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- PDB-4n74: Crystal Structure of Outer Membrane Protein TamA beta-barrel Doma... -

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Basic information

Entry
Database: PDB / ID: 4n74
TitleCrystal Structure of Outer Membrane Protein TamA beta-barrel Domain in E.coli
ComponentsPredicted outer membrane protein and surface antigen
KeywordsMEMBRANE PROTEIN / Beta-barrel / Autotransporter biogenesis / Membrane
Function / homologymembrane protein fhac: a member of the omp85/tpsb transporter family / Porin / Beta Barrel / Mainly Beta / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsWang, Y.
CitationJournal: To be Published
Title: Structural Basis of BamA-mediate Outer Membrane Protein Biogenesis
Authors: Huang, Y.H.
History
DepositionOct 14, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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: Predicted outer membrane protein and surface antigen


Theoretical massNumber of molelcules
Total (without water)35,3441
Polymers35,3441
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.071, 71.071, 143.341
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Predicted outer membrane protein and surface antigen


Mass: 35344.324 Da / Num. of mol.: 1 / Fragment: beta-barrel domain, UNP residues 264-577 / Mutation: E265Q, M291V, F371L, M391V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / MC4100 / BW2952 / Production host: Escherichia coli (E. coli) / References: UniProt: C4ZR96

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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: 2.96 Å3/Da / Density % sol: 58.4 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1M Glycine pH 9.0, 31% PEG 400, 0.15M magnesium chloride, 0.4M sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 49230 / Num. obs: 48998 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.9-3199.9
3-3.12199.8
3.12-3.27199.8
3.27-3.44199.9
3.44-3.65199.7
3.65-3.94199.8
3.94-4.33199
4.33-4.96197.2
4.96-6.24199.5
6.24-50195.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(Phaser-MR: 1.8.1_1168)model building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX(Phaser-MR: 1.8.1_1168)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→28.514 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8054 / SU ML: 0.37 / σ(F): 0.11 / Phase error: 25.83 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2813 963 10.03 %RANDOM
Rwork0.2317 ---
obs0.2368 9604 98.09 %-
all-9794 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.77 Å2 / Biso mean: 54.8397 Å2 / Biso min: 34.41 Å2
Refinement stepCycle: LAST / Resolution: 2.9→28.514 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2502 0 0 0 2502
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082573
X-RAY DIFFRACTIONf_angle_d1.2193500
X-RAY DIFFRACTIONf_dihedral_angle_d14.949914
X-RAY DIFFRACTIONf_chiral_restr0.08369
X-RAY DIFFRACTIONf_plane_restr0.005447
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9001-3.05290.32521320.2534120597
3.0529-3.24390.30241340.2358122898
3.2439-3.4940.26641340.2232119799
3.494-3.84480.27521380.2273122299
3.8448-4.39940.30021350.2223125399
4.3994-5.53610.2831450.2191123398
5.5361-28.51540.26021450.2505130397
Refinement TLS params.Method: refined / Origin x: 22.0691 Å / Origin y: -23.6701 Å / Origin z: 1.7491 Å
111213212223313233
T0.5355 Å2-0.1543 Å2-0.0354 Å2-0.4342 Å2-0.0234 Å2--0.3283 Å2
L2.8732 °2-0.2037 °2-1.6042 °2-1.3155 °2-0.3789 °2--2.168 °2
S0.0563 Å °0.0846 Å °0.1225 Å °-0.02 Å °-0.0443 Å °0.1775 Å °-0.097 Å °-0.0475 Å °-0.0203 Å °
Refinement TLS groupSelection details: all

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