HEADER TOXIN INHIBITOR 13-MAR-12 3VPV TITLE CRYSTAL STRUCTURE OF PSEUDOMONAS AERUGINOSA TSI2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TSE2 SPECIFIC IMMUNITY PROTEIN 2; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 3 ORGANISM_TAXID: 208964; SOURCE 4 STRAIN: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228; SOURCE 5 GENE: PA2703; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: B834(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS TOXIN INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR W.WANG,J.DING,D.C.WANG REVDAT 1 28-MAR-12 3VPV 0 JRNL AUTH W.WANG,J.DING,D.C.WANG JRNL TITL CRYSTAL STRUCTURE OF PSEUDOMONAS AERUGINOSA TSI2 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7_650) 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.080 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 12131 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.850 REMARK 3 FREE R VALUE TEST SET COUNT : 588 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 19.7956 - 2.8553 0.97 2916 154 0.1727 0.1943 REMARK 3 2 2.8553 - 2.2673 0.96 2897 138 0.1901 0.2354 REMARK 3 3 2.2673 - 1.9810 0.96 2911 150 0.1835 0.2133 REMARK 3 4 1.9810 - 1.8000 0.94 2819 146 0.2178 0.2560 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.72 REMARK 3 K_SOL : 0.41 REMARK 3 B_SOL : 71.09 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.310 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.88 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.23 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.44480 REMARK 3 B22 (A**2) : 1.74310 REMARK 3 B33 (A**2) : -1.29830 REMARK 3 B12 (A**2) : 1.31700 REMARK 3 B13 (A**2) : 1.67020 REMARK 3 B23 (A**2) : 1.86560 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 : 0.005 1303 REMARK 3 ANGLE : 0.742 1775 REMARK 3 CHIRALITY : 0.050 197 REMARK 3 PLANARITY : 0.004 244 REMARK 3 DIHEDRAL : 13.816 491 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 3VPV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-MAR-12. REMARK 100 THE RCSB ID CODE IS RCSB095351. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-NOV-11 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BSRF REMARK 200 BEAMLINE : 3W1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12200 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 19.794 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.02200 REMARK 200 R SYM (I) : 0.02200 REMARK 200 FOR THE DATA SET : 36.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.04700 REMARK 200 R SYM FOR SHELL (I) : 0.04700 REMARK 200 FOR SHELL : 16.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX (PHENIX.REFINE: 1.7_650) REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG 3350, 0.1MM SODIUM ACETATE, PH REMARK 280 5.