HEADER LYASE 12-NOV-10 3PKV TITLE CRYSTAL STRUCTURE OF TOXOFLAVIN LYASE (TFLA) COMPND MOL_ID: 1; COMPND 2 MOLECULE: TOXOFLAVIN LYASE (TFLA); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PAENIBACILLUS POLYMYXA; SOURCE 3 ORGANISM_TAXID: 1406; SOURCE 4 STRAIN: JH2; SOURCE 5 GENE: TFLA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS METALLOENZYME, VICINAL OXYGEN CHELATE SUPERFAMILY, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR M.K.FENWICK,B.PHILMUS,T.P.BEGLEY,S.E.EALICK REVDAT 4 21-FEB-24 3PKV 1 REMARK REVDAT 3 08-NOV-17 3PKV 1 REMARK REVDAT 2 23-FEB-11 3PKV 1 JRNL REVDAT 1 12-JAN-11 3PKV 0 JRNL AUTH M.K.FENWICK,B.PHILMUS,T.P.BEGLEY,S.E.EALICK JRNL TITL TOXOFLAVIN LYASE REQUIRES A NOVEL 1-HIS-2-CARBOXYLATE FACIAL JRNL TITL 2 TRIAD . JRNL REF BIOCHEMISTRY V. 50 1091 2011 JRNL REFN ISSN 0006-2960 JRNL PMID 21166463 JRNL DOI 10.1021/BI101741V REMARK 2 REMARK 2 RESOLUTION. 1.34 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.6.1_357 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.34 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.140 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 57477 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 2820 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 27.7915 - 2.8820 0.99 5594 301 0.1604 0.1699 REMARK 3 2 2.8820 - 2.2879 1.00 5672 295 0.1714 0.1796 REMARK 3 3 2.2879 - 1.9988 1.00 5689 298 0.1598 0.1726 REMARK 3 4 1.9988 - 1.8160 1.00 5627 290 0.1690 0.1957 REMARK 3 5 1.8160 - 1.6859 0.99 5646 302 0.1731 0.1913 REMARK 3 6 1.6859 - 1.5865 0.98 5528 259 0.1710 0.1734 REMARK 3 7 1.5865 - 1.5071 0.96 5476 284 0.1758 0.2047 REMARK 3 8 1.5071 - 1.4415 0.94 5353 267 0.1882 0.2087 REMARK 3 9 1.4415 - 1.3860 0.92 5176 272 0.2092 0.2211 REMARK 3 10 1.3860 - 1.3400 0.86 4896 252 0.2300 0.2260 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.41 REMARK 3 B_SOL : 61.81 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.69 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.08190 REMARK 3 B22 (A**2) : -2.08190 REMARK 3 B33 (A**2) : 4.16390 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 1817 REMARK 3 ANGLE : 1.085 2484 REMARK 3 CHIRALITY : 0.071 283 REMARK 3 PLANARITY : 0.005 328 REMARK 3 DIHEDRAL : 13.455 673 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3PKV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-NOV-10. REMARK 100 THE DEPOSITION ID IS D_1000062496. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUN-10 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : CRYO-COOLED SI(111) DOUBLE REMARK 200 CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 59565 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.340 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.04300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.34 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.41600 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: SAD REMARK 200 SOFTWARE USED: SHELX, SHELXD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2M NAH2PO4, 0.8M K2HPO4, 0.1M CAPS REMARK 280 (PH 10.5), 0.2M LI2SO4, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K, PH 6.1 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 55.29050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 31.92199 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 19.35633 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 55.29050 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 31.92199 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 19.35633 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 55.29050 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 31.92199 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 19.35633 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 63.84397 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 