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Yorodumi- PDB-3x3m: Crystal structure of EccB1 of Mycobacterium tuberculosis in space... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3x3m | ||||||
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Title | Crystal structure of EccB1 of Mycobacterium tuberculosis in spacegroup P212121 | ||||||
Components | ESX-1 secretion system protein EccB1 | ||||||
Keywords | PROTEIN TRANSPORT / alpha-beta-alpha sandwich / beta-sheet / ATPase | ||||||
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 H37Rv (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Zhang, X.L. / Li, D.F. / Zhang, X.E. / Bi, L.J. / Wang, D.C. | ||||||
Citation | Journal: Faseb J. / Year: 2015 Title: Core component EccB1 of the Mycobacterium tuberculosis type VII secretion system is a periplasmic ATPase. Authors: Zhang, X.L. / Li, D.F. / Fleming, J. / Wang, L.W. / Zhou, Y. / Wang, D.C. / Zhang, X.E. / 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 | 3x3m.cif.gz | 174.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3x3m.ent.gz | 134 KB | Display | PDB format |
PDBx/mmJSON format | 3x3m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3x3m_validation.pdf.gz | 428.2 KB | Display | wwPDB validaton report |
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Full document | 3x3m_full_validation.pdf.gz | 429.4 KB | Display | |
Data in XML | 3x3m_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | 3x3m_validation.cif.gz | 31.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x3/3x3m ftp://data.pdbj.org/pub/pdb/validation_reports/x3/3x3m | HTTPS FTP |
-Related structure data
Related structure data | 3x3nSC 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 H37Rv (bacteria) Strain: H37Rv / Gene: LH57_21080, P425_04028, Rv3869, RVBD_3869 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: I6Y4Q7, UniProt: P9WNR7*PLUS | ||
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#2: Chemical | #3: 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: 2.15 Å3/Da / Density % sol: 42.91 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20mM Tris-Cl pH 7.5, 100mM magnesium formate, 15% [w/v] PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-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: May 3, 2013 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→39.42 Å / Num. all: 32078 / Num. obs: 31116 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 5.4 / Num. unique all: 3779 / Rsym value: 0.227 / % possible all: 84.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3X3N Resolution: 1.9→36.021 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): 0 / Phase error: 20.7 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.978 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.9→36.021 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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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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