HEADER MEMBRANE PROTEIN 02-OCT-07 2JW1 TITLE STRUCTURAL CHARACTERIZATION OF THE TYPE III PILOTIN-SECRETIN TITLE 2 INTERACTION IN SHIGELLA FLEXNERI BY NMR SPECTROSCOPY COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIPOPROTEIN MXIM; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: OUTER MEMBRANE PROTEIN MXID; COMPND 7 CHAIN: B; COMPND 8 FRAGMENT: SEQUENCE DATABASE RESIDUES 549-566; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SHIGELLA FLEXNERI; SOURCE 3 ORGANISM_TAXID: 623; SOURCE 4 GENE: MXIM; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET28A; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630 KEYWDS PROTEIN-PROTEIN INTERACTION, LIPOPROTEIN, MEMBRANE, OUTER MEMBRANE, KEYWDS 2 PALMITATE, PLASMID, VIRULENCE, PROTEIN TRANSPORT, TRANSPORT, KEYWDS 3 MEMBRANE PROTEIN EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR M.S.OKON,P.I.LARIO,L.CREAGH,Y.M.T.JUNG,A.T.MAURELLI,N.C.J.STRYNADKA, AUTHOR 2 L.P.MCINTOSH REVDAT 4 19-FEB-20 2JW1 1 SOURCE REMARK LINK REVDAT 3 24-FEB-09 2JW1 1 VERSN REVDAT 2 04-NOV-08 2JW1 1 JRNL REVDAT 1 02-SEP-08 2JW1 0 JRNL AUTH M.OKON,T.F.MORAES,P.I.LARIO,A.L.CREAGH,C.A.HAYNES, JRNL AUTH 2 N.C.STRYNADKA,L.P.MCINTOSH JRNL TITL STRUCTURAL CHARACTERIZATION OF THE TYPE-III PILOT-SECRETIN JRNL TITL 2 COMPLEX FROM SHIGELLA FLEXNERI JRNL REF STRUCTURE V. 16 1544 2008 JRNL REFN ISSN 0969-2126 JRNL PMID 18940609 JRNL DOI 10.1016/J.STR.2008.08.006 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE, ARIA 2.1 REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX REMARK 3 (NMRPIPE), LINGE, O'DONOGHUE AND NILGES (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ADDITIONAL WATER REFINEMENT WAS MADE REMARK 3 FOR EACH OF SUBMITTED CONFORMERS REMARK 4 REMARK 4 2JW1 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-OCT-07. REMARK 100 THE DEPOSITION ID IS D_1000100361. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 20 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.3 -0.5 MM [U-95% 13C; U-95% REMARK 210 15N] MXIM(28-142), 0.5 - 0.7 MM REMARK 210 MXID(553-570), 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D CBCA(CO)NH; REMARK 210 3D HNCO; 3D HNCA; 3D HN(CO)CA; REMARK 210 3D HCCH-TOCSY; 3D 1H-15N NOESY; REMARK 210 3D 1H-13C NOESY; 13C/15N_F1,F2- REMARK 210 FILTERED_NOESY; 13C/15N_F1,F2- REMARK 210 FILTERED_TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEW 5.0.4 REMARK 210 METHOD USED : SIMULATED ANNEALING, MOLECULAR REMARK 210 DYNAMICS, TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 HZ PHE A 78 HD13 LEU B 564 1.15 REMARK 500 HG LEU B 558 HA LEU B 564 1.28 REMARK 500 O VAL B 565 H ASN B 569 1.58 REMARK 500 HZ3 LYS A 130 OD1 ASP A 131 1.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 6 TYR A 76 CE1 TYR A 76 CZ 0.078 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 SER A 30 71.78 -178.13 REMARK 500 1 SER A 32 -143.94 -123.45 REMARK 500 1 PRO A 49 -176.92 -51.60 REMARK 500 1 ASP A 51 116.15 175.09 REMARK 500 1 LYS A 61 72.96 56.53 REMARK 500 1 MET A 97 -112.04 36.44 REMARK 500 1 ASP A 98 -48.28 -131.48 REMARK 500 1 LYS A 118 162.88 154.27 REMARK 500 1 ASP A 131 33.18 74.44 REMARK 500 1 ILE A 139 151.10 75.91 REMARK 500 1 THR B 556 -53.87 -137.31 REMARK 500 1 LEU B 557 -148.73 70.49 REMARK 500 1 LEU B 558 49.33 88.21 