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- PDB-4k3b: The crystal structure of BamA from Neisseria gonorrhoeae -

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Basic information

Entry
Database: PDB / ID: 4k3b
TitleThe crystal structure of BamA from Neisseria gonorrhoeae
ComponentsOuter membrane protein assembly factor BamA
KeywordsMEMBRANE PROTEIN / beta-barrel membrane protein / insertase
Function / homology
Function and homology information


Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / cell outer membrane / membrane => GO:0016020
Similarity search - Function
membrane protein fhac: a member of the omp85/tpsb transporter family / 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 ...membrane protein fhac: a member of the omp85/tpsb transporter family / 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 / Porin / Ubiquitin-like (UB roll) / Roll / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Outer membrane protein assembly factor BamA
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsNoinaj, N. / Lukacik, P. / Chang, H. / Easley, N. / Buchanan, S.K.
CitationJournal: Nature / Year: 2013
Title: Structural insight into the biogenesis of beta-barrel membrane proteins.
Authors: Noinaj, N. / Kuszak, A.J. / Gumbart, J.C. / Lukacik, P. / Chang, H. / Easley, N.C. / Lithgow, T. / Buchanan, S.K.
History
DepositionApr 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Oct 2, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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


Theoretical massNumber of molelcules
Total (without water)88,0471
Polymers88,0471
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)59.525, 270.206, 190.618
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Outer membrane protein assembly factor BamA


Mass: 88047.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Strain: FA 1090 / Gene: bamA, NGO1801 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5F5W8

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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: 4.35 Å3/Da / Density % sol: 71.74 %
Crystal growTemperature: 295 K / pH: 7.5
Details: 0.1 M NaCl, 0.1 M K-phosphate 7.0, 32% PEG 300, and 200 mM Na-malonate, pH 7.5, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 1, 2011
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 26110 / Num. obs: 25674 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.2 % / Rsym value: 0.14 / Net I/σ(I): 17.2
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 2582 / Rsym value: 0.957 / % possible all: 99.2

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIXmodel building
PHENIX(phenix.refine: dev_1103)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→14.999 Å / SU ML: 0.53 / σ(F): 1.35 / Phase error: 30.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2779 1964 7.65 %random
Rwork0.232 ---
obs0.2356 25674 99.8 %-
all-26110 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→14.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5748 0 0 0 5748
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125885
X-RAY DIFFRACTIONf_angle_d2.0427999
X-RAY DIFFRACTIONf_dihedral_angle_d20.5952051
X-RAY DIFFRACTIONf_chiral_restr0.139889
X-RAY DIFFRACTIONf_plane_restr0.0091048
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.27920.39511380.37031675X-RAY DIFFRACTION100
3.2792-3.36690.37771390.33481673X-RAY DIFFRACTION100
3.3669-3.46480.36791390.30621675X-RAY DIFFRACTION100
3.4648-3.57520.32831370.29281650X-RAY DIFFRACTION100
3.5752-3.70120.34021390.27681680X-RAY DIFFRACTION100
3.7012-3.84690.32351390.25711674X-RAY DIFFRACTION100
3.8469-4.01880.31541380.24931675X-RAY DIFFRACTION100
4.0188-4.22620.26181400.22431694X-RAY DIFFRACTION100
4.2262-4.48430.24421390.19161683X-RAY DIFFRACTION100
4.4843-4.81990.22091400.17921687X-RAY DIFFRACTION100
4.8199-5.28560.26611420.18771700X-RAY DIFFRACTION100
5.2856-6.0070.25691430.21291736X-RAY DIFFRACTION100
6.007-7.41290.28331430.23821722X-RAY DIFFRACTION100
7.4129-14.99920.22951480.20191786X-RAY DIFFRACTION99
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)
10.96681.1578-0.2493.3019-0.55120.76320.21240.1034-0.09180.7621-0.18010.3826-0.12890.0246-0.06210.79990.00270.02150.6843-0.28451.07667.3522-45.0053-2.5746
21.66620.3240.00283.7602-0.59041.08820.1780.5057-0.819-0.66590.17170.71790.15030.1345-0.13081.5722-0.0476-0.03511.0438-0.11580.80144.7544-26.7775-32.3541
32.42710.0555-0.75772.5593-0.39713.48-0.1136-0.0114-0.0275-0.82180.0027-0.33140.26680.06680.0220.7617-0.04530.14670.5686-0.00790.597-15.867711.7795-24.224
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 283 )
2X-RAY DIFFRACTION2chain 'A' and (resid 284 through 414 )
3X-RAY DIFFRACTION3chain 'A' and (resid 415 through 792 )

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