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Yorodumi- PDB-2wee: Crystal structure of Rv0371c from Mycobacterium tuberculosis H37Rv -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wee | ||||||
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Title | Crystal structure of Rv0371c from Mycobacterium tuberculosis H37Rv | ||||||
Components | MOBA-RELATED PROTEIN | ||||||
Keywords | UNKNOWN FUNCTION | ||||||
Function / homology | MobA-like NTP transferase / MobA-like NTP transferase domain / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / metal ion binding / Alpha Beta / MobA-like NTP transferase domain-containing protein Function and homology information | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS H37RV (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Cho, H.J. / Kang, B.S. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Rv0371C from Mycobacterium Tuberculosis H37Rv Authors: Cho, H.J. / Kang, B.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wee.cif.gz | 94 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wee.ent.gz | 72 KB | Display | PDB format |
PDBx/mmJSON format | 2wee.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wee_validation.pdf.gz | 452.2 KB | Display | wwPDB validaton report |
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Full document | 2wee_full_validation.pdf.gz | 454.7 KB | Display | |
Data in XML | 2wee_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | 2wee_validation.cif.gz | 29 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/we/2wee ftp://data.pdbj.org/pub/pdb/validation_reports/we/2wee | HTTPS FTP |
-Related structure data
Related structure data | 2we9SC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 21158.334 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) MYCOBACTERIUM TUBERCULOSIS H37RV (bacteria) References: UniProt: O53706 #2: Chemical | #3: 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: 2.2 Å3/Da / Density % sol: 44 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 0.1 M MES PH 6.0 AND 18% PEG 4000 BY MICRO-SEEDING |
-Data collection
Diffraction | Mean temperature: 294 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 12, 2008 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. obs: 40721 / % possible obs: 89.4 % / Observed criterion σ(I): 1.65 / Redundancy: 7.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 37.6 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.36 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WE9 Resolution: 1.65→31.25 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.926 / SU B: 6.168 / SU ML: 0.104 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.68 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→31.25 Å
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Refine LS restraints |
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