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- PDB-3og5: Crystal Structure of BamA POTRA45 tandem -

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Basic information

Entry
Database: PDB / ID: 3og5
TitleCrystal Structure of BamA POTRA45 tandem
ComponentsOuter membrane protein assembly complex, YaeT protein
KeywordsPROTEIN BINDING / POTRA fold / Insertion of outer membrane proteins
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 / SAD / Resolution: 2.69 Å
AuthorsGatzeva-Topalova, P.Z. / Warner, L.R. / Pardi, A. / Sousa, M.C.
CitationJournal: Structure / Year: 2010
Title: Structure and Flexibility of the Complete Periplasmic Domain of BamA: The Protein Insertion Machine of the Outer Membrane
Authors: Gatzeva-Topalova, P.Z. / Warner, L.R. / Pardi, A. / Sousa, M.C.
History
DepositionAug 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer membrane protein assembly complex, YaeT protein
B: Outer membrane protein assembly complex, YaeT protein


Theoretical massNumber of molelcules
Total (without water)37,8732
Polymers37,8732
Non-polymers00
Water90150
1
A: Outer membrane protein assembly complex, YaeT protein


Theoretical massNumber of molelcules
Total (without water)18,9361
Polymers18,9361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Outer membrane protein assembly complex, YaeT protein


Theoretical massNumber of molelcules
Total (without water)18,9361
Polymers18,9361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.492, 118.492, 69.992
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 Outer membrane protein assembly complex, YaeT protein


Mass: 18936.482 Da / Num. of mol.: 2 / Fragment: POTRA45 DOMAIN (unp residues 264-424)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yaeT / Plasmid: pMS487 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: D5CVA9, UniProt: P0A940*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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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: 3.75 Å3/Da / Density % sol: 67.16 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 1.68M ammonium sulfate, 3% PEG 400, 0.25M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 23, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.69→40 Å / Num. obs: 29399 / % possible obs: 96.8 % / Redundancy: 1.5 % / Rmerge(I) obs: 0.084 / Χ2: 1.34 / Net I/σ(I): 8.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.69-2.81.40.24229181.18897.3
2.8-2.911.50.20429721.17297.5
2.91-3.041.50.16629671.20897.8
3.04-3.21.50.13129681.22197.2
3.2-3.41.50.10929571.34597.8
3.4-3.661.50.09329551.41397
3.66-4.031.40.07529341.54496.7
4.03-4.621.40.06629451.56596.3
4.62-5.811.40.06328561.41494.9
5.81-401.40.05429271.35195.5

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
MOLREPphasing
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.69→38.786 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8206 / SU ML: 0.4 / σ(F): 0.08 / Phase error: 25.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2603 2828 9.96 %
Rwork0.2115 --
obs0.2163 28390 93.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.374 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso max: 218.24 Å2 / Biso mean: 42.8419 Å2 / Biso min: 2.62 Å2
Baniso -1Baniso -2Baniso -3
1-8.3412 Å2-0 Å2-0 Å2
2--8.3412 Å20 Å2
3----12.9726 Å2
Refinement stepCycle: LAST / Resolution: 2.69→38.786 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2301 0 0 50 2351
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092333
X-RAY DIFFRACTIONf_angle_d1.2043143
X-RAY DIFFRACTIONf_chiral_restr0.072346
X-RAY DIFFRACTIONf_plane_restr0.005416
X-RAY DIFFRACTIONf_dihedral_angle_d18.743873
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.69-2.79060.28722620.26582359262187
2.7906-2.90230.3372690.25472487275690
2.9023-3.03440.31772800.24162506278692
3.0344-3.19430.27112820.21122549283193
3.1943-3.39430.25332950.20762597289295
3.3943-3.65620.24242920.19232617290996
3.6562-4.02380.21282800.17312627290796
4.0238-4.60520.22572880.1732638292696
4.6052-5.7990.23832950.19262553284894
5.799-38.78960.28262850.2452629291495

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