HEADER MEMBRANE PROTEIN 15-APR-05 1ZDX TITLE SOLUTION STRUCTURE OF THE TYPE 1 PILUS ASSEMBLY PLATFORM FIMD(25-125) COMPND MOL_ID: 1; COMPND 2 MOLECULE: OUTER MEMBRANE USHER PROTEIN FIMD; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN RESIDUES 70-170; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: FIMD; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BETA SHEET, ALPHA HELIX, MEMBRANE PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.NISHIYAMA,R.HORST,T.HERRMANN,M.VETSCH,P.BETTENDORFF,O.IGNATOV, AUTHOR 2 M.GRUTTER,K.WUTHRICH,R.GLOCKSHUBER,G.CAPITANI REVDAT 4 02-MAR-22 1ZDX 1 REMARK REVDAT 3 24-FEB-09 1ZDX 1 VERSN REVDAT 2 28-JUN-05 1ZDX 1 JRNL REVDAT 1 14-JUN-05 1ZDX 0 JRNL AUTH M.NISHIYAMA,R.HORST,O.EIDAM,T.HERRMANN,O.IGNATOV,M.VETSCH, JRNL AUTH 2 P.BETTENDORFF,I.JELESAROV,R.GLOCKSHUBER,G.CAPITANI JRNL TITL STRUCTURAL BASIS OF CHAPERONE-SUBUNIT COMPLEX RECOGNITION BY JRNL TITL 2 THE TYPE 1 PILUS ASSEMBLY PLATFORM FIMD. JRNL REF EMBO J. V. 24 2075 2005 JRNL REFN ISSN 0261-4189 JRNL PMID 15920478 JRNL DOI 10.1038/SJ.EMBOJ.7600693 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.5, ATHNOS/CANDID REMARK 3 AUTHORS : BRUKER (XWINNMR), HERRMANN (ATHNOS/CANDID) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1ZDX COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-APR-05. REMARK 100 THE DEPOSITION ID IS D_1000032610. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : UNIFORM LABELING WITH 13C, 15N; REMARK 210 90 % H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 750 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : DRX; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ATHNOS/CANDID REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 11 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 ASP A 55 HG SER A 56 1.59 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 4 ARG A 34 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 5 LEU A 69 CB - CG - CD1 ANGL. DEV. = 12.2 DEGREES REMARK 500 10 ARG A 66 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 11 ARG A 34 CD - NE - CZ ANGL. DEV. = 8.9 DEGREES REMARK 500 11 ARG A 34 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 11 ARG A 66 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 13 VAL A 97 CA - CB - CG2 ANGL. DEV. = 10.7 DEGREES REMARK 500 16 TYR A 33 CB - CG - CD1 ANGL. DEV. = 4.1 DEGREES REMARK 500 16 ARG A 34 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 17 ARG A 110 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 18 TYR A 33 CB - CG - CD1 ANGL. DEV. = 3.7 DEGREES REMARK 500 20 ARG A 66 NE - CZ - NH2 ANGL. DEV. = -3.2 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 1 GLU A 27 14.06 -140.10 REMARK 500 1 MET A 44 -62.32 -109.21 REMARK 500 1 SER A 56 178.82 163.20 REMARK 500 1 GLU A 57 -64.93 -25.93 REMARK 500 1 ALA A 80 96.10 -63.66 REMARK 500 1 ASP A 99 -28.12 71.73 REMARK 500 1 PHE A 119 38.44 -94.36 REMARK 500 1 ASN A 122 -26.98 172.93 REMARK 500 2 GLN A 26 113.40 -164.36 REMARK 500 2 GLU A 27 13.69 -141.25 REMARK 500 2 LEU A 28 115.11 -160.02 REMARK 500 2 THR A 50 98.27 -69.30 REMARK 500 2 ASP A 55 90.92 67.76 REMARK 500 2 SER A 56 -154.08 -145.50 REMARK 500 2 MET A 72 9.95 -68.12 REMARK 500 2 ASN A 83 17.69 -66.05 REMARK 500 2 ASN A 122 -34.64 -176.09 REMARK 500 3 GLN A 26 146.49 -179.17 REMARK 500 3 GLU A 27 14.44 -162.63 REMARK 500 3 MET