HEADER VIRAL PROTEIN 09-DEC-19 6V7U TITLE STRUCTURE OF A PHAGE-ENCODED QUORUM SENSING ANTI-ACTIVATOR, AQS1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: QUORUM SENSING ANTI-ACTIVATOR PROTEIN AQS1; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS VIRUS DMS3; SOURCE 3 ORGANISM_TAXID: 389469; SOURCE 4 GENE: DMS3-3; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693 KEYWDS PROPHAGE PROTEIN, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.SHAH,T.F.MORAES,K.L.MAXWELL REVDAT 3 06-MAR-24 6V7U 1 REMARK REVDAT 2 30-JUN-21 6V7U 1 JRNL REVDAT 1 16-DEC-20 6V7U 0 JRNL AUTH M.SHAH,V.L.TAYLOR,D.BONA,Y.TSAO,S.Y.STANLEY, JRNL AUTH 2 S.M.PIMENTEL-ELARDO,M.MCCALLUM,J.BONDY-DENOMY,P.L.HOWELL, JRNL AUTH 3 J.R.NODWELL,A.R.DAVIDSON,T.F.MORAES,K.L.MAXWELL JRNL TITL A PHAGE-ENCODED ANTI-ACTIVATOR INHIBITS QUORUM SENSING IN JRNL TITL 2 PSEUDOMONAS AERUGINOSA. JRNL REF MOL.CELL V. 81 571 2021 JRNL REFN ISSN 1097-2765 JRNL PMID 33412111 JRNL DOI 10.1016/J.MOLCEL.2020.12.011 REMARK 2 REMARK 2 RESOLUTION. 2.08 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.08 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.25 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.930 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 12960 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.890 REMARK 3 FREE R VALUE TEST SET COUNT : 1191 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 4.1600 - 3.3000 1.00 2574 135 0.1885 0.2411 REMARK 3 2 3.3000 - 2.8800 1.00 2575 127 0.2214 0.2824 REMARK 3 3 2.8800 - 2.6200 1.00 2568 136 0.2203 0.2723 REMARK 3 4 2.6200 - 2.4300 0.99 2595 125 0.2222 0.2876 REMARK 3 5 2.4300 - 2.2900 1.00 2553 132 0.2367 0.2704 REMARK 3 6 2.2900 - 2.1700 0.99 2589 139 0.2419 0.2526 REMARK 3 7 2.1700 - 2.0800 0.99 2537 132 0.2688 0.3054 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.204 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.521 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.13 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.13 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 : 0.006 945 REMARK 3 ANGLE : 0.693 1285 REMARK 3 CHIRALITY : 0.035 152 REMARK 3 PLANARITY : 0.004 165 REMARK 3 DIHEDRAL : 8.132 569 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 2:63) REMARK 3 ORIGIN FOR THE GROUP (A): 3.6564 36.6177 37.7420 REMARK 3 T TENSOR REMARK 3 T11: 0.3464 T22: 0.2896 REMARK 3 T33: 0.0851 T12: 0.0471 REMARK 3 T13: 0.0111 T23: -0.0316 REMARK 3 L TENSOR REMARK 3 L11: 6.8200 L22: 2.3718 REMARK 3 L33: 3.4615 L12: -1.7510 REMARK 3 L13: 2.1888 L23: -0.1836 REMARK 3 S TENSOR REMARK 3 S11: -0.2200 S12: -0.0945 S13: 0.1648 REMARK 3 S21: 0.1808 S22: 0.0639 S23: 0.1469 REMARK 3 S31: -0.4380 S32: -0.3753 S33: 0.1453 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN B AND RESID 4:62) REMARK 3 ORIGIN FOR THE GROUP (A): 0.9458 35.8304 26.9366 REMARK 3 T TENSOR REMARK 3 T11: 0.2396 T22: 0.2879 REMARK 3 T33: 0.0865 T12: 0.0749 REMARK 3 T13: -0.0025 T23: 0.0102 REMARK 3 L TENSOR REMARK 3 L11: 7.1917 L22: 4.3039 REMARK 3 L33: 7.4111 L12: 2.7930 REMARK 3 L13: 2.7493 L23: 0.5694 REMARK 3 S TENSOR REMARK 3 S11: -0.1189 S12: 0.1747 S13: -0.1256 REMARK 3 S21: -0.1215 S22: 0.0358 S23: -0.1356 REMARK 3 S31: -0.1427 S32: 0.1075 S33: 0.0388 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 6V7U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-DEC-19. REMARK 100 THE DEPOSITION ID IS D_1000245784. