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Yorodumi- PDB-6khr: Structure of glycinamide-RNase-transformylase T from Mycobacteriu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6khr | ||||||
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Title | Structure of glycinamide-RNase-transformylase T from Mycobacterium tuberculosis | ||||||
Components | Formate-dependent phosphoribosylglycinamide formyltransferase | ||||||
Keywords | TRANSFERASE / purine salvag pathway | ||||||
Function / homology | Function and homology information purine ribonucleotide biosynthetic process / phosphoribosylglycinamide formyltransferase activity / magnesium ion binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis H37Rv (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.786 Å | ||||||
Authors | Chen, C. / Wang, J. | ||||||
Citation | Journal: Emerg Microbes Infect / Year: 2020 Title: Structural characterization of glycinamide-RNase-transformylase T fromMycobacterium tuberculosis. Authors: Chen, C. / Liu, Z. / Liu, L. / Wang, J. / Jin, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6khr.cif.gz | 259.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6khr.ent.gz | 208.9 KB | Display | PDB format |
PDBx/mmJSON format | 6khr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6khr_validation.pdf.gz | 451.1 KB | Display | wwPDB validaton report |
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Full document | 6khr_full_validation.pdf.gz | 465.7 KB | Display | |
Data in XML | 6khr_validation.xml.gz | 25.4 KB | Display | |
Data in CIF | 6khr_validation.cif.gz | 34.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kh/6khr ftp://data.pdbj.org/pub/pdb/validation_reports/kh/6khr | HTTPS FTP |
-Related structure data
Related structure data | 1eyzS S: Starting model for refinement |
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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: 43815.633 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Strain: H37Rv / Gene: purT, Rv0389 / Production host: Escherichia coli (E. coli) / References: UniProt: P95197 #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: 2.6 Å3/Da / Density % sol: 52.78 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.06 M sodium acetate, pH4.6, 6.0% PEG4000, 32% glycerol. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.978 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.786→48.719 Å / Num. obs: 23300 / % possible obs: 99.4 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.266 / Rpim(I) all: 0.098 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.79→2.94 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.874 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 27385 / Rpim(I) all: 0.32 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EYZ Resolution: 2.786→48.719 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.22
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 207.35 Å2 / Biso mean: 63.7125 Å2 / Biso min: 22.93 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.786→48.719 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 44.3701 Å / Origin y: -14.0443 Å / Origin z: -8.2524 Å
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Refinement TLS group |
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