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Yorodumi- PDB-7wgk: Crystal structure of Adenosine triphosphate phosphoribosyltransfe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wgk | ||||||
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Title | Crystal structure of Adenosine triphosphate phosphoribosyltransferase (HisG) from Acinetobacter baumannii at 3.13 A resolution | ||||||
Components | ATP phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / Catalytic Domain of ATP-PRT / HisG | ||||||
Function / homology | Function and homology information ATP phosphoribosyltransferase / ATP phosphoribosyltransferase activity / L-histidine biosynthetic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Acinetobacter baumannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.13 Å | ||||||
Authors | Ahmad, N. / Maurya, A. / Singh, P.K. / Viswanathan, V. / Sharma, P. / Singh, T.P. / Sharma, S. | ||||||
Funding support | India, 1items
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Citation | Journal: To Be Published Title: Crystal structure of Adenosine triphosphate phosphoribosyltransferase (HisG) from Acinetobacter baumannii at 3.13 A resolution Authors: Ahmad, N. / Maurya, A. / Singh, P.K. / Viswanathan, V. / Sharma, P. / Singh, T.P. / Sharma, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wgk.cif.gz | 103.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wgk.ent.gz | 76.1 KB | Display | PDB format |
PDBx/mmJSON format | 7wgk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wg/7wgk ftp://data.pdbj.org/pub/pdb/validation_reports/wg/7wgk | HTTPS FTP |
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-Related structure data
Related structure data | 5m8hS 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: 25113.203 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: hisG / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: V5VGC6, ATP phosphoribosyltransferase #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: 2.97 Å3/Da / Density % sol: 58.66 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1M Sodium Acetate Trihydrate (pH 4.6), 2M Sodium Formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 3.13→59.49 Å / Num. obs: 11022 / % possible obs: 99.8 % / Redundancy: 14.9 % / Biso Wilson estimate: 69.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.109 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 3.13→3.18 Å / Redundancy: 15 % / Rmerge(I) obs: 1.249 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 532 / CC1/2: 0.93 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5M8H Resolution: 3.13→59.488 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.847 / SU B: 26.73 / SU ML: 0.436 / Cross valid method: FREE R-VALUE / ESU R Free: 0.553 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.246 Å2
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Refinement step | Cycle: LAST / Resolution: 3.13→59.488 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: 20
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