HEADER HYDROLASE 16-NOV-09 2WYD TITLE THE QUORUM QUENCHING N-ACYL HOMOSERINE LACTONE ACYLASE PVDQ IN COMPLEX TITLE 2 WITH DODECANOIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACYL-HOMOSERINE LACTONE ACYLASE PVDQ SUBUNIT ALPHA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ACYL-HSL ACYLASE PVDQ SUBUNIT ALPHA; COMPND 5 EC: 3.5.1.97; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: ACYL-HOMOSERINE LACTONE ACYLASE PVDQ SUBUNIT BETA; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: ACYL-HSL ACYLASE PVDQ SUBUNIT BETA; COMPND 11 EC: 3.5.1.97; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 3 ORGANISM_TAXID: 208964; SOURCE 4 STRAIN: PAO1; SOURCE 5 ATCC: 15692; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 316385; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: K-12 SUBSTR. DH10B; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMCTNDE; SOURCE 10 OTHER_DETAILS: HOLLOWAY COLLECTION; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 13 ORGANISM_TAXID: 208964; SOURCE 14 STRAIN: PAO1; SOURCE 15 ATCC: 15692; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 316385; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: K-12 SUBSTR. DH10B; SOURCE 19 EXPRESSION_SYSTEM_PLASMID: PMCTNDE; SOURCE 20 OTHER_DETAILS: HOLLOWAY COLLECTION KEYWDS ZYMOGEN, HYDROLASE, PERIPLASM EXPDTA X-RAY DIFFRACTION AUTHOR M.BOKHOVE,P.NADAL JIMENEZ,W.J.QUAX,B.W.DIJKSTRA REVDAT 3 13-NOV-24 2WYD 1 REMARK REVDAT 2 26-JAN-10 2WYD 1 JRNL REVDAT 1 29-DEC-09 2WYD 0 JRNL AUTH M.BOKHOVE,P.NADAL JIMENEZ,W.J.QUAX,B.W.DIJKSTRA JRNL TITL THE QUORUM-QUENCHING N-ACYL HOMOSERINE LACTONE ACYLASE PVDQ JRNL TITL 2 IS AN NTN-HYDROLASE WITH AN UNUSUAL SUBSTRATE-BINDING POCKET JRNL REF PROC.NATL.ACAD.SCI.USA V. 107 686 2010 JRNL REFN ISSN 0027-8424 JRNL PMID 20080736 JRNL DOI 10.1073/PNAS.0911839107 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0096 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.13 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 73309 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 3686 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4429 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.71 REMARK 3 BIN R VALUE (WORKING SET) : 0.2500 REMARK 3 BIN FREE R VALUE SET COUNT : 237 REMARK 3 BIN FREE R VALUE : 0.2840 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5526 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 76 REMARK 3 SOLVENT ATOMS : 432 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.77 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.08300 REMARK 3 B22 (A**2) : 0.75300 REMARK 3 B33 (A**2) : -0.67000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.120 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.112 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.075 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.684 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5840 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7937 ; 1.144 