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Yorodumi- PDB-3h6p: Crystal structure of Rv3019c-Rv3020c from Mycobacterium tuberculosis -
+Open data
-Basic information
Entry | Database: PDB / ID: 3h6p | ||||||
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Title | Crystal structure of Rv3019c-Rv3020c from Mycobacterium tuberculosis | ||||||
Components |
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Keywords | structural genomics / unknown function / Four-helix bundle / PSI-2 / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC / Integrated Center for Structure and Function Innovation / ISFI | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.91 Å | ||||||
Authors | Chan, S. / Arbing, M. / Phan, T. / Kaufmann, M. / Cascio, D. / Eisenberg, D. / TB Structural Genomics Consortium (TBSGC) / Integrated Center for Structure and Function Innovation (ISFI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of Rv3019c-Rv3020c from Mycobacterium tuberculosis Authors: Chan, S. / Arbing, M. / Phan, T. / Kaufmann, M. / Cascio, D. / Eisenberg, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3h6p.cif.gz | 61.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h6p.ent.gz | 44.9 KB | Display | PDB format |
PDBx/mmJSON format | 3h6p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3h6p_validation.pdf.gz | 460.9 KB | Display | wwPDB validaton report |
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Full document | 3h6p_full_validation.pdf.gz | 462.8 KB | Display | |
Data in XML | 3h6p_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 3h6p_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/3h6p ftp://data.pdbj.org/pub/pdb/validation_reports/h6/3h6p | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 11570.802 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: esxS, Rv3019c, Rv3020c / Plasmid: pET46EkLIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: Q6MX18 #2: Protein | Mass: 10317.367 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: esxR, MT3104, MTV012.33c, Rv3019c, Rv3020c / Plasmid: pET46-EkLIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: P64093, UniProt: P9WNI9*PLUS #3: Chemical | ChemComp-GOL / | #4: 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 grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 26% PEG1500, 0.1 M MMT pH 7.0, , VAPOR DIFFUSION, HANGING DROP, temperature 293K |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97849 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 1, 2009 |
Radiation | Monochromator: Cryo-Cooled Si(111) double crystal. / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97849 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→80 Å / Num. all: 18085 / Num. obs: 18085 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 13.7 % / Rsym value: 0.073 / Net I/σ(I): 25.5 |
Reflection shell | Resolution: 1.91→1.98 Å / Redundancy: 13.9 % / Mean I/σ(I) obs: 6.1 / Rsym value: 0.472 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.91→51.57 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.914 / SU B: 6.463 / SU ML: 0.096 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.156 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.911 Å2
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Refinement step | Cycle: LAST / Resolution: 1.91→51.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.912→1.962 Å / Total num. of bins used: 20
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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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