+Open data
-Basic information
Entry | Database: PDB / ID: 5waq | ||||||
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Title | Structure of BamD from Neisseria gonorrhoeae | ||||||
Components | Outer membrane protein assembly factor BamD | ||||||
Keywords | MEMBRANE PROTEIN / beta-barrel assembly machinery / BAM complex / lipoprotein / tetratrico peptide repeat / TPR domain | ||||||
Function / homology | Function and homology information protein insertion into membrane / Gram-negative-bacterium-type cell outer membrane assembly / cell outer membrane Similarity search - Function | ||||||
Biological species | Neisseria gonorrhoeae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.501 Å | ||||||
Authors | Korotkov, K.V. / Buchanan, S.K. / Noinaj, N. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2018 Title: Structural and functional insights into the role of BamD and BamE within the beta-barrel assembly machinery in Neisseria gonorrhoeae. Authors: Sikora, A.E. / Wierzbicki, I.H. / Zielke, R.A. / Ryner, R.F. / Korotkov, K.V. / Buchanan, S.K. / Noinaj, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5waq.cif.gz | 94.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5waq.ent.gz | 71.6 KB | Display | PDB format |
PDBx/mmJSON format | 5waq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5waq_validation.pdf.gz | 424.8 KB | Display | wwPDB validaton report |
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Full document | 5waq_full_validation.pdf.gz | 425.6 KB | Display | |
Data in XML | 5waq_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 5waq_validation.cif.gz | 11.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wa/5waq ftp://data.pdbj.org/pub/pdb/validation_reports/wa/5waq | HTTPS FTP |
-Related structure data
Related structure data | 5wamC 2yhcS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29193.723 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090) (bacteria) Strain: ATCC 700825 / FA 1090 / Gene: bamD, NGO_0277 / Plasmid: pET20bHT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5F9W0 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.39 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.0M LITHIUM CHLORIDE, 0.1M HEPES PH 7.0, 10% PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 1, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal cryo-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. obs: 12840 / % possible obs: 99.9 % / Redundancy: 8.1 % / Biso Wilson estimate: 74.45 Å2 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.04 / Rrim(I) all: 0.112 / Χ2: 1.036 / Net I/σ(I): 6.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YHC Resolution: 2.501→45.548 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.01 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 202.23 Å2 / Biso mean: 91.47 Å2 / Biso min: 46.03 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.501→45.548 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %
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