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- PDB-6izt: Crystal structure of Haemophilus Influenzae BamA POTRA3-5 -

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Basic information

Entry
Database: PDB / ID: 6izt
TitleCrystal structure of Haemophilus Influenzae BamA POTRA3-5
ComponentsOuter membrane protein assembly factor BamA
KeywordsTRANSPORT PROTEIN / beta-barrel assembly machinery / poly-POTRAs / OMP recruitment / lipo-partners
Function / homology
Function and homology information


Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / cell outer membrane
Similarity search - Function
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
Similarity search - Domain/homology
Outer membrane protein assembly factor BamA
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsMa, X. / Wang, Q. / Li, Y. / Tan, P. / Wu, H. / Wang, P. / Dong, X. / Hong, L. / Meng, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China81770142 China
CitationJournal: Faseb J. / Year: 2019
Title: How BamA recruits OMP substratesviapoly-POTRAs domain.
Authors: Ma, X. / Wang, Q. / Li, Y. / Tan, P. / Wu, H. / Wang, P. / Dong, X. / Hong, L. / Meng, G.
History
DepositionDec 20, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 18, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Outer membrane protein assembly factor BamA
B: Outer membrane protein assembly factor BamA


Theoretical massNumber of molelcules
Total (without water)60,1332
Polymers60,1332
Non-polymers00
Water6,539363
1
A: Outer membrane protein assembly factor BamA


Theoretical massNumber of molelcules
Total (without water)30,0661
Polymers30,0661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Outer membrane protein assembly factor BamA


Theoretical massNumber of molelcules
Total (without water)30,0661
Polymers30,0661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.680, 89.900, 110.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Outer membrane protein assembly factor BamA / 80 kDa D15 antigen / D-15-Ag / Outer membrane protein D15 / Protective surface antigen D15


Mass: 30066.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: bamA / Production host: Escherichia coli (E. coli) / References: UniProt: P46024
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.58 Å3/Da / Density % sol: 52.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.03→55.1 Å / Num. obs: 41023 / % possible obs: 99.9 % / Redundancy: 22 % / CC1/2: 0.99 / Rsym value: 0.183 / Net I/σ(I): 15.1
Reflection shellResolution: 2.03→2.1 Å / Num. unique obs: 4041 / CC1/2: 0.72 / Rsym value: 1.09

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J09

6j09


Resolution: 2.03→55.1 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.31
RfactorNum. reflection% reflection
Rfree0.2385 2074 5.06 %
Rwork0.2097 --
obs0.2111 40985 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.03→55.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4014 0 0 363 4377
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044072
X-RAY DIFFRACTIONf_angle_d0.875500
X-RAY DIFFRACTIONf_dihedral_angle_d14.9212468
X-RAY DIFFRACTIONf_chiral_restr0.051614
X-RAY DIFFRACTIONf_plane_restr0.004726
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.07620.31471440.29222540X-RAY DIFFRACTION100
2.0762-2.12820.29371380.26652542X-RAY DIFFRACTION100
2.1282-2.18570.24031590.24642559X-RAY DIFFRACTION100
2.1857-2.250.30011320.2422559X-RAY DIFFRACTION100
2.25-2.32270.22261410.24222549X-RAY DIFFRACTION100
2.3227-2.40570.26711410.23712570X-RAY DIFFRACTION100
2.4057-2.5020.29711530.23252554X-RAY DIFFRACTION100
2.502-2.61590.26831370.23752582X-RAY DIFFRACTION100
2.6159-2.75380.23721030.23782602X-RAY DIFFRACTION100
2.7538-2.92630.25751540.23522561X-RAY DIFFRACTION100
2.9263-3.15230.25441310.22142617X-RAY DIFFRACTION100
3.1523-3.46950.25251380.19492602X-RAY DIFFRACTION100
3.4695-3.97150.18131360.17562635X-RAY DIFFRACTION100
3.9715-5.00350.18931230.14912663X-RAY DIFFRACTION100
5.0035-55.10.23811440.21832776X-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)
10.1034-0.0166-0.01370.0180.01650.0529-0.03630.0667-0.00430.05970.0244-0.00870.2635-0.0515-00.2992-0.039-0.01120.222-0.01730.2304-32.1789-24.5799-8.5057
20.12550.04030.04470.16510.03930.0331-0.0115-0.00290.00620.0282-0.0283-0.09150.0368-0.004300.2204-0.02730.00440.21970.00590.2377-35.5079-2.4883-0.3743
30.04680.01990.05130.0410.00170.0602-0.01330.0175-0.0324-0.2057-0.0506-0.01470.0984-0.07270.00010.275-0.04560.02660.2926-0.03470.2762-50.75096.8009-15.7901
40.18640.05020.15280.17880.19580.22110.00260.0344-0.006-0.00780.0166-0.013-0.0362-0.0392-00.16750.00470.00360.21030.00160.1883-21.176917.9803-6.3301
50.0775-0.0357-0.01940.0224-0.01320.1501-0.30540.23390.2535-0.25940.18130.167-0.14880.0035-0.11660.4204-0.2366-0.17670.35120.06150.2639-13.4236-8.4907-22.516
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 91 )
2X-RAY DIFFRACTION2chain 'A' and (resid 92 through 207 )
3X-RAY DIFFRACTION3chain 'A' and (resid 208 through 266 )
4X-RAY DIFFRACTION4chain 'B' and (resid 13 through 188 )
5X-RAY DIFFRACTION5chain 'B' and (resid 189 through 266 )

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