+Open data
-Basic information
Entry | Database: PDB / ID: 6jd5 | ||||||||||||||||||||||||
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Title | ATPase | ||||||||||||||||||||||||
Components | ESX conserved component EccC2. ESX-2 type VII secretion system protein. Possible membrane protein | ||||||||||||||||||||||||
Keywords | MOTOR PROTEIN / ATPase | ||||||||||||||||||||||||
Function / homology | Function and homology information cell wall / membrane => GO:0016020 / DNA binding / ATP binding / plasma membrane Similarity search - Function | ||||||||||||||||||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||||||||||||||||||||
Authors | Wang, S.H. / Li, J. / Rao, Z.H. | ||||||||||||||||||||||||
Funding support | China, 7items
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Citation | Journal: Protein Cell / Year: 2020 Title: Structural insights into substrate recognition by the type VII secretion system. Authors: Wang, S. / Zhou, K. / Yang, X. / Zhang, B. / Zhao, Y. / Xiao, Y. / Yang, X. / Yang, H. / Guddat, L.W. / Li, J. / Rao, Z. | ||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jd5.cif.gz | 121.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jd5.ent.gz | 91.4 KB | Display | PDB format |
PDBx/mmJSON format | 6jd5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jd/6jd5 ftp://data.pdbj.org/pub/pdb/validation_reports/jd/6jd5 | HTTPS FTP |
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-Related structure data
Related structure data | 6j17C 6j18C 6j19C 6jd4C 4nh0S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30066.225 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: eccC2, Rv3894c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O05450 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.75 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.1 M BIS-TRIS pH 6.5, 45% (v/v) PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→74.674 Å / Num. all: 26929 / Num. obs: 26929 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rpim(I) all: 0.037 / Rrim(I) all: 0.099 / Rsym value: 0.091 / Net I/av σ(I): 7.3 / Net I/σ(I): 13.5 / Num. measured all: 184657 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NH0 Resolution: 2.2→38.707 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.86 / 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: 80.55 Å2 / Biso mean: 40.4184 Å2 / Biso min: 22.18 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→38.707 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
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