HEADER PROTEIN TRANSPORT 25-NOV-11 3UTK TITLE STRUCTURE OF THE PILOTIN OF THE TYPE II SECRETION SYSTEM COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIPOPROTEIN OUTS; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DICKEYA DADANTII; SOURCE 3 ORGANISM_TAXID: 198628; SOURCE 4 STRAIN: 3937; SOURCE 5 GENE: OUTS, DDA3937_02411; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX KEYWDS NESTED (PERPENDICULAR) ALPHA-HELICAL HAIRPINS, PROTEIN TRANSPORT, KEYWDS 2 PILOT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.REHMAN,R.W.PICKERSGILL REVDAT 2 24-JAN-18 3UTK 1 JRNL REVDAT 1 14-DEC-11 3UTK 0 JRNL AUTH S.GU,S.REHMAN,X.WANG,V.E.SHEVCHIK,R.W.PICKERSGILL JRNL TITL STRUCTURE OF THE PILOTIN OF THE TYPE II SECRETION SYSTEM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.3_473) 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 31358 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.890 REMARK 3 FREE R VALUE TEST SET COUNT : 1533 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 46.7812 - 3.5544 1.00 3245 165 0.2119 0.2670 REMARK 3 2 3.5544 - 2.8213 1.00 3114 160 0.1961 0.2445 REMARK 3 3 2.8213 - 2.4647 1.00 3053 174 0.1827 0.2045 REMARK 3 4 2.4647 - 2.2394 0.99 3030 156 0.1789 0.2403 REMARK 3 5 2.2394 - 2.0788 0.99 2975 159 0.1887 0.2518 REMARK 3 6 2.0788 - 1.9563 0.98 2996 157 0.1868 0.2496 REMARK 3 7 1.9563 - 1.8583 0.95 2845 170 0.1906 0.2654 REMARK 3 8 1.8583 - 1.7774 0.96 2863 145 0.1807 0.2556 REMARK 3 9 1.7774 - 1.7090 0.95 2888 129 0.2029 0.2716 REMARK 3 10 1.7090 - 1.6500 0.93 2816 118 0.2379 0.3335 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.83 REMARK 3 K_SOL : 0.37 REMARK 3 B_SOL : 47.19 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.990 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.18050 REMARK 3 B22 (A**2) : -1.91790 REMARK 3 B33 (A**2) : -5.36990 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 : 0.006 1490 REMARK 3 ANGLE : 0.918 2021 REMARK 3 CHIRALITY : 0.057 237 REMARK 3 PLANARITY : 0.004 263 REMARK 3 DIHEDRAL : 12.483 561 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 3UTK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-NOV-11. REMARK 100 THE DEPOSITION ID IS D_1000069191. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0718 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : SILICON MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32440 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 46.780 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 7.800 REMARK 200 R MERGE (I) : 0.20000 REMARK 200 R SYM (I) : 0.20000 REMARK 200 FOR THE DATA SET : 6.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.33600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD 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 (%): 45.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2M AMMONIUM SULFATE, 2% PEG 400, 0.1 M REMARK 280 HEPES PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 24.85000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.36750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.54750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.36750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.85000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.54750 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 MET A 1 REMARK 465 HIS A 2 REMARK 465 VAL A 3 REMARK 465 SER A 4 REMARK 465 SER A 5 REMARK 465 LEU A 6 REMARK 465 LYS A 7 REMARK 465 VAL A 8 REMARK 465 VAL A 9 REMARK 465 LEU A 10 REMARK 465 PHE A 11 REMARK 465 GLY A 12 REMARK 465 VAL A 13 REMARK 465 CYS A 14 REMARK 465 