HEADER CELL INVASION 24-JUL-15 5CUK TITLE CRYSTAL STRUCTURE OF THE PSCP SS DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: RULER PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TRANSLOCATION PROTEIN IN TYPE III SECRETION; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA (STRAIN ATCC 15692 / SOURCE 3 PAO1 / 1C / PRS 101 / LMG 12228); SOURCE 4 ORGANISM_TAXID: 208964; SOURCE 5 STRAIN: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228; SOURCE 6 GENE: PSCP, PA1695; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MOLECULAR RULER SECRETION SYSTEM, CELL INVASION EXPDTA X-RAY DIFFRACTION AUTHOR J.R.C.BERGERON,N.C.J.STRYNADKA REVDAT 3 06-MAR-24 5CUK 1 JRNL REMARK REVDAT 2 03-FEB-16 5CUK 1 JRNL REVDAT 1 02-DEC-15 5CUK 0 JRNL AUTH J.R.BERGERON,L.FERNANDEZ,G.A.WASNEY,M.VUCKOVIC, JRNL AUTH 2 F.REFFUVEILLE,R.E.HANCOCK,N.C.STRYNADKA JRNL TITL THE STRUCTURE OF A TYPE 3 SECRETION SYSTEM (T3SS) RULER JRNL TITL 2 PROTEIN SUGGESTS A MOLECULAR MECHANISM FOR NEEDLE LENGTH JRNL TITL 3 SENSING. JRNL REF J.BIOL.CHEM. V. 291 1676 2016 JRNL REFN ESSN 1083-351X JRNL PMID 26589798 JRNL DOI 10.1074/JBC.M115.684423 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 3 NUMBER OF REFLECTIONS : 6154 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.680 REMARK 3 FREE R VALUE TEST SET COUNT : 288 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 2.6461 - 2.1003 0.93 2886 141 0.2475 0.2961 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.130 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 : 0.012 750 REMARK 3 ANGLE : 1.693 1016 REMARK 3 CHIRALITY : 0.076 118 REMARK 3 PLANARITY : 0.007 137 REMARK 3 DIHEDRAL : 19.458 291 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 5CUK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000212212. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-DEC-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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) : 0.97949 REMARK 200 MONOCHROMATOR : NULL 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 : 6182 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 39.207 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.2000 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) : 2.17 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.57600 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CITRIC ACID, 20% PEG 60000, PH REMARK 280 5.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 51.57000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.24000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 51.57000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.24000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 KCAL/MOL 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 250 REMARK 465 SER A 251 REMARK 465 HIS A 252 REMARK 465 MET A 253 REMARK 465 GLY A 254 REMARK 465 SER A 255 REMARK 465 GLN A 350 REMARK 465 ASP A 351 REMARK 465 SER A 352 REMARK 465 GLY A 353 REMARK 465 GLN A 354 REMARK 465 ARG A 355 REMARK 465 SER A 356 REMARK 465 ARG A 357 REMARK 465 GLN A 358 REMARK 465 ARG A 359 REMARK 465 ARG A 360 REMARK 465 TYR A 361 REMARK 465 LEU A 362 REMARK 465 HIS A 363 REMARK 465 GLU A 364 REMARK 465 GLU A 365 REMARK 465 TRP A 366 REMARK 465 GLN A 367 REMARK 465 ALA A 368 REMARK 465 GLU A 369 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 NE ARG A 273 O HOH A 501 1.80 REMARK 500 NH1 ARG A 286 O HOH A 502 2.05 REMARK 500 OE1 GLU A 311 O HOH A 503 2.07 REMARK 500 OE2 GLU A 331 NH2 ARG A 335 2.07 REMARK 500 NH1 ARG A 326 O HOH A 504 2.12 REMARK 500 O HOH A 530 O HOH A 532 2.12 REMARK 500 O GLY A 304 O HOH A 505 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 256 CA - CB - CG ANGL. DEV. = -13.9 DEGREES REMARK 500 PRO A 257 C - N - CA ANGL. DEV. = 10.1 DEGREES 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 ALA A 279 52.27 -98.30 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5CUL RELATED DB: PDB DBREF 5CUK A 254 369 UNP Q9I332 Q9I332_PSEAE 254 369 SEQADV 5CUK GLY A 250 UNP Q9I332 EXPRESSION TAG SEQADV 5CUK SER A 251 UNP Q9I332 EXPRESSION TAG SEQADV 5CUK HIS A 252 UNP Q9I332 EXPRESSION TAG SEQADV 5CUK MET A 253 UNP Q9I332 EXPRESSION TAG SEQRES 1 A 120 GLY SER HIS MET GLY SER ARG PRO LEU PRO LEU ALA ASP SEQRES 2 A 120 LEU ALA ARG LEU LEU ASP ALA VAL GLN GLY ARG ILE GLN SEQRES 3 A 120 VAL ALA SER ALA ALA GLU SER HIS ALA ALA ARG LEU GLN SEQRES 4 A 120 VAL ARG LEU PRO GLN LEU GLY ALA VAL GLU VAL GLN VAL SEQRES 5 A 120 LEU HIS GLY HIS GLY GLN LEU GLN ILE GLU ILE SER ALA SEQRES 6 A 120 SER PRO GLY SER LEU ALA LEU LEU GLN GLN ALA ARG GLY SEQRES 7 A 120 GLU LEU LEU GLU ARG LEU GLN ARG LEU HIS PRO GLU GLN SEQRES 8 A 120 PRO VAL GLN LEU THR PHE ASN GLN GLN GLN ASP SER GLY SEQRES 9 A 120 GLN ARG SER ARG GLN ARG ARG TYR LEU HIS GLU GLU TRP SEQRES 10 A 120 GLN ALA GLU HET GOL A 401 6 HET GOL A 402 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 2(C3 H8 O3) FORMUL 4 HOH *33(H2 O) HELIX 1 AA1 PRO A 259 ALA A 279 1 21 HELIX 2 AA2 SER A 315 ALA A 325 1 11 HELIX 3 AA3 ALA A 325 HIS A 337 1 13 SHEET 1 AA1 4 ALA A 284 LEU A 291 0 SHEET 2 AA1 4 GLY A 295 HIS A 303 -1 O GLY A 295 N LEU A 291 SHEET 3 AA1 4 LEU A 308 ALA A 314 -1 O GLU A 311 N GLN A 300 SHEET 4 AA1 4 VAL A 342 GLN A 348 1 O GLN A 343 N ILE A 310 SITE 1 AC1 4 GLN A 323 ARG A 326 THR A 345 PHE A 346 SITE 1 AC2 5 ILE A 274 SER A 278 HIS A 303 HIS A 337 SITE 2 AC2 5 GLN A 340 CRYST1 103.140 42.480 25.860 90.00 99.07 90.00 C 1 2 1 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 0.009696 0.000000 0.001548 0.00000 SCALE2 0.000000 0.023540 0.000000 0.00000 SCALE3 0.000000 0.000000 0.039159 0.00000