HEADER LYASE 17-AUG-09 3IP8 TITLE CRYSTAL STRUCTURE OF ARYLMALONATE DECARBOXYLASE (AMDASE) FROM TITLE 2 BORDATELLA BRONCHISEPTIC IN COMPLEX WITH BENZYLPHOSPHONATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ARYLMALONATE DECARBOXYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: AMDASE; COMPND 5 EC: 4.1.1.76; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BORDETELLA BRONCHISEPTICA; SOURCE 3 ORGANISM_TAXID: 518; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS ARYLMALONATE DECARBOXYLASE BENZYLPHOSPHONATE COMPLEX, DECARBOXYLASE, KEYWDS 2 LYASE EXPDTA X-RAY DIFFRACTION AUTHOR K.OKRASA,C.LEVY,D.LEYS,J.MICKLEFIELD REVDAT 2 21-FEB-24 3IP8 1 REMARK SEQADV REVDAT 1 06-OCT-09 3IP8 0 JRNL AUTH K.OKRASA,C.LEVY,M.WILDING,M.GOODALL,N.BAUDENDISTEL,B.HAUER, JRNL AUTH 2 D.LEYS,J.MICKLEFIELD JRNL TITL STRUCTURE-GUIDED DIRECTED EVOLUTION OF ALKENYL AND JRNL TITL 2 ARYLMALONATE DECARBOXYLASES. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 48 7691 2009 JRNL REFN ISSN 1433-7851 JRNL PMID 19739187 JRNL DOI 10.1002/ANIE.200904112 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 29863 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.159 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.181 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 1511 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 32.9629 - 3.3307 0.90 2497 149 0.1413 0.1423 REMARK 3 2 3.3307 - 2.6440 0.93 2550 143 0.1580 0.1674 REMARK 3 3 2.6440 - 2.3099 0.95 2597 123 0.1603 0.1939 REMARK 3 4 2.3099 - 2.0988 0.96 2599 145 0.1532 0.1792 REMARK 3 5 2.0988 - 1.9484 0.97 2643 132 0.1567 0.1873 REMARK 3 6 1.9484 - 1.8335 0.96 2620 129 0.1572 0.2120 REMARK 3 7 1.8335 - 1.7417 0.95 2580 142 0.1566 0.1945 REMARK 3 8 1.7417 - 1.6659 0.96 2605 144 0.1604 0.2167 REMARK 3 9 1.6659 - 1.6017 0.96 2586 140 0.1751 0.1961 REMARK 3 10 1.6017 - 1.5465 0.96 2581 134 0.1818 0.2323 REMARK 3 11 1.5465 - 1.4980 0.92 2494 130 0.2034 0.2552 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 : 0.39 REMARK 3 B_SOL : 72.63 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 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) : 16.15 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.99100 REMARK 3 B22 (A**2) : -4.29400 REMARK 3 B33 (A**2) : 2.55600 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.61000 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 : 0.009 1710 REMARK 3 ANGLE : 1.351 2330 REMARK 3 CHIRALITY : 0.085 279 REMARK 3 PLANARITY : 0.007 303 REMARK 3 DIHEDRAL : 15.551 607 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 3IP8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-AUG-09. REMARK 100 THE DEPOSITION ID IS D_1000054692. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUL-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9756 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29865 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.498 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 (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.6000 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: WELL SOLUTION 0.1M TRIS PH 8.0 AND 30% REMARK 280 PEG 10K, PROTEIN 10-15MG/ML IN TRIS PH 7.