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 733 ; 5.615 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 285 ;35.650 ;23.298 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 912 ;12.503 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 60 ;15.984 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 836 ; 0.076 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4591 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3611 ; 0.450 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5781 ; 0.850 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2229 ; 1.630 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2155 ; 2.761 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 323 B 480 REMARK 3 ORIGIN FOR THE GROUP (A): 32.9090 68.4140 31.2930 REMARK 3 T TENSOR REMARK 3 T11: 0.2647 T22: 0.1441 REMARK 3 T33: 0.1122 T12: 0.0301 REMARK 3 T13: 0.0267 T23: 0.0112 REMARK 3 L TENSOR REMARK 3 L11: 0.8593 L22: 1.5109 REMARK 3 L33: 2.1199 L12: 0.6174 REMARK 3 L13: -0.8963 L23: -0.7413 REMARK 3 S TENSOR REMARK 3 S11: -0.0238 S12: 0.2762 S13: 0.0432 REMARK 3 S21: -0.3375 S22: 0.0887 S23: -0.0933 REMARK 3 S31: -0.1467 S32: -0.0819 S33: -0.0648 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 51 A 95 REMARK 3 RESIDUE RANGE : A 129 A 168 REMARK 3 RESIDUE RANGE : B 75 B 155 REMARK 3 RESIDUE RANGE : B 206 B 250 REMARK 3 ORIGIN FOR THE GROUP (A): 44.8200 34.8600 47.1770 REMARK 3 T TENSOR REMARK 3 T11: 0.0150 T22: 0.0149 REMARK 3 T33: 0.0313 T12: 0.0063 REMARK 3 T13: 0.0020 T23: 0.0036 REMARK 3 L TENSOR REMARK 3 L11: 2.0827 L22: 0.4280 REMARK 3 L33: 0.7917 L12: -0.1310 REMARK 3 L13: -0.4849 L23: -0.0161 REMARK 3 S TENSOR REMARK 3 S11: -0.0396 S12: 0.0272 S13: -0.1159 REMARK 3 S21: -0.0344 S22: 0.0067 S23: -0.0483 REMARK 3 S31: 0.0689 S32: 0.0792 S33: 0.0329 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 6 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 6 A 50 REMARK 3 RESIDUE RANGE : A 96 A 128 REMARK 3 RESIDUE RANGE : B 1 B 74 REMARK 3 RESIDUE RANGE : B 156 B 205 REMARK 3 RESIDUE RANGE : B 251 B 322 REMARK 3 RESIDUE RANGE : B 481 B 546 REMARK 3 ORIGIN FOR THE GROUP (A): 30.1200 56.7090 60.7990 REMARK 3 T TENSOR REMARK 3 T11: 0.0432 T22: 0.0094 REMARK 3 T33: 0.0144 T12: 0.0074 REMARK 3 T13: 0.0028 T23: -0.0102 REMARK 3 L TENSOR REMARK 3 L11: 1.0178 L22: 0.8756 REMARK 3 L33: 0.9332 L12: 0.1032 REMARK 3 L13: -0.1339 L23: 0.0174 REMARK 3 S TENSOR REMARK 3 S11: 0.0135 S12: -0.0865 S13: 0.1161 REMARK 3 S21: 0.0470 S22: 0.0159 S23: -0.0167 REMARK 3 S31: -0.1928 S32: -0.0222 S33: -0.0293 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL PLUS MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2WYD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-NOV-09. REMARK 100 THE DEPOSITION ID IS D_1290041731. