HEADER HYDROLASE 31-MAR-24 8YWO TITLE CRYSTAL STRUCTURE OF L-AZETIDINE-2-CARBOXYLATE HYDROLASE SOAKED IN TITLE 2 (S)-AZETIDINE-2-CARBOXYLIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: (S)-2-HALOACID DEHALOGENASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 2-HALOALKANOIC ACID DEHALOGENASE,HALOCARBOXYLIC ACID COMPND 5 HALIDOHYDROLASE,L-2-HALOACID DEHALOGENASE,L-AZETIDINE-2-CARBOXYLATE COMPND 6 HYDROLASE; COMPND 7 EC: 3.8.1.2; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS SP. A2C; SOURCE 3 ORGANISM_TAXID: 533317; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BLR KEYWDS AZETIDINE-2-CARBOXYLATE, DEHALOGENASE, ALPHA/BETA HYDROLASE, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.TOYODA,K.MIZUTANI,B.MIKAMI,L.P.WACKETT,N.ESAKI,T.KURIHARA REVDAT 1 08-MAY-24 8YWO 0 JRNL AUTH M.TOYODA,K.JITSUMORI,B.MIKAMI,K.MIZUTANI,N.ESAKI, JRNL AUTH 2 L.P.WACKETT,T.KURIHARA JRNL TITL RESEARCH FOR THE CRYSTAL STRUCTURE OF JRNL TITL 2 L-AZETIDINE-2-CARBOXYLATE HYDROLASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.58 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.52 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 32192 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.134 REMARK 3 R VALUE (WORKING SET) : 0.132 REMARK 3 FREE R VALUE : 0.183 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1609 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 25.5200 - 3.5000 0.99 2863 150 0.1305 0.1569 REMARK 3 2 3.5000 - 2.7800 1.00 2845 150 0.1296 0.1679 REMARK 3 3 2.7800 - 2.4300 1.00 2829 149 0.1267 0.1803 REMARK 3 4 2.4300 - 2.2100 0.99 2829 149 0.1189 0.1808 REMARK 3 5 2.2100 - 2.0500 1.00 2813 148 0.1145 0.1635 REMARK 3 6 2.0500 - 1.9300 1.00 2826 149 0.1235 0.1959 REMARK 3 7 1.9300 - 1.8300 1.00 2825 148 0.1417 0.2263 REMARK 3 8 1.8300 - 1.7500 1.00 2800 148 0.1385 0.2082 REMARK 3 9 1.7500 - 1.6900 1.00 2833 149 0.1400 0.2317 REMARK 3 10 1.6900 - 1.6300 0.97 2733 144 0.1597 0.2271 REMARK 3 11 1.6300 - 1.5800 0.85 2387 125 0.2096 0.2823 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.169 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.954 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.53 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.13 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 : 0.006 2104 REMARK 3 ANGLE : 0.781 2875 REMARK 3 CHIRALITY : 0.052 303 REMARK 3 PLANARITY : 0.006 385 REMARK 3 DIHEDRAL : 14.229 816 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 8YWO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-APR-24. REMARK 100 THE DEPOSITION ID IS D_1300044826. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-FEB-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 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) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32195 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 REMARK 200 RESOLUTION RANGE LOW (A) : 40.