HEADER IMMUNE SYSTEM 26-APR-16 5JKP TITLE CRYSTAL STRUCTURE OF IMMUNITY PROTEIN PA5087 FROM PSEUDOMONAS TITLE 2 AERUGINOSA COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA PAO1; SOURCE 3 ORGANISM_TAXID: 208964; SOURCE 4 STRAIN: PAO1; SOURCE 5 GENE: PA5087; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX KEYWDS IMMUNITY PROTEIN, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR Z.Q.LI,Z.Q.GAO,Z.SHE,Y.H.DONG REVDAT 2 08-NOV-23 5JKP 1 JRNL REMARK REVDAT 1 31-AUG-16 5JKP 0 JRNL AUTH X.Y.YANG,Z.Q.LI,Z.SHE,Z.GENG,J.H.XU,Z.Q.GAO,Y.H.DONG JRNL TITL STRUCTURAL ANALYSIS OF PSEUDOMONAS AERUGINOSA H3-T6SS JRNL TITL 2 IMMUNITY PROTEINS JRNL REF FEBS LETT. V. 590 2787 2016 JRNL REFN ISSN 0014-5793 JRNL PMID 27397502 JRNL DOI 10.1002/1873-3468.12291 REMARK 2 REMARK 2 RESOLUTION. 2.11 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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) : 2.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 16056 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 804 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 27.4973 - 3.8246 1.00 2688 127 0.1669 0.1984 REMARK 3 2 3.8246 - 3.0370 1.00 2556 128 0.2004 0.2412 REMARK 3 3 3.0370 - 2.6534 1.00 2507 135 0.2261 0.2801 REMARK 3 4 2.6534 - 2.4110 1.00 2511 152 0.2144 0.2722 REMARK 3 5 2.4110 - 2.2383 1.00 2494 128 0.2297 0.2498 REMARK 3 6 2.2383 - 2.1063 1.00 2496 134 0.2095 0.2653 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.260 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 : 0.003 2161 REMARK 3 ANGLE : 0.670 2946 REMARK 3 CHIRALITY : 0.044 298 REMARK 3 PLANARITY : 0.006 385 REMARK 3 DIHEDRAL : 12.018 1288 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 19.1207 -10.4724 74.4852 REMARK 3 T TENSOR REMARK 3 T11: 0.1698 T22: 0.2392 REMARK 3 T33: 0.2102 T12: 0.0218 REMARK 3 T13: 0.0105 T23: -0.0149 REMARK 3 L TENSOR REMARK 3 L11: 0.6875 L22: 1.7399 REMARK 3 L33: 0.7219 L12: 0.6517 REMARK 3 L13: -0.3078 L23: -0.6374 REMARK 3 S TENSOR REMARK 3 S11: 0.0046 S12: -0.0314 S13: 0.0370 REMARK 3 S21: 0.0132 S22: -0.0246 S23: 0.0399 REMARK 3 S31: 0.0125 S32: -0.0027 S33: 0.0014 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 5JKP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-APR-16. REMARK 100 THE DEPOSITION ID IS D_1000220717. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9778 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16110 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.5600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 0.48000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.220 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: 5JJO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M CALCIUM ACETATE, 0.1M MES, 15% REMARK 280 PEG400, PH 6.