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-APR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM16 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 73345 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 39.130 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 4.240 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.89 REMARK 200 R MERGE FOR SHELL (I) : 0.47000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.630 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: NULL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24% PEG 6000, 100 MM BICINE PH 9.6 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.15650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.15650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 60.38750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 83.18300 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 60.38750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 83.18300 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 47.15650 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 60.38750 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 83.18300 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 47.15650 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 60.38750 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 83.18300 REMARK 290 SMTRY3 8 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -45.1 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 ASP A 1 REMARK 465 MET A 2 REMARK 465 PRO A 3 REMARK 465 ARG A 4 REMARK 465 PRO A 5 REMARK 465 VAL A 170 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 LYS A 169 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE1 GLU A 149 O HOH A 2121 2.02 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 ASN A 42 26.02 -143.37 REMARK 500 ASN A 84 41.08 -102.03 REMARK 500 ARG B 42 -11.88 -145.06 REMARK 500 PRO B 54 42.60 -84.95 REMARK 500 LYS B 137 -59.37 -134.24 REMARK 500 ASN B 141 -155.89 -109.48 REMARK 500 TRP B 186 27.89 -153.39 REMARK 500 ASN B 202 52.98 -94.35 REMARK 500 ASP B 263 -79.11 -95.02 REMARK 500 SER B 480 -95.80 -139.08 REMARK 500 SER B 501 162.98 76.55 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 GOL B 1547 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1170 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1548 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1171 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1549 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1550 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1172 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1551 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DAO B 1552 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DAO B 1553 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2WYC RELATED DB: PDB REMARK 900 THE QUORUM QUENCHING N-ACYL HOMOSERINE LACTONE ACYLASE PVDQ IN REMARK 900 COMPLEX WITH 3-OXO -LAURIC ACID REMARK 900 RELATED ID: 2WYB RELATED DB: PDB REMARK 900 THE QUORUM QUENCHING N-ACYL HOMOSERINE LACTONE ACYLASE PVDQ WITH A REMARK 900 COVALENTLY BOUND DODECANOIC ACID REMARK 900 RELATED ID: 2WYE RELATED DB: PDB REMARK 900 THE QUORUM QUENCHING N-ACYL