HEADER LIGASE 07-JAN-10 3LAX TITLE THE CRYSTAL STRUCTURE OF A DOMAIN OF PHENYLACETATE-COENZYME TITLE 2 A LIGASE FROM BACTEROIDES VULGATUS ATCC 8482 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHENYLACETATE-COENZYME A LIGASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 327-432; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACTEROIDES VULGATUS; SOURCE 3 ORGANISM_TAXID: 435590; SOURCE 4 STRAIN: ATCC 8482; SOURCE 5 GENE: BACTEROIDES VULGATUS, BVU_1668; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: PPK1037; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PMCSG19 KEYWDS STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE INITIATIVE, KEYWDS 2 MIDWEST CENTER FOR STRUCTURAL GENOMICS, MCSG EXPDTA X-RAY DIFFRACTION AUTHOR K.TAN,R.WU,G.COBB,A.JOACHIMIAK,MIDWEST CENTER FOR STRUCTURAL AUTHOR 2 GENOMICS (MCSG) REVDAT 2 02-FEB-10 3LAX 1 SPRSDE REVDAT 1 19-JAN-10 3LAX 0 SPRSDE 02-FEB-10 3LAX 3GXS JRNL AUTH K.TAN,R.WU,G.COBB,A.JOACHIMIAK JRNL TITL THE CRYSTAL STRUCTURE OF A DOMAIN OF JRNL TITL 2 PHENYLACETATE-COENZYME A LIGASE FROM BACTEROIDES JRNL TITL 3 VULGATUS ATCC 8482 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.43 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.5_2) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.19 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 19197 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.140 REMARK 3 FREE R VALUE TEST SET COUNT : 986 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 30.1934 - 2.7313 0.95 2683 121 0.2008 0.2180 REMARK 3 2 2.7313 - 2.1681 1.00 2663 145 0.1445 0.2212 REMARK 3 3 2.1681 - 1.8941 1.00 2624 140 0.1318 0.1889 REMARK 3 4 1.8941 - 1.7209 1.00 2594 150 0.1341 0.2112 REMARK 3 5 1.7209 - 1.5976 1.00 2576 154 0.1510 0.2541 REMARK 3 6 1.5976 - 1.5034 0.99 2572 141 0.1626 0.2285 REMARK 3 7 1.5034 - 1.4281 0.96 2499 135 0.1992 0.2697 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 : 60.16 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 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) : 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 : 0.007 945 REMARK 3 ANGLE : 1.090 1295 REMARK 3 CHIRALITY : 0.072 163 REMARK 3 PLANARITY : 0.004 163 REMARK 3 DIHEDRAL : 16.925 397 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 3LAX COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JAN-10. REMARK 100 THE RCSB ID CODE IS RCSB057052. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-DEC-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97926 REMARK 200 MONOCHROMATOR : SI 111 CRYSTAL REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19292 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.428 REMARK 200 RESOLUTION RANGE LOW (A) : 37.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 39.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.43 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 0.70900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.960 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXD/MLPHARE/DM/ARP/WARP/HKL3000 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM ACETATE, 0.1M HEPES, REMARK 280 45% W/V MPD, PH 8.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 289K 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 16.86850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.80050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.16700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.80050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.86850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.16700 REMARK 290 SMTRY3 4 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 300 REMARK: EXPERIMENTALLY UNKNOWN. THE DOMAIN IS LIKELY A MONOMER. 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 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 GLU A 419 REMARK 465 GLY A 420 REMARK 465 LYS A 421 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 GLU A 364 -103.14 57.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3GXS RELATED DB: PDB REMARK 900 THIS DEPOSIT IS TO REPLACE 3GXS. REMARK 900 RELATED ID: APC62324.1 RELATED DB: TARGETDB DBREF 3LAX A 327 432 UNP A6L0Y5 A6L0Y5_BACV8 327 432 SEQADV 3LAX SER A 324 UNP A6L0Y5 EXPRESSION TAG SEQADV 3LAX ASN A 325 UNP A6L0Y5 EXPRESSION TAG SEQADV 3LAX ALA A 326 UNP A6L0Y5 EXPRESSION TAG SEQRES 1 A 109 SER ASN ALA ASP ASP MSE ILE ILE LEU LYS GLY VAL ASN SEQRES 2 A 109 ILE PHE PRO ILE GLN ILE GLU THR ILE LEU LEU GLN PHE SEQRES 3 A 109 LYS GLU LEU GLY SER ASP TYR LEU ILE THR LEU GLU THR SEQRES 4 A 109 ALA GLU SER ASN ASP GLU MSE THR VAL GLU VAL GLU LEU SEQRES 5 A 109 SER GLN LEU PHE THR ASP ASP TYR GLY ARG LEU GLN ALA SEQRES 6 A 109 LEU THR ARG GLU ILE THR ARG GLN LEU LYS ASP GLU ILE SEQRES 7 A 109 LEU VAL THR PRO ARG VAL LYS LEU VAL PRO LYS GLY ALA SEQRES 8 A 109 LEU PRO LYS SER GLU GLY LYS ALA VAL ARG VAL LYS ASP SEQRES 9 A 109 LEU ARG LYS THR PHE MODRES 3LAX MSE A 329 MET SELENOMETHIONINE MODRES 3LAX MSE A 369 MET SELENOMETHIONINE HET MSE A 329 8 HET MSE A 369 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 2 HOH *90(H2 O) HELIX 1 1 SER A 324 ASP A 328 5 5 HELIX 2 2 PHE A 338 GLN A 348 1 11 HELIX 3 3 ASP A 382 LEU A 402 1 21 SHEET 1 A 2 ILE A 330 LEU A 332 0 SHEET 2 A 2 VAL A 335 ILE A 337 -1 O ILE A 337 N ILE A 330 SHEET 1 B 4 ARG A 406 VAL A 410 0 SHEET 2 B 4 ASN A 366 LEU A 375 1 N VAL A 371 O ARG A 406 SHEET 3 B 4 LEU A 352 ALA A 363 -1 N GLY A 353 O GLU A 374 SHEET 4 B 4 VAL A 425 ASP A 427 1 O LYS A 426 N ILE A 358 LINK C ASP A 328 N MSE A 329 1555 1555 1.33 LINK C MSE A 329 N ILE A 330 1555 1555 1.33 LINK C GLU A 368 N MSE A 369 1555 1555 1.33 LINK C MSE A 369 N THR A 370 1555 1555 1.33 CRYST1 33.737 44.334 67.601 90.00 90.00 90.00 P 21 21 21 4 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 0.029641 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022556 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014793 0.00000 MASTER 230 0 2 3 6 0 0 6 0 0 0 9 END