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: 1520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 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 MSE A 1 REMARK 465 MSE B 1 REMARK 465 HIS B 81 REMARK 465 HIS B 82 REMARK 465 HIS B 83 REMARK 465 HIS B 84 REMARK 465 HIS B 85 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 O HOH A 196 O HOH A 213 1.99 REMARK 500 O HOH B 156 O HOH B 162 2.06 REMARK 500 NE2 GLN A 13 O HOH A 199 2.06 REMARK 500 O HOH A 225 O HOH B 178 2.09 REMARK 500 N ASN B 2 O HOH B 185 2.09 REMARK 500 O HOH A 140 O HOH A 192 2.10 REMARK 500 O HOH B 136 O HOH B 182 2.15 REMARK 500 O HOH A 134 O HOH A 218 2.17 REMARK 500 O HOH A 119 O HOH A 129 2.17 REMARK 500 O HOH A 189 O HOH A 198 2.17 REMARK 500 O HOH A 215 O HOH A 219 2.18 REMARK 500 O HOH B 141 O HOH B 159 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 218 O HOH B 172 1655 1.88 REMARK 500 REMARK 500 REMARK: NULL DBREF 3VPV A 1 77 UNP Q9I0D9 Q9I0D9_PSEAE 1 77 DBREF 3VPV B 1 77 UNP Q9I0D9 Q9I0D9_PSEAE 1 77 SEQADV 3VPV LEU A 78 UNP Q9I0D9 EXPRESSION TAG SEQADV 3VPV GLU A 79 UNP Q9I0D9 EXPRESSION TAG SEQADV 3VPV HIS A 80 UNP Q9I0D9 EXPRESSION TAG SEQADV 3VPV HIS A 81 UNP Q9I0D9 EXPRESSION TAG SEQADV 3VPV HIS A 82 UNP Q9I0D9 EXPRESSION TAG SEQADV 3VPV HIS A 83 UNP Q9I0D9 EXPRESSION TAG SEQADV 3VPV HIS A 84 UNP Q9I0D9 EXPRESSION TAG SEQADV 3VPV HIS A 85 UNP Q9I0D9 EXPRESSION TAG SEQADV 3VPV LEU B 78 UNP Q9I0D9 EXPRESSION TAG SEQADV 3VPV GLU B 79 UNP Q9I0D9 EXPRESSION TAG SEQADV 3VPV HIS B 80 UNP Q9I0D9 EXPRESSION TAG SEQADV 3VPV HIS B 81 UNP Q9I0D9 EXPRESSION TAG SEQADV 3VPV HIS B 82 UNP Q9I0D9 EXPRESSION TAG SEQADV 3VPV HIS B 83 UNP Q9I0D9 EXPRESSION TAG SEQADV 3VPV HIS B 84 UNP Q9I0D9 EXPRESSION TAG SEQADV 3VPV HIS B 85 UNP Q9I0D9 EXPRESSION TAG SEQRES 1 A 85 MSE ASN LEU LYS PRO GLN THR LEU MSE VAL ALA ILE GLN SEQRES 2 A 85 CYS VAL ALA ALA ARG THR ARG GLU LEU ASP ALA GLN LEU SEQRES 3 A 85 GLN ASN ASP ASP PRO GLN ASN ALA ALA GLU LEU GLU GLN SEQRES 4 A 85 LEU LEU VAL GLY TYR ASP LEU ALA ALA ASP ASP LEU LYS SEQRES 5 A 85 ASN ALA TYR GLU GLN ALA LEU GLY GLN TYR SER GLY LEU SEQRES 6 A 85 PRO PRO TYR ASP ARG LEU ILE GLU GLU PRO ALA SER LEU SEQRES 7 A 85 GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 85 MSE ASN LEU LYS PRO GLN THR LEU MSE VAL ALA ILE GLN SEQRES 2 B 85 CYS VAL ALA ALA ARG THR ARG GLU LEU ASP ALA GLN LEU SEQRES 3 B 85 GLN ASN ASP ASP PRO GLN ASN ALA ALA GLU LEU GLU GLN SEQRES 4 B 85 LEU LEU VAL GLY TYR ASP LEU ALA ALA ASP ASP LEU LYS SEQRES 5 B 85 ASN ALA TYR GLU GLN ALA LEU GLY GLN TYR SER GLY LEU SEQRES 6 B 85 PRO PRO TYR ASP ARG LEU ILE GLU GLU PRO ALA SER LEU SEQRES 7 B 85 GLU HIS HIS HIS HIS HIS HIS MODRES 3VPV MSE A 9 MET SELENOMETHIONINE MODRES 3VPV MSE B 9 MET SELENOMETHIONINE HET MSE A 9 8 HET MSE B 9 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 3 HOH *218(H2 O) HELIX 1 1 LYS A 4 GLN A 27 1 24 HELIX 2 2 ASN A 33 ALA A 58 1 26 HELIX 3 3 PRO A 67 ILE A 72 1 6 HELIX 4 4 GLU A 74 GLU A 79 5 6 HELIX 5 5 LYS B 4 ALA B 24 1 21 HELIX 6 6 GLN B 25 ASP B 29 5 5 HELIX 7 7 ASP B 30 GLY B 60 1 31 HELIX 8 8 PRO B 67 GLU B 73 1 7 HELIX 9 9 PRO B 75 GLU B 79 5 5 LINK C LEU A 8 N MSE A 9 1555 1555 1.33 LINK C MSE A 9 N VAL A 10 1555 1555 1.33 LINK C LEU B 8 N MSE B 9 1555 1555 1.33 LINK C MSE B 9 N VAL B 10 1555 1555 1.33 CRYST1 28.380 34.920 38.490 110.37 95.98 95.61 P 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 0.035236 0.003461 0.005303 0.00000 SCALE2 0.000000 0.028775 0.011173 0.00000 SCALE3 0.000000 0.000000 0.028023 0.00000