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 32.80000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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 1 REMARK 465 GLN A 2 REMARK 465 GLN A 3 REMARK 465 ALA A 4 REMARK 465 SER A 5 REMARK 465 THR A 6 REMARK 465 GLU A 239 REMARK 465 SER A 240 REMARK 465 LEU A 241 REMARK 465 GLU A 242 REMARK 465 HIS A 243 REMARK 465 HIS A 244 REMARK 465 HIS A 245 REMARK 465 HIS A 246 REMARK 465 HIS A 247 REMARK 465 HIS A 248 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 ASP A 238 CG OD1 OD2 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 MET A 93 SD MET A 93 CE -0.404 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 CYS A 188 111.76 142.94 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 B85 A 249 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3DG9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MALONATE DECARBOXYLASE FROM BORDATELLA REMARK 900 BRONCHISEPTICA DBREF 3IP8 A 1 240 UNP Q05115 AMDA_BORBR 1 240 SEQADV 3IP8 LEU A 241 UNP Q05115 EXPRESSION TAG SEQADV 3IP8 GLU A 242 UNP Q05115 EXPRESSION TAG SEQADV 3IP8 HIS A 243 UNP Q05115 EXPRESSION TAG SEQADV 3IP8 HIS A 244 UNP Q05115 EXPRESSION TAG SEQADV 3IP8 HIS A 245 UNP Q05115 EXPRESSION TAG SEQADV 3IP8 HIS A 246 UNP Q05115 EXPRESSION TAG SEQADV 3IP8 HIS A 247 UNP Q05115 EXPRESSION TAG SEQADV 3IP8 HIS A 248 UNP Q05115 EXPRESSION TAG SEQRES 1 A 248 MET GLN GLN ALA SER THR PRO THR ILE GLY MET ILE VAL SEQRES 2 A 248 PRO PRO ALA ALA GLY LEU VAL PRO ALA ASP GLY ALA ARG SEQRES 3 A 248 LEU TYR PRO ASP LEU PRO PHE ILE ALA SER GLY LEU GLY SEQRES 4 A 248 LEU GLY SER VAL THR PRO GLU GLY TYR ASP ALA VAL ILE SEQRES 5 A 248 GLU SER VAL VAL ASP HIS ALA ARG ARG LEU GLN LYS GLN SEQRES 6 A 248 GLY ALA ALA VAL VAL SER LEU MET GLY THR SER LEU SER SEQRES 7 A 248 PHE TYR ARG GLY ALA ALA PHE ASN ALA ALA LEU THR VAL SEQRES 8 A 248 ALA MET ARG GLU ALA THR GLY LEU PRO CYS THR THR MET SEQRES 9 A 248 SER THR ALA VAL LEU ASN GLY LEU ARG ALA LEU GLY VAL SEQRES 10 A 248 ARG ARG VAL ALA LEU ALA THR ALA TYR ILE ASP ASP VAL SEQRES 11 A 248 ASN GLU ARG LEU ALA ALA PHE LEU ALA GLU GLU SER LEU SEQRES 12 A 248 VAL PRO THR GLY CYS ARG SER LEU GLY ILE THR GLY VAL SEQRES 13 A 248 GLU ALA MET ALA ARG VAL ASP THR ALA THR LEU VAL ASP SEQRES 14 A 248 LEU CYS VAL ARG ALA PHE GLU ALA ALA PRO ASP SER ASP SEQRES 15 A 248 GLY ILE LEU LEU SER CYS GLY GLY LEU LEU THR LEU ASP SEQRES 16 A 248 ALA ILE PRO GLU VAL GLU ARG ARG LEU GLY VAL PRO VAL SEQRES 17 A 248 VAL SER SER SER PRO ALA GLY PHE TRP ASP ALA VAL ARG SEQRES 18 A 248 LEU ALA GLY GLY GLY ALA LYS ALA ARG PRO GLY TYR GLY SEQRES 19 A 248 ARG LEU PHE ASP GLU SER LEU GLU HIS HIS HIS HIS HIS SEQRES 20 A 248 HIS HET B85 A 249 11 HETNAM B85 BENZYLPHOSPHONIC ACID FORMUL 2 B85 C7 H9 O3 P FORMUL 3 HOH *293(H2 O) HELIX 1 1 ALA A 22 TYR A 28 1 7 HELIX 2 2 THR A 44 ILE A 52 1 9 HELIX 3 3 SER A 54 GLN A 65 1 12 HELIX 4 4 THR A 75 TYR A 80 1 6 HELIX 5 5 GLY A 82 GLY A 98 1 17 HELIX 6 6 MET A 104 LEU A 115 1 12 HELIX 7 7 ILE A 127 GLU A 141 1 15 HELIX 8 8 VAL A 156 VAL A 162 5 7 HELIX 9 9 ASP A 163 ALA A 178 1 16 HELIX 10 10 ASP A 195 GLY A 205 1 11 HELIX 11 11 SER A 211 GLY A 224 1 14 HELIX 12 12 GLY A 234 ASP A 238 5 5 SHEET 1 A 4 PHE A 33 GLY A 37 0 SHEET 2 A 4 ILE A 9 VAL A 13 1 N VAL A 13 O SER A 36 SHEET 3 A 4 VAL A 69 LEU A 72 1 O VAL A 69 N GLY A 10 SHEET 4 A 4 CYS A 101 THR A 103 1 O THR A 102 N LEU A 72 SHEET 1 B 4 VAL A 144 SER A 150 0 SHEET 2 B 4 ARG A 119 THR A 124 1 N LEU A 122 O GLY A 147 SHEET 3 B 4 GLY A 183 SER A 187 1 O LEU A 185 N ALA A 123 SHEET 4 B 4 VAL A 208 SER A 210 1 O VAL A 209 N ILE A 184 SITE 1 AC1 10 PRO A 14 GLY A 74 THR A 75 SER A 76 SITE 2 AC1 10 TYR A 126 VAL A 156 CYS A 188 GLY A 189 SITE 3 AC1 10 GLY A 190 HOH A 355 CRYST1 38.640 65.600 41.880 90.00 110.42 90.00 P 1 21 1 2 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 0.025880 0.000000 0.009635 0.00000 SCALE2 0.000000 0.015244 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025479 0.00000