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- PDB-3efc: Crystal Structure of YaeT periplasmic domain -

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Basic information

Entry
Database: PDB / ID: 3efc
TitleCrystal Structure of YaeT periplasmic domain
ComponentsOuter membrane protein assembly factor yaeT
KeywordsMEMBRANE PROTEIN / POTRA fold / Cell membrane / Cell outer membrane / Membrane
Function / homology
Function and homology information


Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / cell outer membrane / cell adhesion / membrane
Similarity search - Function
membrane protein fhac / Outer membrane protein assembly factor BamA / 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) ...membrane protein fhac / Outer membrane protein assembly factor BamA / 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
Outer membrane protein assembly factor BamA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.3 Å
AuthorsGatzeva-Topalova, P.Z. / Walton, T.A. / Sousa, M.C.
CitationJournal: Structure / Year: 2008
Title: Crystal structure of YaeT: conformational flexibility and substrate recognition.
Authors: Gatzeva-Topalova, P.Z. / Walton, T.A. / Sousa, M.C.
History
DepositionSep 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer membrane protein assembly factor yaeT


Theoretical massNumber of molelcules
Total (without water)44,1881
Polymers44,1881
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.509, 92.509, 142.429
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Outer membrane protein assembly factor yaeT / Omp85


Mass: 44187.598 Da / Num. of mol.: 1 / Fragment: periplasmic domain (UNP residues 21-410)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yaeT, yzzN, yzzY, b0177, JW0172 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P0A940

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.98 Å3/Da / Density % sol: 69.11 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.3-1.6M (NH4)2SO4, 3-6% polyethylene glycol 400, 10% Dioxane, 0.1M MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289.15K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.111
SYNCHROTRONALS 8.2.120.9796, 0.9797, 0.9643
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDAug 3, 2007
ADSC QUANTUM 3152CCDAug 3, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97961
30.97971
40.96431
ReflectionResolution: 3.3→50 Å / Num. obs: 11035 / % possible obs: 99.6 % / Redundancy: 3.5 % / Rsym value: 0.056 / Net I/σ(I): 20.6
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 1069 / Rsym value: 0.424 / % possible all: 99.9

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Processing

Software
NameClassification
BOSdata collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 3.3→47.5 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.295 1126 10.2 %RANDOM
Rwork0.267 ---
all-11061 --
obs-11004 99.55 %-
Displacement parametersBiso mean: 95.5 Å2
Refinement stepCycle: LAST / Resolution: 3.3→47.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2514 0 0 0 2514
LS refinement shellResolution: 3.3→3.45 Å
RfactorNum. reflection
Rfree0.421 130
Rwork0.367 -
obs-1344

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