HOMOSERINE LACTONE ACYLASE PVDQ IS AN REMARK 900 NTN-HYDROLASE WITH AN UNUSUAL SUBSTRATE-BINDING POCKET DBREF 2WYD A 1 170 UNP Q9I194 PVDQ_PSEAE 24 193 DBREF 2WYD B 1 546 UNP Q9I194 PVDQ_PSEAE 217 762 SEQRES 1 A 170 ASP MET PRO ARG PRO THR GLY LEU ALA ALA ASP ILE ARG SEQRES 2 A 170 TRP THR ALA TYR GLY VAL PRO HIS ILE ARG ALA LYS ASP SEQRES 3 A 170 GLU ARG GLY LEU GLY TYR GLY ILE GLY TYR ALA TYR ALA SEQRES 4 A 170 ARG ASP ASN ALA CYS LEU LEU ALA GLU GLU ILE VAL THR SEQRES 5 A 170 ALA ARG GLY GLU ARG ALA ARG TYR PHE GLY SER GLU GLY SEQRES 6 A 170 LYS SER SER ALA GLU LEU ASP ASN LEU PRO SER ASP ILE SEQRES 7 A 170 PHE TYR ALA TRP LEU ASN GLN PRO GLU ALA LEU GLN ALA SEQRES 8 A 170 PHE TRP GLN ALA GLN THR PRO ALA VAL ARG GLN LEU LEU SEQRES 9 A 170 GLU GLY TYR ALA ALA GLY PHE ASN ARG PHE LEU ARG GLU SEQRES 10 A 170 ALA ASP GLY LYS THR THR SER CYS LEU GLY GLN PRO TRP SEQRES 11 A 170 LEU ARG ALA ILE ALA THR ASP ASP LEU LEU ARG LEU THR SEQRES 12 A 170 ARG ARG LEU LEU VAL GLU GLY GLY VAL GLY GLN PHE ALA SEQRES 13 A 170 ASP ALA LEU VAL ALA ALA ALA PRO PRO GLY ALA GLU LYS SEQRES 14 A 170 VAL SEQRES 1 B 546 SER ASN ALA ILE ALA VAL GLY SER GLU ARG SER ALA ASP SEQRES 2 B 546 GLY LYS GLY MET LEU LEU ALA ASN PRO HIS PHE PRO TRP SEQRES 3 B 546 ASN GLY ALA MET ARG PHE TYR GLN MET HIS LEU THR ILE SEQRES 4 B 546 PRO GLY ARG LEU ASP VAL MET GLY ALA SER LEU PRO GLY SEQRES 5 B 546 LEU PRO VAL VAL ASN ILE GLY PHE SER ARG HIS LEU ALA SEQRES 6 B 546 TRP THR HIS THR VAL ASP THR SER SER HIS PHE THR LEU SEQRES 7 B 546 TYR ARG LEU ALA LEU ASP PRO LYS ASP PRO ARG ARG TYR SEQRES 8 B 546 LEU VAL ASP GLY ARG SER LEU PRO LEU GLU GLU LYS SER SEQRES 9 B 546 VAL ALA ILE GLU VAL ARG GLY ALA ASP GLY LYS LEU SER SEQRES 10 B 546 ARG VAL GLU HIS LYS VAL TYR GLN SER ILE TYR GLY PRO SEQRES 11 B 546 LEU VAL VAL TRP PRO GLY LYS LEU ASP TRP ASN ARG SER SEQRES 12 B 546 GLU ALA TYR ALA LEU ARG ASP ALA ASN LEU GLU ASN THR SEQRES 13 B 546 ARG VAL LEU GLN GLN TRP TYR SER ILE ASN GLN ALA SER SEQRES 14 B 546 ASP VAL ALA ASP LEU ARG ARG ARG VAL GLU ALA LEU GLN SEQRES 15 B 546 GLY ILE PRO TRP VAL ASN THR LEU ALA ALA ASP GLU GLN SEQRES 16 B 546 GLY ASN ALA LEU TYR MET ASN GLN SER VAL VAL PRO TYR SEQRES 17 B 546 LEU LYS PRO GLU LEU ILE PRO ALA CYS ALA ILE PRO GLN SEQRES 18 B 546 LEU VAL ALA GLU GLY LEU PRO ALA LEU GLN GLY GLN ASP SEQRES 19 B 546 SER ARG CYS ALA TRP SER ARG ASP PRO ALA ALA ALA GLN SEQRES 20 B 546 ALA GLY ILE THR PRO ALA ALA GLN LEU PRO VAL LEU LEU SEQRES 21 B 546 ARG ARG ASP PHE VAL GLN ASN SER ASN ASP SER ALA TRP SEQRES 22 B 546 LEU THR ASN PRO ALA SER PRO LEU GLN GLY PHE SER PRO SEQRES 23 B 546 LEU VAL SER GLN GLU LYS PRO ILE GLY PRO ARG ALA ARG SEQRES 24 B 546 TYR ALA LEU SER ARG LEU GLN GLY LYS GLN PRO LEU GLU SEQRES 25 B 546 ALA LYS THR LEU GLU GLU MET VAL THR ALA ASN HIS VAL SEQRES 26 B 546 PHE SER ALA ASP GLN VAL LEU PRO ASP LEU LEU ARG LEU SEQRES 27 B 546 CYS ARG ASP ASN GLN GLY GLU LYS SER LEU ALA ARG ALA SEQRES 28 B 546 CYS ALA ALA LEU ALA GLN TRP ASP ARG