REMARK 500 2 SER A 30 -168.03 -168.74 REMARK 500 2 SER A 32 -107.35 -84.26 REMARK 500 2 PRO A 49 179.61 -53.93 REMARK 500 2 ASP A 51 107.10 -169.44 REMARK 500 2 SER A 71 112.76 -172.51 REMARK 500 2 MET A 97 -114.72 38.37 REMARK 500 2 LYS A 118 162.22 153.43 REMARK 500 2 ASN A 123 -64.92 -136.22 REMARK 500 2 ASP A 124 40.89 -98.45 REMARK 500 2 ILE A 139 145.62 77.11 REMARK 500 2 THR B 556 -53.16 -138.74 REMARK 500 2 LEU B 557 -149.12 69.25 REMARK 500 2 LEU B 558 50.86 87.53 REMARK 500 3 SER A 30 102.81 -54.52 REMARK 500 3 ASN A 31 63.31 -179.33 REMARK 500 3 LYS A 34 104.67 -55.82 REMARK 500 3 PRO A 49 -176.68 -51.24 REMARK 500 3 ASP A 51 113.68 -178.37 REMARK 500 3 MET A 97 -136.06 40.37 REMARK 500 3 LYS A 118 163.29 158.58 REMARK 500 3 ASN A 123 -80.41 -131.49 REMARK 500 3 ASP A 124 54.51 -101.99 REMARK 500 3 ASP A 131 -1.22 82.63 REMARK 500 3 ILE A 139 143.97 79.84 REMARK 500 3 THR B 556 -53.55 -140.44 REMARK 500 3 LEU B 557 -153.64 69.71 REMARK 500 3 LEU B 558 58.61 91.05 REMARK 500 4 ASN A 31 54.82 -150.41 REMARK 500 4 SER A 32 -131.28 -88.12 REMARK 500 4 PRO A 49 178.98 -48.57 REMARK 500 4 ASP A 51 105.86 -165.12 REMARK 500 4 LYS A 61 67.90 63.51 REMARK 500 4 SER A 71 104.36 -164.23 REMARK 500 4 PHE A 96 36.19 -95.35 REMARK 500 4 MET A 97 -109.67 32.58 REMARK 500 4 ASP A 98 -48.68 -133.23 REMARK 500 4 LYS A 118 167.20 156.47 REMARK 500 REMARK 500 THIS ENTRY HAS 225 RAMACHANDRAN OUTLIERS. 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 3 TYR A 76 0.06 SIDE CHAIN REMARK 500 6 TYR A 76 0.07 SIDE CHAIN REMARK 500 15 TYR A 76 0.06 SIDE CHAIN 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 ACE B 552 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 15504 RELATED DB: BMRB DBREF 2JW1 A 28 142 UNP P0A1X2 MXIM_SHIFL 28 142 DBREF 2JW1 B 553 570 UNP Q04641 MXID_SHIFL 549 566 SEQRES 1 A 115 SER SER SER ASN SER GLU LYS GLU TRP HIS ILE VAL PRO SEQRES 2 A 115 VAL SER LYS ASP TYR PHE SER ILE PRO ASN ASP LEU LEU SEQRES 3 A 115 TRP SER PHE ASN THR THR ASN LYS SER ILE ASN VAL TYR SEQRES 4 A 115 SER LYS CYS ILE SER GLY LYS ALA VAL TYR SER PHE ASN SEQRES 5 A 115 ALA GLY LYS PHE MET GLY ASN PHE ASN VAL LYS GLU VAL SEQRES 6 A 115 ASP GLY CYS PHE MET ASP ALA GLN LYS ILE ALA ILE ASP SEQRES 7 A 115 LYS LEU PHE SER MET LEU LYS ASP GLY VAL VAL LEU LYS SEQRES 8 A 115 GLY ASN LYS ILE ASN ASP THR ILE LEU ILE GLU LYS ASP SEQRES 9 A 115 GLY GLU VAL LYS LEU LYS LEU ILE ARG GLY ILE SEQRES 1 B 19 ACE SER GLU THR THR LEU LEU GLU ASP GLU LYS SER LEU SEQRES 2 B 19 VAL SER TYR LEU ASN TYR HET ACE B 552 6 HETNAM ACE ACETYL GROUP FORMUL 2 ACE C2 H4 O HELIX 1 1 SER A 42 PHE A 46 5 5 HELIX 2 2 ASP A 98 VAL A 115 1 18 HELIX 3 3 ASP B 560 ASN B 569 1 10 SHEET 1 A 8 LYS A 82 GLU A 91 0 SHEET 2 A 8 ILE A 70 ASN A 79 -1 N LYS A 73 O ASN A 88 SHEET 3 A 8 SER A 62 SER A 67 -1 N VAL A 65 O GLY A 72 SHEET 4 A 8 LEU A 52 ASN A 57 -1 N ASN A 57 O SER A 62 SHEET 5 A 8 TRP A 36 PRO A 40 -1 N TRP A 36 O TRP A 54 SHEET 6 A 8 VAL A 134 LEU A 138 -1 O LYS A 137 N VAL A 39 SHEET 7 A 8 ILE A 126 GLU A 129 -1 N ILE A 126 O LEU A 138 SHEET 8 A 8 VAL A 116 LEU A 117 -1 N VAL A 116 O GLU A 129 SSBOND 1 CYS A 69 CYS A 95 1555 1555 2.03 LINK N SER B 553 C ACE B 552 1555 1555 1.33 SITE 1 AC1 1 SER B 553 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