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 29.00750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.36000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.34300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.36000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.00750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.34300 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 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 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 SER A 24 REMARK 465 LYS A 25 REMARK 465 LYS A 290 REMARK 465 PRO A 291 REMARK 465 GLY A 292 REMARK 465 GLN A 293 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 TRP A 92 111.37 -165.37 REMARK 500 PRO A 93 -92.36 0.32 REMARK 500 GLU A 97 -9.84 171.54 REMARK 500 LYS A 98 111.92 34.84 REMARK 500 GLU A 168 78.25 -108.72 REMARK 500 ASP A 283 115.30 -167.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5JJO RELATED DB: PDB DBREF 5JKP A 24 293 UNP Q9HU96 Q9HU96_PSEAE 20 289 SEQRES 1 A 270 SER LYS PRO PHE VAL CYS ALA ASN GLU LYS ASP HIS LEU SEQRES 2 A 270 PRO PRO LEU ASP PRO GLN ALA ASP ALA TRP TYR ARG GLU SEQRES 3 A 270 ALA ALA ALA LEU ALA LYS PRO ASP THR LEU ARG PRO TRP SEQRES 4 A 270 GLY ARG ILE VAL GLU ILE TYR SER LYS ALA VAL GLU ARG SEQRES 5 A 270 GLY HIS TRP LYS ALA MET HIS ASN LEU ALA ASN LEU TYR SEQRES 6 A 270 ARG THR GLY TRP PRO GLY GLY VAL GLU LYS ASP PRO GLN SEQRES 7 A 270 LYS ALA LEU ASP LEU TYR GLN LYS MET ILE ASP LEU ASP SEQRES 8 A 270 VAL PRO GLN GLY PHE TYR ASP MET GLY ALA MET ILE GLY SEQRES 9 A 270 ASN ARG ALA GLY VAL LYS ASN PRO ALA THR ASP GLY LEU SEQRES 10 A 270 THR PHE LEU ASP LYS ALA ALA SER LEU GLY ASN PRO PRO SEQRES 11 A 270 ALA LEU THR GLU LEU GLY LYS LEU TYR ILE TYR VAL ALA SEQRES 12 A 270 LYS GLU LYS GLU LEU GLY LEU ALA TYR ALA SER CYS ALA SEQRES 13 A 270 SER SER GLN GLY TYR ALA PRO ALA SER TYR GLU LEU GLY SEQRES 14 A 270 SER TYR TYR GLU LEU VAL GLU ASN ASN TYR PRO LYS ALA SEQRES 15 A 270 LEU SER TYR TYR GLN VAL SER VAL SER GLN GLY GLY ARG SEQRES 16 A 270 SER ALA ALA PHE PHE LEU SER ARG VAL PHE GLY LYS ARG SEQRES 17 A 270 THR PRO PRO SER SER ALA MET TRP TYR THR PRO ASP GLU SEQRES 18 A 270 LYS LEU GLU LYS PHE TYR TYR SER LEU TYR LEU GLN ILE SEQRES 19 A 270 ASP ALA ASP PRO ASP LEU ARG PHE PRO ASN LEU VAL LYS SEQRES 20 A 270 TYR ASN PRO LEU PRO PRO HIS PRO VAL GLN GLY TYR ASP SEQRES 21 A 270 ALA ALA ARG PRO ASP TRP LYS PRO GLY GLN FORMUL 2 HOH *135(H2 O) HELIX 1 AA1 ASN A 31 LEU A 36 5 6 HELIX 2 AA2 ASP A 40 ALA A 54 1 15 HELIX 3 AA3 PRO A 61 ARG A 75 1 15 HELIX 4 AA4 HIS A 77 THR A 90 1 14 HELIX 5 AA5 ASP A 99 LEU A 113 1 15 HELIX 6 AA6 VAL A 115 GLY A 127 1 13 HELIX 7 AA7 ASN A 128 VAL A 132 5 5 HELIX 8 AA8 ASN A 134 ASP A 138 5 5 HELIX 9 AA9 THR A 141 LEU A 149 1 9 HELIX 10 AB1 ASN A 151 VAL A 165 1 15 HELIX 11 AB2 GLU A 168 GLN A 182 1 15 HELIX 12 AB3 TYR A 184 VAL A 198 1 15 HELIX 13 AB4 ASN A 201 GLN A 215 1 15 HELIX 14 AB5 GLY A 217 PHE A 228 1 12 HELIX 15 AB6 ASP A 243 ASP A 260 1 18 HELIX 16 AB7 ASN A 267 ASN A 272 1 6 SSBOND 1 CYS A 29 CYS A 178 1555 1555 2.03 CISPEP 1 VAL A 96 GLU A 97 0 -18.99 CRYST1 58.015 58.686 78.720 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 0.017237 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017040 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012703 0.00000