HEADER MEMBRANE PROTEIN 07-APR-08 3CRE TITLE ELECTRON MICROSCOPY MODEL OF THE SAF PILUS- TYPE A COMPND MOL_ID: 1; COMPND 2 MOLECULE: OUTER MEMBRANE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CORE PILIN DOMAIN, N-TERMINAL DELETED, UNP RESIDUES 48-170; COMPND 5 SYNONYM: SAFA PILUS SUBUNIT; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: OUTER MEMBRANE PROTEIN; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: CORE PILIN DOMAIN, UNP RESIDUES 27-170; COMPND 11 SYNONYM: SAFA PILUS SUBUNIT; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: OUTER MEMBRANE PROTEIN; COMPND 15 CHAIN: C; COMPND 16 FRAGMENT: N-TERMINAL EXTENSION, UNP RESIDUES 27-45; COMPND 17 SYNONYM: SAFA N-TERMINAL EXTENSION; COMPND 18 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SALMONELLA TYPHIMURIUM; SOURCE 3 STRAIN: LT2; SOURCE 4 GENE: SAFA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: C600; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PTRC99A; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: SALMONELLA TYPHIMURIUM; SOURCE 11 STRAIN: LT2; SOURCE 12 GENE: SAFA; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_STRAIN: C600; SOURCE 15 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 16 EXPRESSION_SYSTEM_PLASMID: PTRC99A; SOURCE 17 MOL_ID: 3; SOURCE 18 SYNTHETIC: YES; SOURCE 19 OTHER_DETAILS: SAFANTE - N-TERMINAL EXTENSION KEYWDS SAFA PROTEIN POLYMER, TYPE A SAF PILUS, FIBRIL PROTEIN, MEMBRANE KEYWDS 2 PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR O.SALIH,H.REMAUT,G.WAKSMAN,E.V.ORLOVA REVDAT 4 21-FEB-24 3CRE 1 REMARK REVDAT 3 18-JUL-18 3CRE 1 REMARK REVDAT 2 24-FEB-09 3CRE 1 VERSN REVDAT 1 20-MAY-08 3CRE 0 JRNL AUTH O.SALIH,H.REMAUT,G.WAKSMAN,E.V.ORLOVA JRNL TITL STRUCTURAL ANALYSIS OF THE SAF PILUS BY ELECTRON MICROSCOPY JRNL TITL 2 AND IMAGE PROCESSING. JRNL REF J.MOL.BIOL. V. 379 174 2008 JRNL REFN ISSN 0022-2836 JRNL PMID 18448124 JRNL DOI 10.1016/J.JMB.2008.03.056 REMARK 2 REMARK 2 RESOLUTION. 17.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : URO, IMAGIC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 2CO4 REMARK 3 REFINEMENT SPACE : RECIPROCAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT REMARK 3 REFINEMENT TARGET : CORRELATION COEFFICIENT REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : REFINEMENT PROTOCOL--RIGID BODY REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 17.00 REMARK 3 NUMBER OF PARTICLES : 5000 REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 3CRE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-APR-08. REMARK 100 THE DEPOSITION ID IS D_1000047121. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : HELICAL REMARK 245 SPECIMEN TYPE : NEGATIVE STAIN REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : FILAMENT REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : WILD-TYPE SAFA PILI REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.00 REMARK 245 SAMPLE SUPPORT DETAILS : CONTINUOUS-CARBON FILM REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : 10 MM TRIS-HCL (PH 8) AND 10 MM REMARK 245 NACL REMARK 245 PH : 8.00 REMARK 245 SAMPLE DETAILS : STAINED WITH 2% AMMONIUM REMARK 245 MOLYBDATE. TYPE A SAF PILUS. FIBRE. REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 23-APR-04 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TECNAI 10 REMARK 245 DETECTOR TYPE : KODAK SO-163 FILM REMARK 245 MINIMUM DEFOCUS (NM) : 400.