CYS A 15 REMARK 465 LEU A 16 REMARK 465 SER A 17 REMARK 465 LEU A 18 REMARK 465 ALA A 19 REMARK 465 ALA A 20 REMARK 465 CYS A 21 REMARK 465 GLN A 22 REMARK 465 THR A 23 REMARK 465 PRO A 24 REMARK 465 ALA A 25 REMARK 465 PRO A 26 REMARK 465 VAL A 27 REMARK 465 LYS A 28 REMARK 465 ASN A 29 REMARK 465 THR A 30 REMARK 465 ALA A 31 REMARK 465 SER A 32 REMARK 465 ARG A 33 REMARK 465 SER A 34 REMARK 465 ALA A 35 REMARK 465 ALA A 36 REMARK 465 SER A 37 REMARK 465 ARG A 133 REMARK 465 MET B 1 REMARK 465 HIS B 2 REMARK 465 VAL B 3 REMARK 465 SER B 4 REMARK 465 SER B 5 REMARK 465 LEU B 6 REMARK 465 LYS B 7 REMARK 465 VAL B 8 REMARK 465 VAL B 9 REMARK 465 LEU B 10 REMARK 465 PHE B 11 REMARK 465 GLY B 12 REMARK 465 VAL B 13 REMARK 465 CYS B 14 REMARK 465 CYS B 15 REMARK 465 LEU B 16 REMARK 465 SER B 17 REMARK 465 LEU B 18 REMARK 465 ALA B 19 REMARK 465 ALA B 20 REMARK 465 CYS B 21 REMARK 465 GLN B 22 REMARK 465 THR B 23 REMARK 465 PRO B 24 REMARK 465 ALA B 25 REMARK 465 PRO B 26 REMARK 465 VAL B 27 REMARK 465 LYS B 28 REMARK 465 ASN B 29 REMARK 465 THR B 30 REMARK 465 ALA B 31 REMARK 465 SER B 32 REMARK 465 ARG B 33 REMARK 465 SER B 34 REMARK 465 ALA B 35 REMARK 465 ALA B 36 REMARK 465 SER B 37 REMARK 465 ARG B 133 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 SER A 92 37.45 -91.49 REMARK 500 REMARK 500 REMARK: NULL DBREF 3UTK A 1 133 UNP Q01567 OUTS_DICD3 1 133 DBREF 3UTK B 1 133 UNP Q01567 OUTS_DICD3 1 133 SEQRES 1 A 133 MET HIS VAL SER SER LEU LYS VAL VAL LEU PHE GLY VAL SEQRES 2 A 133 CYS CYS LEU SER LEU ALA ALA CYS GLN THR PRO ALA PRO SEQRES 3 A 133 VAL LYS ASN THR ALA SER ARG SER ALA ALA SER VAL PRO SEQRES 4 A 133 ALA ASN GLU GLN ILE SER GLN LEU ALA SER LEU VAL ALA SEQRES 5 A 133 ALA SER LYS TYR LEU ARG VAL GLN CYS GLU ARG SER ASP SEQRES 6 A 133 LEU PRO ASP ASP GLY THR ILE LEU LYS THR ALA VAL ASN SEQRES 7 A 133 VAL ALA VAL GLN LYS GLY TRP ASP THR GLY ARG TYR GLN SEQRES 8 A 133 SER LEU PRO GLN LEU SER GLU ASN LEU TYR GLN GLY LEU SEQRES 9 A 133 LEU LYS ASP GLY THR PRO LYS ALA THR GLN CYS SER SER SEQRES 10 A 133 PHE ASN ARG THR MET THR PRO PHE LEU ASP ALA MET ARG SEQRES 11 A 133 THR VAL ARG SEQRES 1 B 133 MET HIS VAL SER SER LEU LYS VAL VAL LEU PHE GLY VAL SEQRES 2 B 133 CYS CYS LEU SER LEU ALA ALA CYS GLN THR PRO ALA PRO SEQRES 3 B 133 VAL LYS ASN THR ALA SER ARG SER ALA ALA SER VAL PRO SEQRES 4 B 133 ALA ASN GLU GLN ILE SER GLN LEU ALA SER LEU VAL ALA SEQRES 5 B 133 ALA SER LYS TYR LEU ARG VAL GLN CYS GLU ARG SER ASP SEQRES 6 B 133 LEU PRO ASP ASP GLY THR ILE LEU LYS THR ALA VAL ASN SEQRES 7 B 133 VAL ALA VAL GLN LYS GLY TRP ASP THR GLY ARG TYR GLN SEQRES 8 B 133 SER LEU PRO GLN LEU SER GLU ASN LEU TYR GLN GLY LEU SEQRES 9 B 133 LEU LYS ASP GLY THR PRO LYS ALA THR GLN CYS SER SER SEQRES 10 B 133 PHE ASN ARG THR MET THR PRO PHE LEU ASP ALA MET ARG SEQRES 11 B 133 THR VAL ARG FORMUL 3 HOH *195(H2 O) HELIX 1 1 PRO A 39 CYS A 61 1 23 HELIX 2 2 ASP A 68 LYS A 83 1 16 HELIX 3 3 LEU A 93 ASP A 107 1 15 HELIX 4 4 PRO A 110 MET A 122 1 13 HELIX 5 5 MET A 122 VAL A 132 1 11 HELIX 6 6 PRO B 39 CYS B 61 1 23 HELIX 7 7 ASP B 68 LYS B 83 1 16 HELIX 8 8 ASP B 86 TYR B 90 5 5 HELIX 9 9 SER B 92 ASP B 107 1 16 HELIX 10 10 PRO B 110 MET B 122 1 13 HELIX 11 11 MET B 122 ARG B 130 1 9 SSBOND 1 CYS A 61 CYS A 115 1555 1555 2.03 SSBOND 2 CYS B 61 CYS B 115 1555 1555 2.02 CRYST1 49.700 53.095 98.735 90.00 90.00 90.00 P 21 21 21 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 0.020121 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018834 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010128 0.00000