HEADER LYASE 26-AUG-15 5DFG TITLE CRYSTAL STRUCTURE OF C-AS LYASE WITH MUTATIONS Y100H AND V102F COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYOXALASE/BLEOMYCIN RESISTANCE PROTEIN/DIOXYGENASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOMONOSPORA CURVATA (STRAIN ATCC 19995 / SOURCE 3 DSM 43183 / JCM 3096 / NCIMB 10081); SOURCE 4 ORGANISM_TAXID: 471852; SOURCE 5 STRAIN: ATCC 19995 / DSM 43183 / JCM 3096 / NCIMB 10081; SOURCE 6 GENE: TCUR_4156; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LYASE, CUPIN FOLD EXPDTA X-RAY DIFFRACTION AUTHOR S.VENKADESH,M.YOSHINAGA,P.KANDAVELU,B.SANKARAN,B.P.ROSEN REVDAT 4 27-SEP-23 5DFG 1 REMARK REVDAT 3 25-DEC-19 5DFG 1 REMARK REVDAT 2 06-SEP-17 5DFG 1 REMARK REVDAT 1 21-SEP-16 5DFG 0 JRNL AUTH S.VENKADESH,M.YOSHINAGA,P.KANDAVELU,B.SANKARAN,B.P.ROSEN JRNL TITL CRYSTAL STRUCTURE OF C-AS LYASE WITH MUTATIONS Y100H AND JRNL TITL 2 F102V JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.2_1309 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) : 1.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 8754 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.750 REMARK 3 FREE R VALUE TEST SET COUNT : 416 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 27.6411 - 2.8421 0.97 2850 138 0.1908 0.2252 REMARK 3 2 2.8421 - 2.2562 1.00 2778 131 0.2323 0.2593 REMARK 3 3 2.2562 - 1.9711 0.99 2710 147 0.1950 0.2816 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.700 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 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 : 0.005 929 REMARK 3 ANGLE : 1.097 1277 REMARK 3 CHIRALITY : 0.078 147 REMARK 3 PLANARITY : 0.005 169 REMARK 3 DIHEDRAL : 13.864 325 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 5DFG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000212945. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : SI(IIII) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8832 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.970 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 (%) : 98.7 REMARK 200 DATA REDUNDANCY : 25.10 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 40.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.04 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 27.00 REMARK 200 R MERGE FOR SHELL (I) : 0.26900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 13.60 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 5C4P REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 1000, 0.2 M AMMONIUM SULFATE, REMARK 280 0.1 M NA ACETATE, 0.1 M TCEP, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.29200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 22.09000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 22.09000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 88.93800 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 22.09000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 22.09000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 29.64600 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 22.09000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 22.09000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 88.93800 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 22.09000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 22.09000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 29.64600 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 59.29200 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 KCAL/MOL 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 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 GLY A 1 REMARK 465 SER A 2 REMARK 465 ALA A 97 REMARK 465 CYS A 98 REMARK 465 CYS A 99 REMARK 465 LYS A 122 REMARK 465 GLY A 123 REMARK 465 ASP A 124 REMARK 465 ALA A 125 REMARK 465 ASP A 126 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 HIS A 3 CG ND1 CD2 CE1 NE2 REMARK 470 ASP A 59 CG OD1 OD2 REMARK 470 ARG A 62 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 71 CG CD OE1 OE2 REMARK 470 LYS A 84 CG CD CE NZ REMARK 470 GLU A 85 CG CD OE1 OE2 REMARK 470 THR A 96 OG1 CG2 REMARK 470 GLN A 103 O CG CD OE1 NE2 REMARK 470 VAL A 121 CG1 CG2 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 259 O HOH A 260 5444 2.17 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 ALA A 56 -34.32 63.05 REMARK 500 REMARK 500 REMARK: NULL DBREF 5DFG A 4 126 UNP D1A230 D1A230_THECD 1 123 SEQADV 5DFG GLY A 1 UNP D1A230 EXPRESSION TAG SEQADV 5DFG SER A 2 UNP D1A230 EXPRESSION TAG SEQADV 5DFG HIS A 3 UNP D1A230 EXPRESSION TAG SEQADV 5DFG HIS A 100 UNP D1A230 TYR 97 ENGINEERED MUTATION SEQADV 5DFG PHE A 102 UNP D1A230 VAL 99 ENGINEERED MUTATION SEQRES 1 A 126 GLY SER HIS MET SER ARG VAL GLN LEU ALA LEU ARG VAL SEQRES 2 A 126 PRO ASP LEU GLU ALA SER ILE GLY PHE TYR SER LYS LEU SEQRES 3 A 126 PHE GLY THR GLY PRO ALA LYS VAL ARG PRO GLY TYR ALA SEQRES 4 A 126 ASN PHE ALA ILE ALA GLU PRO PRO LEU LYS LEU VAL LEU SEQRES 5 A 126 ILE GLU GLY ALA GLY GLU ASP ALA THR ARG LEU ASP HIS SEQRES 6 A 126 LEU GLY VAL GLU VAL GLU ASP SER ALA GLN VAL GLY HIS SEQRES 7 A 126 ALA ALA ARG ARG LEU LYS GLU SER GLY LEU ALA THR VAL SEQRES 8 A 126 GLU GLU ASN ASP THR ALA CYS CYS HIS ALA PHE GLN ASP SEQRES 9 A 126 LYS VAL TRP VAL THR GLY PRO GLY GLY GLU PRO TRP GLU SEQRES 10 A 126 VAL TYR VAL VAL LYS GLY ASP ALA ASP FORMUL 2 HOH *61(H2 O) HELIX 1 AA1 ASP A 15 GLY A 28 1 14 HELIX 2 AA2 ASP A 72 SER A 86 1 15 SHEET 1 AA1 8 LYS A 33 ARG A 35 0 SHEET 2 AA1 8 TYR A 38 ILE A 43 -1 O TYR A 38 N ARG A 35 SHEET 3 AA1 8 LEU A 48 GLU A 54 -1 O LEU A 52 N ALA A 39 SHEET 4 AA1 8 SER A 5 VAL A 13 1 N LEU A 11 O ILE A 53 SHEET 5 AA1 8 ARG A 62 VAL A 70 -1 O ASP A 64 N ALA A 10 SHEET 6 AA1 8 PRO A 115 VAL A 120 1 O TYR A 119 N VAL A 70 SHEET 7 AA1 8 LYS A 105 THR A 109 -1 N VAL A 108 O TRP A 116 SHEET 8 AA1 8 VAL A 91 GLU A 93 -1 N GLU A 93 O LYS A 105 CISPEP 1 GLU A 45 PRO A 46 0 -0.47 CRYST1 44.180 44.180 118.584 90.00 90.00 90.00 P 43 21 2 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 0.022635 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022635 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008433 0.00000