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 900.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.40 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 2500.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 44000 REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : TUNGSTEN HAIRPIN REMARK 245 ACCELERATION VOLTAGE (KV) : 100 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 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 CB ALA B 130 OG SER C 19 1.67 REMARK 500 NZ LYS A 79 OD1 ASP B 14 2.19 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 60 NE - CZ - NH1 ANGL. DEV. = 7.1 DEGREES REMARK 500 ARG A 75 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 95 NE - CZ - NH2 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 96 NE - CZ - NH2 ANGL. DEV. = 3.6 DEGREES REMARK 500 MET A 109 CG - SD - CE ANGL. DEV. = 9.9 DEGREES REMARK 500 ASP A 115 CB - CG - OD1 ANGL. DEV. = 8.9 DEGREES REMARK 500 ASP A 131 N - CA - CB ANGL. DEV. = -11.3 DEGREES REMARK 500 ARG B 60 NE - CZ - NH1 ANGL. DEV. = 6.6 DEGREES REMARK 500 ARG B 75 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 ARG B 95 NE - CZ - NH2 ANGL. DEV. = 4.9 DEGREES REMARK 500 TRP B 103 CE2 - CD2 - CG ANGL. DEV. = -4.9 DEGREES REMARK 500 TRP B 108 CE2 - CD2 - CG ANGL. DEV. = -5.1 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 PRO A 124 -172.15 -66.05 REMARK 500 ALA A 125 77.45 -51.29 REMARK 500 THR A 129 53.36 -60.13 REMARK 500 SER B 18 76.43 -61.23 REMARK 500 ASP B 22 -152.87 -144.93 REMARK 500 SER B 51 -160.94 -173.01 REMARK 500 THR B 52 62.60 -64.23 REMARK 500 LYS B 55 -83.77 -94.21 REMARK 500 THR B 72 40.53 71.85 REMARK 500 SER B 97 150.19 -43.20 REMARK 500 LYS B 102 63.42 -119.87 REMARK 500 TRP B 103 106.07 -40.09 REMARK 500 SER B 113 56.59 -66.09 REMARK 500 ASN B 114 66.90 -152.84 REMARK 500 PRO B 124 159.68 -45.05 REMARK 500 SER C 2 -174.32 179.97 REMARK 500 ASN C 6 -37.23 -36.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ALA B 39 PRO B 40 147.06 REMARK 500 GLY B 123 PRO B 124 112.31 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 60 0.10 SIDE CHAIN REMARK 500 ARG A 95 0.09 SIDE CHAIN REMARK 500 PHE B 57 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-1494 RELATED DB: EMDB REMARK 900 STRUCTURAL ANALYSIS OF THE SAF PILUS BY ELECTRON MICROSCOPY AND REMARK 900 IMAGE PROCESSING - 3D RECONSTRUCTION OF THE TYPE A SAF PILUS, ONE REMARK 900 OF TWO CONFORMATIONS OF THE PILUS REFINED REMARK 900 RELATED ID: EMD-1495 RELATED DB: EMDB REMARK 900 STRUCTURAL ANALYSIS OF THE SAF PILUS BY ELECTRON MICROSCOPY AND REMARK 900 IMAGE PROCESSING - 3D RECONSTRUCTION OF THE TYPE B SAF PILUS, ONE REMARK 900 OF TWO CONFORMATIONS OF THE PILUS REFINED REMARK 900 RELATED ID: 2CO4 RELATED DB: PDB REMARK 900 SALMONELLA ENTERICA SAFA PILIN IN COMPLEX WITH A 19-RESIDUE SAFA REMARK 900 NTE PEPTIDE REMARK 900 RELATED ID: 3CRF RELATED DB: PDB REMARK 900 ELECTRON MICROSCOPY MODEL OF THE SAF PILUS - TYPE