+Open data
-Basic information
Entry | Database: PDB / ID: 3dwm | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis CysO, an antigen | ||||||
Components | 9.5 kDa culture filtrate antigen cfp10A | ||||||
Keywords | TRANSFERASE / Ubiquitin like / Sulfur carrier protein | ||||||
Function / homology | Function and homology information Cysteine synthesis from O-phosphoserine / cysteine biosynthetic process / protein-containing complex / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.69 Å | ||||||
Authors | Jurgenson, C.T. / Burns, K.E. / Begley, T.P. / Ealick, S.E. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Crystal structure of a sulfur carrier protein complex found in the cysteine biosynthetic pathway of Mycobacterium tuberculosis. Authors: Jurgenson, C.T. / Burns, K.E. / Begley, T.P. / Ealick, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dwm.cif.gz | 43.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dwm.ent.gz | 30.9 KB | Display | PDB format |
PDBx/mmJSON format | 3dwm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dw/3dwm ftp://data.pdbj.org/pub/pdb/validation_reports/dw/3dwm | HTTPS FTP |
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-Related structure data
Related structure data | 3dwgSC 3dwiC 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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 2
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-Components
#1: Protein | Mass: 9564.656 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: cfp10A, Rv1335, MT1376.1, MTCY130.20 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A646, UniProt: P9WP33*PLUS #2: 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: 2.4 Å3/Da / Density % sol: 48.83 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2 M NaNO3, 20% w/v PEG 3350, plus Rv3206 in a 1:1 mass ratio, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 14, 2007 |
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: 2.69→39.97 Å / Num. obs: 5022 / % possible obs: 99.2 % / Redundancy: 4 % / Rsym value: 0.145 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.69→2.76 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.392 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3DWG, chain C Resolution: 2.69→39.97 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.909 / SU B: 13.295 / SU ML: 0.264 / Cross valid method: THROUGHOUT / ESU R Free: 0.359 / 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: 49.931 Å2
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Refinement step | Cycle: LAST / Resolution: 2.69→39.97 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.69→2.76 Å / Total num. of bins used: 20
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