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.67 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.980 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: 3SMV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PRECIPITANT: 20% PEG 3350, 0.15 M REMARK 280 MAGNESIUM ACETATE, 0.1 M IMIDAZOLE/HCL BUFFER; SOAKING: THE REMARK 280 PRECIPITANT ABOVE WITH 50 MM L-AZETIDINE-2-CARBOXYLATE, PH 8, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 32.20950 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10920 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 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 13 -60.52 -94.06 REMARK 500 THR A 57 157.56 -48.50 REMARK 500 ASP A 185 -52.84 -124.44 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 PHE A 11 ASP A 12 146.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 723 DISTANCE = 6.14 ANGSTROMS REMARK 525 HOH A 724 DISTANCE = 6.50 ANGSTROMS DBREF 8YWO A 1 240 UNP B2Z3V8 B2Z3V8_9PSED 1 240 SEQRES 1 A 240 MET GLN LEU THR ASP PHE LYS ALA LEU THR PHE ASP CYS SEQRES 2 A 240 TYR GLY THR LEU ILE ASP TRP GLU THR GLY ILE VAL ASN SEQRES 3 A 240 ALA LEU GLN PRO LEU ALA LYS ARG THR GLY LYS THR PHE SEQRES 4 A 240 THR SER ASP GLU LEU LEU GLU VAL PHE GLY ARG ASN GLU SEQRES 5 A 240 SER PRO GLN GLN THR GLU THR PRO GLY ALA LEU TYR GLN SEQRES 6 A 240 ASP ILE LEU ARG ALA VAL TYR ASP ARG ILE ALA LYS GLU SEQRES 7 A 240 TRP GLY LEU GLU PRO ASP ALA ALA GLU ARG GLU GLU PHE SEQRES 8 A 240 GLY THR SER VAL LYS ASN TRP PRO ALA PHE PRO ASP THR SEQRES 9 A 240 VAL GLU ALA LEU GLN TYR LEU LYS LYS HIS TYR LYS LEU SEQRES 10 A 240 VAL ILE LEU SER ASN ILE ASP ARG ASN GLU PHE LYS LEU SEQRES 11 A 240 SER ASN ALA LYS LEU GLY VAL GLU PHE ASP HIS ILE ILE SEQRES 12 A 240 THR ALA GLN ASP VAL GLY SER TYR LYS PRO ASN PRO ASN SEQRES 13 A 240 ASN PHE THR TYR MET ILE ASP ALA LEU ALA LYS ALA GLY SEQRES 14 A 240 ILE GLU LYS LYS ASP ILE LEU HIS THR ALA GLU SER LEU SEQRES 15 A 240 TYR HIS ASP HIS ILE PRO ALA ASN ASP ALA GLY LEU VAL SEQRES 16 A 240 SER ALA TRP ILE TYR ARG ARG HIS GLY LYS GLU GLY TYR SEQRES 17 A 240 GLY ALA THR HIS VAL PRO SER ARG MET PRO ASN VAL ASP SEQRES 18 A 240 PHE ARG PHE ASN SER MET GLY GLU MET ALA GLU ALA HIS SEQRES 19 A 240 LYS GLN ALA LEU LYS GLY HET 02A A 301 7 HETNAM 02A (2S)-AZETIDINE-2-CARBOXYLIC ACID FORMUL 2 02A C4 H7 N O2 FORMUL 3 HOH *324(H2 O) HELIX 1 AA1 GLN A 2 PHE A 6 5 5 HELIX 2 AA2 ASP A 19 THR A 35 1 17 HELIX 3 AA3 THR A 40 SER A 53 1 14 HELIX 4 AA4 PRO A 54 GLN A 56 5 3 HELIX 5 AA5 LEU A 63 TRP A 79 1 17 HELIX 6 AA6 ASP A 84 THR A 93 1 10 HELIX 7 AA7 SER A 94 TRP A 98 5 5 HELIX 8 AA8 ASP A 103 LYS A 113 1 11 HELIX 9 AA9 ASP A 124 ALA A 133 1 10 HELIX 10 AB1 ALA A 145 GLY A 149 1 5 HELIX 11 AB2 ASN A 154 ALA A 168 1 15 HELIX 12 AB3 GLU A 171 LYS A 173 5 3 HELIX 13 AB4 ASP A 185 GLY A 193 1 9 HELIX 14 AB5 SER A 226 GLY A 240 1 15 SHEET 1 AA1 6 HIS A 141 THR A 144 0 SHEET 2 AA1 6 LYS A 116 SER A 121 1 N ILE A 119 O ILE A 143 SHEET 3 AA1 6 ALA A 8 PHE A 11 1 N PHE A 11 O VAL A 118 SHEET 4 AA1 6 ILE A 175 ALA A 179 1 O THR A 178 N THR A 10 SHEET 5 AA1 6 VAL A 195 ILE A 199 1 O VAL A 195 N HIS A 177 SHEET 6 AA1 6 PHE A 222 PHE A 224 1 O PHE A 222 N TRP A 198 CISPEP 1 LYS A 152 PRO A 153 0 13.23 CRYST1 36.105 64.419 54.307 90.00 106.99 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 0.027697 0.000000 0.008463 0.00000 SCALE2 0.000000 0.015523 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019254 0.00000