B DBREF 3CRE A 22 144 UNP Q8ZRK4 Q8ZRK4_SALTY 48 170 DBREF 3CRE B 1 144 UNP Q8ZRK4 Q8ZRK4_SALTY 27 170 DBREF 3CRE C 1 19 UNP Q8ZRK4 Q8ZRK4_SALTY 27 45 SEQRES 1 A 123 ASP LEU THR VAL SER LEU ILE PRO VAL SER GLY LEU LYS SEQRES 2 A 123 ALA GLY LYS ASN ALA PRO SER ALA LYS ILE ALA LYS LEU SEQRES 3 A 123 VAL VAL ASN SER THR THR LEU LYS GLU PHE GLY VAL ARG SEQRES 4 A 123 GLY ILE SER ASN ASN VAL VAL ASP SER THR GLY THR ALA SEQRES 5 A 123 TRP ARG VAL ALA GLY LYS ASN THR GLY LYS GLU ILE GLY SEQRES 6 A 123 VAL GLY LEU SER SER ASP SER LEU ARG ARG SER ASP SER SEQRES 7 A 123 THR GLU LYS TRP ASN GLY VAL ASN TRP MET THR PHE ASN SEQRES 8 A 123 SER ASN ASP THR LEU ASP ILE VAL LEU THR GLY PRO ALA SEQRES 9 A 123 GLN ASN VAL THR ALA ASP THR TYR PRO ILE THR LEU ASP SEQRES 10 A 123 VAL VAL GLY TYR GLN PRO SEQRES 1 B 144 GLY SER PHE LEU PRO ASN SER GLU GLN GLN LYS SER VAL SEQRES 2 B 144 ASP ILE VAL PHE SER SER PRO GLN ASP LEU THR VAL SER SEQRES 3 B 144 LEU ILE PRO VAL SER GLY LEU LYS ALA GLY LYS ASN ALA SEQRES 4 B 144 PRO SER ALA LYS ILE ALA LYS LEU VAL VAL ASN SER THR SEQRES 5 B 144 THR LEU LYS GLU PHE GLY VAL ARG GLY ILE SER ASN ASN SEQRES 6 B 144 VAL VAL ASP SER THR GLY THR ALA TRP ARG VAL ALA GLY SEQRES 7 B 144 LYS ASN THR GLY LYS GLU ILE GLY VAL GLY LEU SER SER SEQRES 8 B 144 ASP SER LEU ARG ARG SER ASP SER THR GLU LYS TRP ASN SEQRES 9 B 144 GLY VAL ASN TRP MET THR PHE ASN SER ASN ASP THR LEU SEQRES 10 B 144 ASP ILE VAL LEU THR GLY PRO ALA GLN ASN VAL THR ALA SEQRES 11 B 144 ASP THR TYR PRO ILE THR LEU ASP VAL VAL GLY TYR GLN SEQRES 12 B 144 PRO SEQRES 1 C 19 GLY SER PHE LEU PRO ASN SER GLU GLN GLN LYS SER VAL SEQRES 2 C 19 ASP ILE VAL PHE SER SER HELIX 1 1 SER A 90 ARG A 96 1 7 HELIX 2 2 SER B 90 SER B 97 1 8 HELIX 3 3 PRO C 5 GLU C 8 5 4 SHEET 1 A 5 THR A 24 PRO A 29 0 SHEET 2 A 5 LYS A 43 ASN A 50 -1 O VAL A 48 N SER A 26 SHEET 3 A 5 ASP A 115 VAL A 120 -1 O ILE A 119 N ALA A 45 SHEET 4 A 5 GLU A 84 LEU A 89 -1 N GLY A 88 O VAL A 120 SHEET 5 A 5 ALA A 73 ALA A 77 -1 N VAL A 76 O ILE A 85 SHEET 1 B 2 GLY A 36 LYS A 37 0 SHEET 2 B 2 ASN A 127 VAL A 128 -1 O VAL A 128 N GLY A 36 SHEET 1 C 5 THR A 100 TRP A 103 0 SHEET 2 C 5 VAL A 106 ASN A 112 -1 O VAL A 106 N TRP A 103 SHEET 3 C 5 GLU A 56 GLY A 61 -1 N PHE A 57 O PHE A 111 SHEET 4 C 5 THR A 132 TYR A 142 -1 O VAL A 140 N GLY A 58 SHEET 5 C 5 GLN B 9 VAL B 16 -1 O ILE B 15 N TYR A 133 SHEET 1 D 6 LEU B 27 PRO B 29 0 SHEET 2 D 6 LYS B 43 VAL B 49 -1 O LYS B 46 N ILE B 28 SHEET 3 D 6 ASP B 115 VAL B 120 -1 O ASP B 115 N VAL B 49 SHEET 4 D 6 GLU B 84 LEU B 89 -1 N GLY B 88 O VAL B 120 SHEET 5 D 6 ALA B 73 ALA B 77 -1 N TRP B 74 O VAL B 87 SHEET 6 D 6 ASN B 65 VAL B 66 -1 N ASN B 65 O ARG B 75 SHEET 1 E 2 GLY B 36 LYS B 37 0 SHEET 2 E 2 ASN B 127 VAL B 128 -1 O VAL B 128 N GLY B 36 SHEET 1 F 5 THR B 100 TRP B 103 0 SHEET 2 F 5 VAL B 106 ASN B 112 -1 O VAL B 106 N TRP B 103 SHEET 3 F 5 GLU B 56 GLY B 61 -1 N PHE B 57 O PHE B 111 SHEET 4 F 5 THR B 132 VAL B 140 -1 O VAL B 140 N GLY B 58 SHEET 5 F 5 GLN C 9 VAL C 16 -1 O GLN C 9 N VAL B 139 SHEET 1 G 2 TYR B 142 GLN B 143 0 SHEET 2 G 2 SER C 2 PHE C 3 -1 O SER C 2 N GLN B 143 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000