELIX 7 7 PRO B 125 GLU B 130 1 6 HELIX 8 8 ASN B 162 THR B 166 5 5 HELIX 9 9 ASN B 168 LEU B 172 5 5 SHEET 1 A 7 GLY A 8 LYS A 17 0 SHEET 2 A 7 GLN A 22 THR A 27 -1 O GLY A 25 N LYS A 13 SHEET 3 A 7 VAL A 58 ILE A 63 -1 O ILE A 63 N GLN A 22 SHEET 4 A 7 CYS A 47 SER A 55 -1 N VAL A 52 O TYR A 60 SHEET 5 A 7 VAL A 41 VAL A 44 -1 N MET A 42 O LEU A 49 SHEET 6 A 7 LYS A 80 GLU A 84 -1 O GLU A 84 N LEU A 43 SHEET 7 A 7 GLY A 8 LYS A 17 -1 N GLY A 10 O VAL A 81 SHEET 1 B 7 VAL A 143 SER A 146 0 SHEET 2 B 7 HIS A 137 ILE A 140 -1 N ILE A 140 O VAL A 143 SHEET 3 B 7 ASP A 177 THR A 182 -1 O GLU A 181 N GLY A 139 SHEET 4 B 7 GLY A 104 GLU A 114 -1 N GLY A 104 O VAL A 180 SHEET 5 B 7 ARG A 117 LYS A 123 -1 O TYR A 121 N ASP A 109 SHEET 6 B 7 ILE A 154 PRO A 160 -1 O ILE A 157 N VAL A 120 SHEET 7 B 7 GLU A 149 SER A 151 -1 N GLU A 149 O PHE A 156 SHEET 1 C 7 GLY B 8 LYS B 17 0 SHEET 2 C 7 GLN B 22 THR B 27 -1 O THR B 27 N ILE B 11 SHEET 3 C 7 VAL B 58 ILE B 63 -1 O ILE B 63 N GLN B 22 SHEET 4 C 7 CYS B 47 SER B 55 -1 N ARG B 53 O TYR B 60 SHEET 5 C 7 VAL B 41 VAL B 44 -1 N MET B 42 O LEU B 49 SHEET 6 C 7 LYS B 80 GLU B 84 -1 O GLU B 84 N LEU B 43 SHEET 7 C 7 GLY B 8 LYS B 17 -1 N GLY B 10 O VAL B 81 SHEET 1 D 7 VAL B 143 SER B 146 0 SHEET 2 D 7 HIS B 137 ILE B 140 -1 N ILE B 138 O HIS B 145 SHEET 3 D 7 ASP B 177 THR B 182 -1 O GLU B 181 N GLY B 139 SHEET 4 D 7 GLY B 104 GLU B 113 -1 N GLY B 104 O VAL B 180 SHEET 5 D 7 ARG B 117 LYS B 123 -1 O LYS B 123 N THR B 107 SHEET 6 D 7 ILE B 154 PRO B 160 -1 O ILE B 157 N VAL B 120 SHEET 7 D 7 GLU B 149 SER B 151 -1 N GLU B 149 O PHE B 156 CISPEP 1 GLY A 94 LYS A 95 0 -24.94 CISPEP 2 LEU A 128 ILE A 129 0 -1.42 CISPEP 3 ASN A 131 ILE A 132 0 -25.64 CISPEP 4 LEU A 183 ASN A 184 0 17.69 CISPEP 5 ASN B 18 ASP B 19 0 28.34 CISPEP 6 PHE B 89 GLY B 90 0 14.42 CISPEP 7 GLY B 90 SER B 91 0 -10.55 CISPEP 8 LEU B 92 LEU B 93 0 1.90 SITE 1 AC1 16 CYS A 47 SER A 48 LEU A 49 THR A 50 SITE 2 AC1 16 ASP A 62 ILE A 63 ASP A 64 GLN A 65 SITE 3 AC1 16 ALA A 66 THR A 69 GLY A 100 ASN A 101 SITE 4 AC1 16 ILE A 102 HOH A 192 HOH A 193 ASP B 31 SITE 1 AC2 17 CYS B 47 SER B 48 LEU B 49 THR B 50 SITE 2 AC2 17 ASP B 62 ILE B 63 ASP B 64 GLN B 65 SITE 3 AC2 17 ALA B 66 THR B 69 GLY B 100 ASN B 101 SITE 4 AC2 17 ILE B 102 LYS B 126 HOH B 246 HOH B 333 SITE 5 AC2 17 HOH B 442 CRYST1 46.288 46.582 161.053 90.00 90.00 90.00 P 21 21 21 8 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 0.021604 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021468 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006209 0.00000