A 44 -47.69 -132.25 REMARK 500 3 ALA A 80 -92.91 -46.31 REMARK 500 3 ASP A 99 -24.56 71.50 REMARK 500 4 GLU A 27 14.71 -150.60 REMARK 500 4 ASP A 48 97.41 -63.65 REMARK 500 4 SER A 56 -165.59 -174.66 REMARK 500 4 ASN A 83 12.88 -59.33 REMARK 500 4 ASP A 99 -30.81 74.54 REMARK 500 4 GLN A 108 18.72 -144.06 REMARK 500 4 GLN A 109 55.29 34.63 REMARK 500 4 SER A 121 42.88 -75.76 REMARK 500 5 GLU A 27 22.75 -165.20 REMARK 500 5 TYR A 43 106.42 24.19 REMARK 500 5 SER A 56 -166.54 176.33 REMARK 500 5 ALA A 80 103.31 -59.10 REMARK 500 5 ASN A 83 12.94 -63.94 REMARK 500 5 ASP A 99 -24.68 84.19 REMARK 500 5 ASN A 122 175.19 143.69 REMARK 500 5 ARG A 123 -67.51 70.51 REMARK 500 5 ALA A 124 81.52 36.37 REMARK 500 6 GLU A 27 14.87 -142.77 REMARK 500 6 TYR A 43 111.58 24.41 REMARK 500 6 MET A 72 8.38 -68.93 REMARK 500 6 ASN A 83 11.29 -63.94 REMARK 500 6 ASP A 99 -15.80 72.15 REMARK 500 6 ASN A 122 -76.96 63.06 REMARK 500 7 GLU A 27 14.90 -158.53 REMARK 500 7 ARG A 47 -179.44 -171.14 REMARK 500 7 ASN A 83 1.24 -67.02 REMARK 500 7 PRO A 92 79.80 -68.52 REMARK 500 7 ASP A 99 -34.04 72.20 REMARK 500 REMARK 500 THIS ENTRY HAS 167 RAMACHANDRAN OUTLIERS. 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 GLN A 26 GLU A 27 17 -132.23 REMARK 500 ALA A 89 CYS A 90 19 148.09 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 1 ARG A 34 0.08 SIDE CHAIN REMARK 500 2 ARG A 66 0.12 SIDE CHAIN REMARK 500 3 ARG A 47 0.09 SIDE CHAIN REMARK 500 4 TYR A 38 0.08 SIDE CHAIN REMARK 500 4 ARG A 110 0.10 SIDE CHAIN REMARK 500 5 ARG A 47 0.09 SIDE CHAIN REMARK 500 5 ARG A 110 0.10 SIDE CHAIN REMARK 500 6 ARG A 125 0.16 SIDE CHAIN REMARK 500 7 ARG A 34 0.11 SIDE CHAIN REMARK 500 10 ARG A 66 0.09 SIDE CHAIN REMARK 500 10 ARG A 110 0.08 SIDE CHAIN REMARK 500 10 ARG A 125 0.10 SIDE CHAIN REMARK 500 11 TYR A 33 0.07 SIDE CHAIN REMARK 500 11 ARG A 66 0.09 SIDE CHAIN REMARK 500 11 ARG A 125 0.08 SIDE CHAIN REMARK 500 12 ARG A 123 0.09 SIDE CHAIN REMARK 500 13 TYR A 33 0.07 SIDE CHAIN REMARK 500 13 ARG A 110 0.08 SIDE CHAIN REMARK 500 14 ARG A 123 0.13 SIDE CHAIN REMARK 500 15 ARG A 110 0.08 SIDE CHAIN REMARK 500 17 ARG A 47 0.11 SIDE CHAIN REMARK 500 19 ARG A 47 0.08 SIDE CHAIN REMARK 500 19 ARG A 110 0.10 SIDE CHAIN REMARK 500 19 ARG A 125 0.12 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ZDV RELATED DB: PDB DBREF 1ZDX A 25 125 UNP P30130 FIMD_ECOLI 70 170 SEQRES 1 A 101 GLY GLN GLU LEU PRO PRO GLY THR TYR ARG VAL ASP ILE SEQRES 2 A 101 TYR LEU ASN ASN GLY TYR MET ALA THR ARG ASP VAL THR SEQRES 3 A 101 PHE ASN THR GLY ASP SER GLU GLN GLY ILE VAL PRO CYS SEQRES 4 A 101 LEU THR ARG ALA GLN LEU ALA SER MET GLY LEU ASN THR SEQRES 5 A 101 ALA SER VAL ALA GLY MET ASN LEU LEU ALA ASP ASP ALA SEQRES 6 A 101 CYS VAL PRO LEU THR THR MET VAL GLN ASP ALA THR ALA SEQRES 7 A 101 HIS LEU ASP VAL GLY GLN GLN ARG LEU ASN LEU THR ILE SEQRES 8 A 101 PRO GLN ALA PHE MET SER ASN ARG ALA ARG HELIX 1 1 THR A 65 MET A 72 1 8 HELIX 2 2 ASN A 75 VAL A 79 5 5 HELIX 3 3 PRO A 92 VAL A 97 1 6 HELIX 4 4 PRO A 116 MET A 120 5 5 SHEET 1 A 5 ILE A 60 PRO A 62 0 SHEET 2 A 5 GLY A 42 THR A 53 -1 N ASN A 52 O VAL A 61 SHEET 3 A 5 GLY A 31 LEU A 39 -1 N ILE A 37 O MET A 44 SHEET 4 A 5 ARG A 110 THR A 114 1 O LEU A 113 N TYR A 38 SHEET 5 A 5 THR A 101 ASP A 105 -1 N ASP A 105 O ARG A 110 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 MODEL 1