HEADER CELL INVASION 09-JUL-12 4G08 TITLE CRYSTAL STRUCTURE OF THE PERIPLASMIC DOMAIN OF INVG COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN INVG; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 22-179; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR SOURCE 3 TYPHIMURIUM; SOURCE 4 ORGANISM_COMMON: SALMONELLA TYPHIMURIUM; SOURCE 5 ORGANISM_TAXID: 90371; SOURCE 6 GENE: INVG, STM2898; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS RING-BUILDING MOTIF, PROTEIN SECRETION, PRGH, CELL INVASION EXPDTA X-RAY DIFFRACTION AUTHOR J.R.C.BERGERON,N.C.J.STRYNADKA REVDAT 4 28-FEB-24 4G08 1 SEQADV REVDAT 3 17-JUL-19 4G08 1 REMARK REVDAT 2 22-MAY-13 4G08 1 JRNL REVDAT 1 08-MAY-13 4G08 0 JRNL AUTH J.R.BERGERON,L.J.WORRALL,N.G.SGOURAKIS,F.DIMAIO, JRNL AUTH 2 R.A.PFUETZNER,H.B.FELISE,M.VUCKOVIC,A.C.YU,S.I.MILLER, JRNL AUTH 3 D.BAKER,N.C.STRYNADKA JRNL TITL A REFINED MODEL OF THE PROTOTYPICAL SALMONELLA SPI-1 T3SS JRNL TITL 2 BASAL BODY REVEALS THE MOLECULAR BASIS FOR ITS ASSEMBLY. JRNL REF PLOS PATHOG. V. 9 03307 2013 JRNL REFN ISSN 1553-7366 JRNL PMID 23633951 JRNL DOI 10.1371/JOURNAL.PPAT.1003307 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.1_1168 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.09 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 11516 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.750 REMARK 3 FREE R VALUE TEST SET COUNT : 547 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 45.0997 - 2.8590 0.99 2876 129 0.1772 0.2114 REMARK 3 2 2.8590 - 2.2693 1.00 2754 139 0.2069 0.2449 REMARK 3 3 2.2693 - 1.9825 0.99 2709 132 0.1975 0.2387 REMARK 3 4 1.9825 - 1.8010 0.98 2630 147 0.2124 0.2673 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.370 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.56 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.91000 REMARK 3 B22 (A**2) : 0.64000 REMARK 3 B33 (A**2) : 0.27000 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 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 : 0.010 1175 REMARK 3 ANGLE : 1.051 1590 REMARK 3 CHIRALITY : 0.067 170 REMARK 3 PLANARITY : 0.021 208 REMARK 3 DIHEDRAL : 15.763 450 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: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 3 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4G08 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JUL-12. REMARK 100 THE DEPOSITION ID IS D_1000073573. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-DEC-10 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08B1-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978170, 0.979310, 0.979100 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11517 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 99.3 REMARK 200 DATA REDUNDANCY : 7.800 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.7000 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 (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : 0.25600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 26.