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- PDB-4c00: Crystal structure of TamA from E. coli -

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Basic information

Entry
Database: PDB / ID: 4c00
TitleCrystal structure of TamA from E. coli
ComponentsTRANSLOCATION AND ASSEMBLY MODULE TAMA
KeywordsTRANSPORT PROTEIN / YTFM / POLYPEPTIDE TRANSPORT-ASSOCIATED / AUTOTRANSPORTER BIOGENESIS / AUTOTRANSPORTER ASSEMBLY / OUTER MEMBRANE PROTEIN
Function / homology
Function and homology information


TAM protein secretion complex / protein localization to outer membrane / protein secretion / cell outer membrane / plasma membrane
Similarity search - Function
TamA, POTRA domain 1 / POTRA domain TamA domain 1 / membrane protein fhac: a member of the omp85/tpsb transporter family / membrane protein fhac / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / Surface antigen D15-like / POTRA domain / POTRA domain profile. / Bacterial surface antigen (D15) ...TamA, POTRA domain 1 / POTRA domain TamA domain 1 / membrane protein fhac: a member of the omp85/tpsb transporter family / membrane protein fhac / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / Surface antigen D15-like / POTRA domain / POTRA domain profile. / Bacterial surface antigen (D15) / Omp85 superfamily domain / Porin / Ubiquitin-like (UB roll) / Roll / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE / Translocation and assembly module subunit TamA
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsGruss, F. / Zaehringer, F. / Jakob, R.P. / Burmann, B.M. / Hiller, S. / Maier, T.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: The Structural Basis of Autotransporter Translocation by Tama
Authors: Gruss, F. / Zaehringer, F. / Jakob, R.P. / Burmann, B.M. / Hiller, S. / Maier, T.
History
DepositionJul 30, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references
Revision 1.2Nov 20, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSLOCATION AND ASSEMBLY MODULE TAMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,97422
Polymers62,9031
Non-polymers11,07121
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.470, 261.060, 57.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein TRANSLOCATION AND ASSEMBLY MODULE TAMA / AUTOTRANSPORTER ASSEMBLY FACTOR TAMA


Mass: 62902.551 Da / Num. of mol.: 1 / Fragment: RESIDUES 22-577
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): OMP3 / References: UniProt: P0ADE4
#2: Chemical
ChemComp-MC3 / 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE


Mass: 677.933 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C36H72NO8P / Comment: phospholipid*YM
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE (MC3): LIPIDS IN STRUCTURE WERE BUILT AS FRAGMENTS OF ...1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE (MC3): LIPIDS IN STRUCTURE WERE BUILT AS FRAGMENTS OF DMPC, WHICH WAS USED IN BICELLE CRYSTALLIZATION
Sequence detailsWITHOUT N-TERMINAL SIGNAL SEQUENCE (AA. 1-21),COMPRISES AA. 22-577,ADDITIONAL N-TERMINAL GLY-ILE-GLN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.66 Å3/Da / Density % sol: 73.63 % / Description: NONE
Crystal growDetails: IMIDAZOLE PH 6.0, NA ACETATE, TRIS, NACL, BETA-OG, DMPC, CHAPSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→74 Å / Num. obs: 55995 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 7.29 % / Biso Wilson estimate: 41.15 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.74
Reflection shellResolution: 2.25→2.39 Å / Redundancy: 7.04 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 2.39 / % possible all: 94.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2QDZ AND 4BZA

2qdz
PDB Unreleased entry

4bza


Resolution: 2.25→74.269 Å / SU ML: 0.27 / σ(F): 1.99 / Phase error: 22.46 / Stereochemistry target values: ML
Details: POTRA DOMAIN 1 AND C-TERMINUS EXHIBIT HIGHER FLEXIBILITY RESP. DISORDER. STRUCTURE OF ISOLATED POTRA DOMAINS FROM PDB 4BZA GUIDED MODEL BUILDING OF POTRA DOMAIN 1
RfactorNum. reflection% reflection
Rfree0.217 1946 3.5 %
Rwork0.1898 --
obs0.1907 55920 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77 Å2
Refinement stepCycle: LAST / Resolution: 2.25→74.269 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4333 0 428 226 4987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034908
X-RAY DIFFRACTIONf_angle_d0.9566587
X-RAY DIFFRACTIONf_dihedral_angle_d14.021952
X-RAY DIFFRACTIONf_chiral_restr0.05666
X-RAY DIFFRACTIONf_plane_restr0.003836
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2501-2.30630.33711470.27363570X-RAY DIFFRACTION93
2.3063-2.36870.28491120.24263687X-RAY DIFFRACTION96
2.3687-2.43840.28991420.23033748X-RAY DIFFRACTION97
2.4384-2.51710.22731370.21393812X-RAY DIFFRACTION98
2.5171-2.60710.23181480.19493853X-RAY DIFFRACTION100
2.6071-2.71150.20151140.1933841X-RAY DIFFRACTION99
2.7115-2.83490.23131420.19023846X-RAY DIFFRACTION99
2.8349-2.98440.24921550.18963831X-RAY DIFFRACTION99
2.9844-3.17130.22111350.18273883X-RAY DIFFRACTION99
3.1713-3.41620.21311450.17753889X-RAY DIFFRACTION99
3.4162-3.760.18231440.16753901X-RAY DIFFRACTION100
3.76-4.3040.20051220.17483946X-RAY DIFFRACTION99
4.304-5.42230.1791480.16793993X-RAY DIFFRACTION100
5.4223-74.30930.23431550.21614174X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0668-0.09320.03240.1353-0.04640.01560.41280.31670.3816-0.1713-0.3198-0.3467-0.42910.0167-0.14361.7225-0.373-0.28921.31520.18441.6972-7.850216.7902-6.1972
22.77561.57550.1781.14580.4370.4594-0.12550.1731-0.3451-0.05820.02390.42060.3665-0.33730.15221.1239-0.53010.01760.83860.14451.628910.974212.610119.5325
32.391.1019-0.52975.3806-0.60171.28040.042-0.1142-0.7544-0.12840.17440.14840.861-0.3276-0.18930.619-0.1353-0.1160.42310.02480.616337.53431.350219.756
42.0726-0.87870.12020.7208-0.42770.7510.09150.0707-0.0616-0.02660.00650.0537-0.0285-0.1424-0.09860.2798-0.0062-0.01180.3586-0.0390.290825.557667.502814.0638
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 25 THROUGH 103 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 104 THROUGH 188 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 189 THROUGH 263)
4X-RAY DIFFRACTION4CHAIN A AND (RESID 264 THROUGH 577 )

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