HEADER CELL INVASION 11-AUG-03 1Q5Z TITLE CRYSTAL STRUCTURE OF THE C-TERMINAL ACTIN BINDING DOMAIN OF SALMONELLA TITLE 2 INVASION PROTEIN A (SIPA) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SIPA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL ACTIN BINDING DOMAIN; COMPND 5 SYNONYM: SIPA; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SALMONELLA TYPHIMURIUM; SOURCE 3 ORGANISM_TAXID: 602; SOURCE 4 GENE: SIPA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-4T-3 KEYWDS CELL INVASION EXPDTA X-RAY DIFFRACTION AUTHOR C.E.STEBBINS,M.LILIC,V.E.GALKIN,A.ORLOVA,M.S.VANLOOCK,E.H.EGELMAN REVDAT 3 14-FEB-24 1Q5Z 1 REMARK REVDAT 2 24-FEB-09 1Q5Z 1 VERSN REVDAT 1 07-OCT-03 1Q5Z 0 JRNL AUTH M.LILIC,V.E.GALKIN,A.ORLOVA,M.S.VANLOOCK,E.H.EGELMAN, JRNL AUTH 2 C.E.STEBBINS JRNL TITL SALMONELLA SIPA POLYMERIZES ACTIN BY STAPLING FILAMENTS WITH JRNL TITL 2 NONGLOBULAR PROTEIN ARMS. JRNL REF SCIENCE V. 301 1918 2003 JRNL REFN ISSN 0036-8075 JRNL PMID 14512630 JRNL DOI 10.1126/SCIENCE.1088433 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 17011 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 836 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.84 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2200 REMARK 3 BIN FREE R VALUE : 0.2600 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 41 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1136 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 220 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.266 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1Q5Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-AUG-03. REMARK 100 THE DEPOSITION ID IS D_1000019958. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-SEP-02 REMARK 200 TEMPERATURE (KELVIN) : 113.15 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X9A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792,0.9794,0.9716 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : X9A REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17011 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL 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) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE, RESOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2M AMMONIUM SULFATE, 1.5% METHYL REMARK 280 -PENTANEDIOL, 0.1M HEPES, PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 28.75000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.95000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.95000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 43.12500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.95000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.95000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 14.37500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.95000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.95000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 43.12500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.95000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.95000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 14.37500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 28.75000 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 GLY A 493 REMARK 465 PRO A 494 REMARK 465 VAL A 495 REMARK 465 ASP A 496 REMARK 465 LYS A 497 REMARK 465 ALA A 498 REMARK 465 GLY A 499 REMARK 465 THR A 500 REMARK 465 THR A 501 REMARK 465 ASP A 502 REMARK 465 ASN A 503 REMARK 465 ASP A 504 REMARK 465 ASN A 505 REMARK 465 SER A 506 REMARK 465 GLN A 507 REMARK 465 THR A 508 REMARK 465 ASP A 509 REMARK 465 LYS A 510 REMARK 465 THR A 511 REMARK 465 GLY A 512 REMARK 465 GLY A 658 REMARK 465 PRO A 659 REMARK 465 ALA A 660 REMARK 465 TYR A 661 REMARK 465 GLU A 662 REMARK 465 SER A 663 REMARK 465 TYR A 664 REMARK 465 LEU A 665 REMARK 465 ASN A 666 REMARK 465 LYS A 667 REMARK 465 PRO A 668 REMARK 465 GLY A 669 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 176 O HOH A 214 1.94 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 514 55.46 -113.15 REMARK 500 ASN A 522 19.53 57.35 REMARK 500 LYS A 635 -127.21 46.69 REMARK 500 REMARK 500 REMARK: NULL DBREF 1Q5Z A 497 669 UNP Q56027 SIPA_SALTY 497 669 SEQRES 1 A 177 GLY PRO VAL ASP LYS ALA GLY THR THR ASP ASN ASP ASN SEQRES 2 A 177 SER GLN THR ASP LYS THR GLY PRO PHE SER GLY LEU LYS SEQRES 3 A 177 PHE LYS GLN ASN SER PHE LEU SER THR VAL PRO SER VAL SEQRES 4 A 177 THR ASN MET HIS SER MET HIS PHE ASP ALA ARG GLU THR SEQRES 5 A 177 PHE LEU GLY VAL ILE ARG LYS ALA LEU GLU PRO ASP THR SEQRES 6 A 177 SER THR PRO PHE PRO VAL ARG ARG ALA PHE ASP GLY LEU SEQRES 7 A 177 ARG ALA GLU ILE LEU PRO ASN ASP THR ILE LYS SER ALA SEQRES 8 A 177 ALA LEU LYS ALA GLN CYS SER ASP ILE ASP LYS HIS PRO SEQRES 9 A 177 GLU LEU LYS ALA LYS MET GLU THR LEU LYS GLU VAL ILE SEQRES 10 A 177 THR HIS HIS PRO GLN LYS GLU LYS LEU ALA GLU ILE ALA SEQRES 11 A 177 LEU GLN PHE ALA ARG GLU ALA GLY LEU THR ARG LEU LYS SEQRES 12 A 177 GLY GLU THR ASP TYR VAL LEU SER ASN VAL LEU ASP GLY SEQRES 13 A 177 LEU ILE GLY ASP GLY SER TRP ARG ALA GLY PRO ALA TYR SEQRES 14 A 177 GLU SER TYR LEU ASN LYS PRO GLY FORMUL 2 HOH *220(H2 O) HELIX 1 1 PHE A 524 VAL A 528 5 5 HELIX 2 2 SER A 530 HIS A 535 1 6 HELIX 3 3 ASP A 540 LEU A 553 1 14 HELIX 4 4 PRO A 560 LEU A 575 1 16 HELIX 5 5 ASP A 578 SER A 590 1 13 HELIX 6 6 ASP A 591 LYS A 594 5 4 HELIX 7 7 HIS A 595 HIS A 611 1 17 HELIX 8 8 GLN A 614 GLY A 630 1 17 HELIX 9 9 LEU A 634 THR A 638 5 5 HELIX 10 10 ASP A 639 ILE A 650 1 12 HELIX 11 11 GLY A 653 ALA A 657 5 5 CRYST1 79.900 79.900 57.500 90.00 90.00 90.00 P 43 21 2 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 0.012516 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012516 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017391 0.00000