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Yorodumi- PDB-4wsp: Racemic crystal structure of Rv1738 from Mycobacterium tuberculos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wsp | ||||||
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Title | Racemic crystal structure of Rv1738 from Mycobacterium tuberculosis (Form-I) | ||||||
Components | protein DL-Rv1738 | ||||||
Keywords | DE NOVO PROTEIN / hypoxic response | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Bunker, R.D. / Mandal, K. / Kent, S.B.H. / Baker, E.N. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 Title: A functional role of Rv1738 in Mycobacterium tuberculosis persistence suggested by racemic protein crystallography. Authors: Bunker, R.D. / Mandal, K. / Bashiri, G. / Chaston, J.J. / Pentelute, B.L. / Lott, J.S. / Kent, S.B. / Baker, E.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wsp.cif.gz | 60.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wsp.ent.gz | 44.4 KB | Display | PDB format |
PDBx/mmJSON format | 4wsp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ws/4wsp ftp://data.pdbj.org/pub/pdb/validation_reports/ws/4wsp | HTTPS FTP |
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-Related structure data
Related structure data | 4wpySC 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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Details | biological unit is the same as asym. |
-Components
#1: Protein | Mass: 10624.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium tuberculosis (bacteria) / References: UniProt: P9WLS3 |
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#2: Chemical | ChemComp-CL / |
#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: 1.66 Å3/Da / Density % sol: 26 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1 microlitre of protein solution containing 9 mg/ml L-Rv1738 and 9 mg/ml D-Rv1738 in water was mixed with 1 microlitre of well solution containing 0.1 M BIS-TRIS pH 5.5, 0.2 M NaCl, 25 % (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-BM-B / Wavelength: 0.97934 Å | |||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 23, 2008 | |||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.65→47.65 Å / Num. obs: 17584 / % possible obs: 98.1 % / Redundancy: 2.8 % / Biso Wilson estimate: 49.07 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.041 / Net I/σ(I): 9.4 / Num. measured all: 49522 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WPY Resolution: 1.65→39.344 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.53 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 137.13 Å2 / Biso mean: 49.4724 Å2 / Biso min: 22.03 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.65→39.344 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: 9
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