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Yorodumi- PDB-5ebc: Crystal structure of EccB1 of Mycobacterium tuberculosis in space... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ebc | ||||||
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Title | Crystal structure of EccB1 of Mycobacterium tuberculosis in spacegroup P21 (state III) | ||||||
Components | ESX-1 secretion system protein eccB1 | ||||||
Keywords | PROTEIN TRANSPORT / ALPHA-BETA-ALPHA SANDWICH / BETA-SHEET / ATPASE / T7SS / ESX-1 SECRETION SYSTEM | ||||||
Function / homology | Function and homology information symbiont-mediated perturbation of host innate immune response / Hydrolases; Acting on acid anhydrides / peptidoglycan-based cell wall / hydrolase activity / extracellular region / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Zhang, X.L. / Qi, C. / Xie, X.Q. / Li, D.F. / Bi, L.J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2016 Title: Crystallographic observation of the movement of the membrane-distal domain of the T7SS core component EccB1 from Mycobacterium tuberculosis. Authors: Xie, X.Q. / Zhang, X.L. / Qi, C. / Li, D.F. / Fleming, J. / Wang, D.C. / Bi, L.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ebc.cif.gz | 162.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ebc.ent.gz | 126.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ebc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ebc_validation.pdf.gz | 438.1 KB | Display | wwPDB validaton report |
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Full document | 5ebc_full_validation.pdf.gz | 442.7 KB | Display | |
Data in XML | 5ebc_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 5ebc_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/5ebc ftp://data.pdbj.org/pub/pdb/validation_reports/eb/5ebc | HTTPS FTP |
-Related structure data
Related structure data | 5ebdC 3x3mS 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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Unit cell |
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-Components
#1: Protein | Mass: 45704.742 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 72-480 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: eccB1, Rv3869 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P9WNR7 |
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#2: Chemical | ChemComp-CA / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.8 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20 mM Tris-Cl pH 7.5, 100 mM magnesium formate, 15% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 26, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→60.1 Å / Num. obs: 8613 / % possible obs: 96.1 % / Redundancy: 3.3 % / Biso Wilson estimate: 85.1 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 2.5 / % possible all: 88.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3X3M Resolution: 3→30.277 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 32.02 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.612 Å2 / ksol: 0.337 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3→30.277 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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