GLY ALA ASN LEU SEQRES 29 B 546 ASP SER GLY SER GLY PHE VAL TYR PHE GLN ARG PHE MET SEQRES 30 B 546 GLN ARG PHE ALA GLU LEU ASP GLY ALA TRP LYS GLU PRO SEQRES 31 B 546 PHE ASP ALA GLN ARG PRO LEU ASP THR PRO GLN GLY ILE SEQRES 32 B 546 ALA LEU ASP ARG PRO GLN VAL ALA THR GLN VAL ARG GLN SEQRES 33 B 546 ALA LEU ALA ASP ALA ALA ALA GLU VAL GLU LYS SER GLY SEQRES 34 B 546 ILE PRO ASP GLY ALA ARG TRP GLY ASP LEU GLN VAL SER SEQRES 35 B 546 THR ARG GLY GLN GLU ARG ILE ALA ILE PRO GLY GLY ASP SEQRES 36 B 546 GLY HIS PHE GLY VAL TYR ASN ALA ILE GLN SER VAL ARG SEQRES 37 B 546 LYS GLY ASP HIS LEU GLU VAL VAL GLY GLY THR SER TYR SEQRES 38 B 546 ILE GLN LEU VAL THR PHE PRO GLU GLU GLY PRO LYS ALA SEQRES 39 B 546 ARG GLY LEU LEU ALA PHE SER GLN SER SER ASP PRO ARG SEQRES 40 B 546 SER PRO HIS TYR ARG ASP GLN THR GLU LEU PHE SER ARG SEQRES 41 B 546 GLN GLN TRP GLN THR LEU PRO PHE SER ASP ARG GLN ILE SEQRES 42 B 546 ASP ALA ASP PRO GLN LEU GLN ARG LEU SER ILE ARG GLU HET GOL A1170 6 HET GOL A1171 6 HET GOL A1172 6 HET GOL B1547 6 HET GOL B1548 6 HET GOL B1549 6 HET GOL B1550 6 HET GOL B1551 6 HET DAO B1552 14 HET DAO B1553 14 HETNAM GOL GLYCEROL HETNAM DAO LAURIC ACID HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL 8(C3 H8 O3) FORMUL 11 DAO 2(C12 H24 O2) FORMUL 13 HOH *432(H2 O) HELIX 1 1 ALA A 16 GLY A 18 5 3 HELIX 2 2 ASP A 26 ARG A 54 1 29 HELIX 3 3 GLU A 56 GLY A 62 1 7 HELIX 4 4 ASP A 72 ASN A 84 1 13 HELIX 5 5 GLN A 85 ALA A 95 1 11 HELIX 6 6 THR A 97 ALA A 118 1 22 HELIX 7 7 ALA A 135 VAL A 148 1 14 HELIX 8 8 GLU A 149 GLN A 154 5 6 HELIX 9 9 PHE A 155 ALA A 161 1 7 HELIX 10 10 ASN B 27 ARG B 31 5 5 HELIX 11 11 ASN B 152 ASN B 155 5 4 HELIX 12 12 ARG B 157 GLN B 167 1 11 HELIX 13 13 ASP B 170 GLN B 182 1 13 HELIX 14 14 LYS B 210 GLU B 212 5 3 HELIX 15 15 LEU B 213 ALA B 218 1 6 HELIX 16 16 ILE B 219 ALA B 224 1 6 HELIX 17 17 ASP B 234 ALA B 238 5 5 HELIX 18 18 PRO B 252 LEU B 256 5 5 HELIX 19 19 GLY B 295 GLN B 306 1 12 HELIX 20 20 GLU B 312 ALA B 322 1 11 HELIX 21 21 SER B 327 ASP B 341 1 15 HELIX 22 22 LEU B 348 TRP B 358 1 11 HELIX 23 23 SER B 368 ALA B 381 1 14 HELIX 24 24 ARG B 407 SER B 428 1 22 HELIX 25 25 ARG B 435 LEU B 439 1 5 HELIX 26 26 ASP B 455 GLY B 459 5 5 HELIX 27 27 ARG B 512 ARG B 520 1 9 HELIX 28 28 SER B 529 ASP B 536 1 8 SHEET 1 BA10 VAL B 258 ARG B 261 0 SHEET 2 BA10 ALA B 198 MET B 201 -1 O ALA B 198 N ARG B 261 SHEET 3 BA10 VAL B 187 ASP B 193 -1 O THR B 189 N MET B 201 SHEET 4 BA10 LEU B 64 VAL B 70 -1 O ALA B 65 N ALA B 192 SHEET 5 BA10 ILE B 58 PHE B 60 -1 O GLY B 59 N TRP B 66 SHEET 6 BA10 LEU B 43 SER B 49 -1 O MET B 46 N PHE B 60 SHEET 7 BA10 TYR B 33 ILE B 39 -1 O TYR B 33 N SER B 49 SHEET 8 BA10 VAL A 19 ARG A 23 1 O PRO A 20 N HIS B 36 SHEET 9 BA10 LEU A 8 THR A 15 -1 O ASP A 11 N ARG A 23 SHEET 10 BA10 GLN B 540 GLU B 546 -1 O GLN B 540 N TRP A 14 SHEET 1 BB 6 PHE B 264 ASN B 267 0 SHEET 2 BB 6 ASN B 2 VAL B 6 -1 O ALA B 3 N ASN B 267 SHEET 3 BB 6 MET B 17 ASN B 21 -1 O MET B 17 N VAL B 6 