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS, PH 8.0, 30% JEFFAMINE M REMARK 280 -600, 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 14.13500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.22000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.33000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.22000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 14.13500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.33000 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 300 REMARK: THOUGH THE CLONED PROTEIN CONSTRUCT THAT WAS CRYSTALLIZED REMARK 300 IS A MONOMER, THE FULL-LENGTH VERSION OF THIS PROTEIN FORMS A 15- REMARK 300 MER. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 GLY A 20 REMARK 465 SER A 21 REMARK 465 GLY A 22 REMARK 465 TYR A 23 REMARK 465 SER A 24 REMARK 465 SER A 25 REMARK 465 GLU A 26 REMARK 465 LYS A 27 REMARK 465 ILE A 28 REMARK 465 PRO A 29 REMARK 465 VAL A 30 REMARK 465 THR A 31 REMARK 465 GLY A 32 REMARK 465 SER A 33 REMARK 465 GLU A 174 REMARK 465 LEU A 175 REMARK 465 GLY A 176 REMARK 465 ARG A 177 REMARK 465 GLN A 178 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 THR A 146 CG2 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 293 O HOH A 298 1.82 REMARK 500 NH2 ARG A 128 O HOH A 289 1.86 REMARK 500 O HOH A 279 O HOH A 291 1.87 REMARK 500 NH1 ARG A 43 O HOH A 206 2.17 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 PHE A 35 119.01 -168.16 REMARK 500 PHE A 74 44.54 -109.01 REMARK 500 ASP A 76 81.55 -160.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 108 0.08 SIDE CHAIN REMARK 500 GLN A 169 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3J1V RELATED DB: PDB REMARK 900 RELATED ID: 4G1I RELATED DB: PDB REMARK 900 RELATED ID: 4G2S RELATED DB: PDB DBREF 4G08 A 22 178 UNP P35672 INVG_SALTY 22 178 SEQADV 4G08 GLY A 20 UNP P35672 EXPRESSION TAG SEQADV 4G08 SER A 21 UNP P35672 EXPRESSION TAG SEQRES 1 A 159 GLY SER GLY TYR SER SER GLU LYS ILE PRO VAL THR GLY SEQRES 2 A 159 SER GLY PHE VAL ALA LYS ASP ASP SER LEU ARG THR PHE SEQRES 3 A 159 PHE ASP ALA MET ALA LEU GLN LEU LYS GLU PRO VAL ILE SEQRES 4 A 159 VAL SER LYS MET ALA ALA ARG LYS LYS ILE THR GLY ASN SEQRES 5 A 159 PHE GLU PHE HIS ASP PRO ASN ALA LEU LEU GLU LYS LEU SEQRES 6 A 159 SER LEU GLN LEU GLY LEU ILE TRP TYR PHE ASP GLY GLN SEQRES 7 A 159 ALA ILE TYR ILE TYR ASP ALA SER GLU MET ARG ASN ALA SEQRES 8 A 159 VAL VAL SER LEU ARG ASN VAL SER LEU ASN GLU PHE ASN SEQRES 9 A 159 ASN PHE LEU LYS ARG SER GLY LEU TYR ASN LYS ASN TYR SEQRES 10 A 159 PRO LEU ARG GLY ASP ASN ARG LYS GLY THR PHE TYR VAL SEQRES 11 A 159 SER GLY PRO PRO VAL TYR VAL ASP MET VAL VAL ASN ALA SEQRES 12 A 159 ALA THR MET MET ASP LYS GLN ASN ASP GLY ILE GLU LEU SEQRES 13 A 159 GLY ARG GLN FORMUL 2 HOH *112(H2 O) HELIX 1 1 LEU A 42 ALA A 50 1 9 HELIX 2 2 LEU A 51 LEU A 53 5 3 HELIX 3 3 SER A 60 ARG A 65 1 6 HELIX 4 4 ASP A 76 GLY A 89 1 14 HELIX 5 5 SER A 105 MET A 107 5 3 HELIX 6 6 SER A 118 SER A 129 1 12 HELIX 7 7 PRO A 152 ASN A 170 1 19 SHEET 1 A 2 PHE A 35 SER A 41 0 SHEET 2 A 2 LYS A 67 PHE A 72 -1 O GLY A 70 N ALA A 37 SHEET 1 B 3 VAL A 57 VAL A 59 0 SHEET 2 B 3 ILE A 99 ASP A 103 1 O ILE A 99 N ILE A 58 SHEET 3 B 3 LEU A 90 PHE A 94 -1 N TYR A 93 O TYR A 100 SHEET 1 C 2 ARG A 108 SER A 113 0 SHEET 2 C 2 THR A 146 GLY A 151 -1 O VAL A 149 N ALA A 110 CRYST1 28.270 56.660 74.440 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 0.035373 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017649 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013434 0.00000