38.71267 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 63.84397 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 38.71267 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 63.84397 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 38.71267 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 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 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 -22 REMARK 465 GLY A -21 REMARK 465 SER A -20 REMARK 465 ASP A -19 REMARK 465 LYS A -18 REMARK 465 ILE A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 SER A -10 REMARK 465 SER A -9 REMARK 465 GLY A -8 REMARK 465 GLU A -7 REMARK 465 ASN A -6 REMARK 465 LEU A -5 REMARK 465 TYR A -4 REMARK 465 PHE A -3 REMARK 465 GLN A -2 REMARK 465 GLY A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 GLU A 223 REMARK 465 HIS A 224 REMARK 465 HIS A 225 REMARK 465 HIS A 226 REMARK 465 HIS A 227 REMARK 465 HIS A 228 REMARK 465 HIS A 229 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 16 CZ NH1 NH2 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 SER A 135 170.41 179.05 REMARK 500 GLN A 176 -112.63 56.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3PKW RELATED DB: PDB REMARK 900 RELATED ID: 3PKX RELATED DB: PDB DBREF 3PKV A -22 229 PDB 3PKV 3PKV -22 229 SEQRES 1 A 252 MET GLY SER ASP LYS ILE HIS HIS HIS HIS HIS HIS SER SEQRES 2 A 252 SER GLY GLU ASN LEU TYR PHE GLN GLY HIS MET THR SER SEQRES 3 A 252 ILE LYS GLN LEU THR LEU TYR THR ALA GLU LEU ASP ARG SEQRES 4 A 252 MET LEU ALA PHE TYR THR ASN MET LEU GLY ALA GLN HIS SEQRES 5 A 252 VAL HIS GLU GLN ALA ASP ALA PHE THR ILE GLN LEU GLY SEQRES 6 A 252 VAL SER GLN ILE GLN PHE ARG ALA ALA ALA ASP GLY THR SEQRES 7 A 252 LYS PRO PHE TYR HIS ILE ALA ILE ASN ILE ALA ALA ASN SEQRES 8 A 252 HIS PHE GLN GLU GLY LYS ALA TRP LEU SER GLY PHE GLY SEQRES 9 A 252 GLU LEU LEU THR GLU ASN ASP GLU ASP GLN ALA TYR PHE SEQRES 10 A 252 PRO PHE PHE ASN ALA TYR SER CYS TYR VAL GLU ASP PRO SEQRES 11 A 252 SER GLY ASN ILE ILE GLU LEU ILE SER ARG GLN GLN ALA SEQRES 12 A 252 ALA PRO VAL LEU ASP LYS PRO PHE SER ALA ASP GLN LEU SEQRES 13 A 252 LEU SER ILE GLY GLU ILE ASN ILE THR THR SER ASP VAL SEQRES 14 A 252 GLU GLN ALA ALA THR ARG LEU LYS GLN ALA GLU LEU PRO SEQRES 15 A 252 VAL LYS LEU ASP GLN ILE GLU PRO ALA GLY LEU ASN PHE SEQRES 16 A 252 ILE GLY ASP GLN ASP LEU PHE LEU LEU LEU GLY PRO PRO SEQRES 17 A 252 GLY ARG ARG TRP LEU PHE SER GLU ARG VAL ALA VAL ILE SEQRES 18 A 252 TYR PRO LEU GLN MET GLU LEU ASP ASN GLY VAL SER LEU SEQRES 19 A 252 ALA ILE THR GLU THR GLY GLU LEU VAL ILE LEU GLU HIS SEQRES 20 A 252 HIS HIS HIS HIS HIS FORMUL 2 HOH *253(H2 O) HELIX 1 1 GLU A 13 GLY A 26 1 14 HELIX 2 2 HIS A 69 SER A 78 1 10 HELIX 3 3 SER A 129 LEU A 133 5 5 HELIX 4 4 ASP A 145 ALA A 156 1 12 HELIX 5 5 LYS A 161 ILE A 165 5 5 SHEET 1 A 7 VAL A 30 GLU A 32 0 SHEET 2 A 7 ALA A 36 LEU A 41 -1 O THR A 38 N HIS A 31 SHEET 3 A 7 SER A 44 ALA A 50 -1 O SER A 44 N LEU A 41 SHEET 4 A 7 ILE A 4 THR A 11 1 N LEU A 7 O GLN A 47 SHEET 5 A 7 LEU A 201 LEU A 205 -1 O GLU A 204 N GLN A 6 SHEET 6 A 7 SER A 210 ILE A 213 -1 O LEU A 211 N MET A 203 SHEET 7 A 7 LEU A 219 ILE A 221 -1 O VAL A 220 N ALA A 212 SHEET 1 B 7 ALA A 92 PHE A 94 0 SHEET 2 B 7 ALA A 99 GLU A 105 -1 O ALA A 99 N PHE A 94 SHEET 3 B 7 ILE A 111 ARG A 117 -1 O SER A 116 N TYR A 100 SHEET 4 B 7 HIS A 60 ILE A 65 1 N ILE A 63 O GLU A 113 SHEET 5 B 7 SER A 135 THR A 142 -1 O GLY A 137 N ALA A 62 SHEET 6 B 7 LEU A 178 GLY A 183 1 O LEU A 181 N ILE A 139 SHEET 7 B 7 ASN A 171 ASP A 175 -1 N ILE A 173 O LEU A 180 CRYST1 110.581 110.581 58.069 90.00 90.00 120.00 H 3 9 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 0.009043 0.005221 0.000000 0.00000 SCALE2 0.000000 0.010442 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017221 0.00000