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUL-16 REMARK 200 TEMPERATURE (KELVIN) : 105 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9796 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : XDS 1.14_3260, XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12983 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.080 REMARK 200 RESOLUTION RANGE LOW (A) : 45.250 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 10.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.8100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.08 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 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: SAD 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 (%): 59.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1M NAH2PO4/K2HPO4, PH 5.6 AND 15% REMARK 280 GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 24.43333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 48.86667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 48.86667 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 24.43333 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: 1800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 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 VAL A 64 REMARK 465 GLY A 65 REMARK 465 GLY A 66 REMARK 465 ASP A 67 REMARK 465 HIS A 68 REMARK 465 GLU A 69 REMARK 465 ALA B 28 REMARK 465 THR B 29 REMARK 465 ASP B 30 REMARK 465 GLU B 31 REMARK 465 SER B 32 REMARK 465 THR B 33 REMARK 465 VAL B 64 REMARK 465 GLY B 65 REMARK 465 GLY B 66 REMARK 465 ASP B 67 REMARK 465 HIS B 68 REMARK 465 GLU B 69 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 LYS B 62 -38.52 -138.20 REMARK 500 REMARK 500 REMARK: NULL DBREF 6V7U A 1 69 UNP A0SML3 A0SML3_9CAUD 1 69 DBREF 6V7U B 1 69 UNP A0SML3 A0SML3_9CAUD 1 69 SEQADV 6V7U ALA A 24 UNP A0SML3 LYS 24 ENGINEERED MUTATION SEQADV 6V7U ALA A 25 UNP A0SML3 GLU 25 ENGINEERED MUTATION SEQADV 6V7U ALA B 24 UNP A0SML3 LYS 24 ENGINEERED MUTATION SEQADV 6V7U ALA B 25 UNP A0SML3 GLU 25 ENGINEERED MUTATION SEQRES 1 A 69 MET THR ASN THR ASP LEU LYS PRO LEU LEU ASP ASN LEU SEQRES 2 A 69 ARG ASN ALA THR GLU PHE TRP ASN LEU VAL ALA ALA ALA SEQRES 3 A 69 SER ALA THR ASP GLU SER THR VAL HIS ASN ARG SER TYR SEQRES 4 A 69 ARG ASP ALA LEU ASP TRP LEU GLU SER ALA ALA LEU ALA SEQRES 5 A 69 LEU GLY ASP ALA LEU ILE ALA GLN ARG LYS ALA VAL GLY SEQRES 6 A 69 GLY ASP HIS GLU SEQRES 1 B 69 MET THR ASN THR ASP LEU LYS PRO LEU LEU ASP ASN LEU SEQRES 2 B 69 ARG ASN ALA THR GLU PHE TRP ASN LEU VAL ALA ALA ALA SEQRES 3 B 69 SER ALA THR ASP GLU SER THR VAL HIS ASN ARG SER TYR SEQRES 4 B 69 ARG ASP ALA LEU ASP TRP LEU GLU SER ALA ALA LEU ALA SEQRES 5 B 69 LEU GLY ASP ALA LEU ILE ALA GLN ARG LYS ALA VAL GLY SEQRES 6 B 69 GLY ASP HIS GLU FORMUL 3 HOH *45(H2 O) HELIX 1 AA1 THR A 2 SER A 27 1 26 HELIX 2 AA2 GLU A 31 LYS A 62 1 32 HELIX 3 AA3 THR B 2 ALA B 26 1 25 HELIX 4 AA4 ASN B 36 ARG B 61 1 26 CRYST1 66.410 66.410 73.300 90.00 90.00 120.00 P 31 2 1 12 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 0.015058 0.008694 0.000000 0.00000 SCALE2 0.000000 0.017387 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013643 0.00000