+Open data
-Basic information
Entry | Database: PDB / ID: 6xmv | |||||||||
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Title | The crystal structure of Neisseria gonorrhoeae DolP (NGO1985) | |||||||||
Components | Hemolysin,Endolysin | |||||||||
Keywords | PROTEIN TRANSPORT / BON domain / lipoprotein / T4 lysozyme | |||||||||
Function / homology | Function and homology information viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium Similarity search - Function | |||||||||
Biological species | Neisseria gonorrhoeae (bacteria) Enterobacteria phage T4 (virus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 Å | |||||||||
Authors | Li, J. / Peterson Brown, L.E. / Reed, R.W. / Wierzbicki, I.H. / Sikora, A.E. / Korotkov, K.V. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: The structure and function of a new component of Bam complex in Neisseria Authors: Wierzbicki, I.H. / Zielke, R.A. / Li, J. / Begum, A.A. / Baarda, B.I. / Peterson Brown, L.E. / Reed, R.W. / Korotkov, K.V. / Jerse, A.E. / Sikora, A.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xmv.cif.gz | 129.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xmv.ent.gz | 99.5 KB | Display | PDB format |
PDBx/mmJSON format | 6xmv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xmv_validation.pdf.gz | 424 KB | Display | wwPDB validaton report |
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Full document | 6xmv_full_validation.pdf.gz | 426.2 KB | Display | |
Data in XML | 6xmv_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | 6xmv_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xm/6xmv ftp://data.pdbj.org/pub/pdb/validation_reports/xm/6xmv | HTTPS FTP |
-Related structure data
Related structure data | 2hukS 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: 37943.969 Da / Num. of mol.: 1 / Mutation: C1054T, C1097A, K1162A Source method: isolated from a genetically manipulated source Details: BamG fragment 46-202 Source: (gene. exp.) Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090) (bacteria), (gene. exp.) Enterobacteria phage T4 (virus) Strain: ATCC 700825 / FA 1090 / Gene: NGO_1985, e, T4Tp126 / Plasmid: pKV1435 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta2 / References: UniProt: Q5F5E4, UniProt: D9IEF7, lysozyme | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.42 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Na acetate pH 4.5, 3M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 18, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.75→57.785 Å / Num. obs: 10641 / % possible obs: 98.6 % / Redundancy: 5.745 % / Biso Wilson estimate: 48.682 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.175 / Rrim(I) all: 0.193 / Χ2: 0.944 / Net I/σ(I): 9.74 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HUK Resolution: 2.75→57.785 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.32 / Phase error: 28.35 / 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: 166.82 Å2 / Biso mean: 55.0817 Å2 / Biso min: 18.05 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.75→57.785 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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