SHEET 4 BB 6 TYR B 481 THR B 486 -1 O GLN B 483 N ALA B 20 SHEET 5 BB 6 LYS B 493 LEU B 498 -1 O LYS B 493 N THR B 486 SHEET 6 BB 6 GLN B 524 LEU B 526 -1 O GLN B 524 N GLY B 496 SHEET 1 BC 2 HIS B 23 PRO B 25 0 SHEET 2 BC 2 HIS B 472 THR B 479 1 O GLY B 478 N PHE B 24 SHEET 1 BD 4 GLU B 447 ALA B 450 0 SHEET 2 BD 4 GLN B 440 ARG B 444 -1 O SER B 442 N ILE B 449 SHEET 3 BD 4 HIS B 472 THR B 479 1 O LEU B 473 N VAL B 441 SHEET 4 BD 4 ILE B 464 LYS B 469 -1 O GLN B 465 N VAL B 476 SHEET 1 BE 4 GLU B 447 ALA B 450 0 SHEET 2 BE 4 GLN B 440 ARG B 444 -1 O SER B 442 N ILE B 449 SHEET 3 BE 4 HIS B 472 THR B 479 1 O LEU B 473 N VAL B 441 SHEET 4 BE 4 HIS B 23 PRO B 25 1 O PHE B 24 N GLY B 478 SHEET 1 BF 2 ILE B 464 LYS B 469 0 SHEET 2 BF 2 HIS B 472 THR B 479 -1 O HIS B 472 N LYS B 469 SHEET 1 BG 4 ARG B 96 PRO B 99 0 SHEET 2 BG 4 ASP B 87 VAL B 93 -1 O TYR B 91 N LEU B 98 SHEET 3 BG 4 PHE B 76 ASP B 84 -1 O ALA B 82 N LEU B 92 SHEET 4 BG 4 ALA B 229 GLN B 231 1 O LEU B 230 N ARG B 80 SHEET 1 BH 7 ARG B 96 PRO B 99 0 SHEET 2 BH 7 ASP B 87 VAL B 93 -1 O TYR B 91 N LEU B 98 SHEET 3 BH 7 PHE B 76 ASP B 84 -1 O ALA B 82 N LEU B 92 SHEET 4 BH 7 GLU B 144 ASP B 150 -1 O ALA B 145 N LEU B 81 SHEET 5 BH 7 GLY B 129 VAL B 132 -1 O PRO B 130 N LEU B 148 SHEET 6 BH 7 LEU B 116 SER B 126 -1 O TYR B 124 N LEU B 131 SHEET 7 BH 7 GLU B 101 ARG B 110 -1 O GLU B 101 N GLN B 125 SHEET 1 BI 2 ALA B 229 GLN B 231 0 SHEET 2 BI 2 PHE B 76 ASP B 84 1 O LEU B 78 N LEU B 230 SHEET 1 BJ 2 TRP B 387 GLU B 389 0 SHEET 2 BJ 2 GLN B 401 ILE B 403 -1 O GLN B 401 N GLU B 389 SSBOND 1 CYS A 44 CYS A 125 1555 1555 2.03 SSBOND 2 CYS B 217 CYS B 237 1555 1555 2.05 SSBOND 3 CYS B 339 CYS B 352 1555 1555 2.04 CISPEP 1 THR B 399 PRO B 400 0 -0.22 SITE 1 AC1 5 LEU A 74 PRO B 40 GLY B 41 HIS B 121 SITE 2 AC1 5 HOH B2292 SITE 1 AC2 6 LYS A 25 ASP A 26 GLU A 70 LEU A 71 SITE 2 AC2 6 ASP A 72 ASP A 157 SITE 1 AC3 9 GLU A 49 SER A 68 ALA A 69 ARG A 145 SITE 2 AC3 9 PRO B 25 ASN B 27 GLY B 28 ALA B 29 SITE 3 AC3 9 MET B 30 SITE 1 AC4 5 TRP A 82 LEU A 83 GLN A 85 ARG A 144 SITE 2 AC4 5 HOH B2088 SITE 1 AC5 7 LEU B 43 ASP B 44 ASN B 166 GLN B 167 SITE 2 AC5 7 ALA B 168 HOH B2034 HOH B2120 SITE 1 AC6 7 PHE B 380 ALA B 381 LEU B 383 GLY B 385 SITE 2 AC6 7 ALA B 386 TRP B 387 HOH B2293 SITE 1 AC7 6 TRP A 93 THR A 136 ASP A 137 HOH A2135 SITE 2 AC7 6 HOH A2136 LYS B 427 SITE 1 AC8 6 ARG B 149 ALA B 238 TRP B 239 ARG B 241 SITE 2 AC8 6 ALA B 248 HOH B2294 SITE 1 AC9 11 THR A 143 LEU A 146 SER B 1 PRO B 22 SITE 2 AC9 11 HIS B 23 PHE B 24 THR B 69 VAL B 70 SITE 3 AC9 11 VAL B 158 TRP B 162 HOH B2295 SITE 1 BC1 11 GLU A 149 GLY A 150 GLN A 154 HIS B 23 SITE 2 BC1 11 PHE B 24 PRO B 25 MET B 30 TRP B 186 SITE 3 BC1 11 GLN B 465 GLY B 477 HOH B2296 CRYST1 120.775 166.366 94.313 90.00 90.00 90.00 C 2 2 21 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 0.008280 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006011 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010603 0.00000