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- PDB-4bza: Crystal structure of TamA POTRA domains 1-3 from E. coli -

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Basic information

Entry
Database: PDB / ID: 4bza
TitleCrystal structure of TamA POTRA domains 1-3 from E. coli
ComponentsTRANSLOCATION AND ASSEMBLY MODULE TAMA
KeywordsTRANSPORT PROTEIN / POLYPEPTIDE TRANSPORT-ASSOCIATED / AUTOTRANSPORTER BIOGENESIS / 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 / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / POTRA domain / POTRA domain profile. / Surface antigen D15-like / Bacterial surface antigen (D15) / Omp85 superfamily domain ...TamA, POTRA domain 1 / POTRA domain TamA domain 1 / membrane protein fhac / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / POTRA domain / POTRA domain profile. / Surface antigen D15-like / Bacterial surface antigen (D15) / Omp85 superfamily domain / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Translocation and assembly module subunit TamA
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.839 Å
AuthorsJakob, R.P. / Gruss, F. / Zaehringer, F. / 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 24, 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 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRANSLOCATION AND ASSEMBLY MODULE TAMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5353
Polymers29,4111
Non-polymers1242
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.050, 83.050, 150.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2087-

HOH

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Components

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


Mass: 29411.166 Da / Num. of mol.: 1 / Fragment: POTRA DOMAINS 1-3, RESIDUES 22-275
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): PRIL PL1SL2 / References: UniProt: P0ADE4
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsWITHOUT N-TERMINAL SIGNAL SEQUENCE (AA. 1-21),COMPRISES AA. 22-275,ADDITIONAL N-TERMINAL ...WITHOUT N-TERMINAL SIGNAL SEQUENCE (AA. 1-21),COMPRISES AA. 22-275,ADDITIONAL N-TERMINAL MET,ADDITIONAL C-TERMINAL 6XHIS

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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: 2.21 Å3/Da / Density % sol: 44.5 %
Description: R VALUE OF 173.1 PERC. NOT ACCEPTED BY INPUT FORM, BUT DUE TO CC ONE HALF 76 PERC. AND I OVER SIGMA 2 AT 12- FOLD REDUNDANCY A REASONABLE RESOLUTION CUTOFF
Crystal growDetails: HEPES PH 7.5, DI-NA TARTRATE, PEG 3350, NACL, GLYCEROL

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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: Mar 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.84→43 Å / Num. obs: 46484 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 12.99 % / Biso Wilson estimate: 37.36 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 31.36
Reflection shellResolution: 1.84→1.95 Å / Redundancy: 12.5 % / Rmerge(I) obs: 1.73 / Mean I/σ(I) obs: 1.99 / % possible all: 99.1

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Processing

Software
NameClassification
XDSdata reduction
XDSdata scaling
SHELXphasing
PHASERphasing
PHENIXrefinement
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 1.839→42.974 Å / SU ML: 0.2 / σ(F): 1.35 / Phase error: 21.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2015 2348 5.1 %
Rwork0.1728 --
obs0.1743 46471 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69 Å2
Refinement stepCycle: LAST / Resolution: 1.839→42.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1930 0 8 290 2228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182037
X-RAY DIFFRACTIONf_angle_d1.4642762
X-RAY DIFFRACTIONf_dihedral_angle_d14.7769
X-RAY DIFFRACTIONf_chiral_restr0.071306
X-RAY DIFFRACTIONf_plane_restr0.008365
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8392-1.87670.28761250.29792484X-RAY DIFFRACTION98
1.8767-1.91750.31721280.27782563X-RAY DIFFRACTION100
1.9175-1.96220.29161280.26312543X-RAY DIFFRACTION100
1.9622-2.01120.27951430.24412555X-RAY DIFFRACTION100
2.0112-2.06560.30281350.24382553X-RAY DIFFRACTION100
2.0656-2.12640.25351340.20172588X-RAY DIFFRACTION100
2.1264-2.1950.19711330.18992564X-RAY DIFFRACTION100
2.195-2.27350.2271440.17262563X-RAY DIFFRACTION100
2.2735-2.36450.20841540.16792566X-RAY DIFFRACTION100
2.3645-2.47210.19941160.15852582X-RAY DIFFRACTION100
2.4721-2.60240.20411300.16412623X-RAY DIFFRACTION100
2.6024-2.76540.21481400.17292586X-RAY DIFFRACTION100
2.7654-2.97890.22411650.17332563X-RAY DIFFRACTION100
2.9789-3.27860.19321480.16872623X-RAY DIFFRACTION100
3.2786-3.75270.20621530.16822631X-RAY DIFFRACTION100
3.7527-4.72710.16021300.14352697X-RAY DIFFRACTION100
4.7271-42.98570.18371420.17382839X-RAY DIFFRACTION100
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)
14.4675-2.7334-0.53694.24822.50633.8340.1332-0.80682.02241.18380.33921.015-1.8158-0.2122-0.09991.51520.2060.43080.6782-0.11941.34169.146559.5417-1.0894
22.82292.5264-1.46198.2766-4.69975.30290.07710.28770.20420.229-0.02140.46-0.1506-0.4126-0.06770.21990.07720.07180.41270.02310.33535.392528.4906-3.3204
32.51011.3755-3.33371.4841-2.75176.2418-0.258-0.0835-0.2251-0.0474-0.1356-0.07480.42090.09530.41340.3476-0.0260.08270.28740.00480.32383.376218.065615.3584
4-0.04740.0323-0.0338-0.0330.0855-0.0281-0.9153-0.76270.2251.37720.4090.8330.3240.08210.55091.52920.25940.31631.2522-0.22670.8085-16.227527.378154.3769
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 25 THROUGH 104 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 105 THROUGH 156 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 157 THROUGH 262 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 263 THROUGH 278 )

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