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Yorodumi- PDB-1vqu: Crystal structure of Anthranilate phosphoribosyltransferase 2 (17... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vqu | ||||||
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Title | Crystal structure of Anthranilate phosphoribosyltransferase 2 (17130499) from Nostoc sp. at 1.85 A resolution | ||||||
Components | Anthranilate phosphoribosyltransferase 2 | ||||||
Keywords | TRANSFERASE / 17130499 / Anthranilate phosphoribosyltransferase 2 / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI | ||||||
Function / homology | Function and homology information anthranilate phosphoribosyltransferase / anthranilate phosphoribosyltransferase activity / tryptophan biosynthetic process / magnesium ion binding Similarity search - Function | ||||||
Biological species | Nostoc sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of Anthranilate phosphoribosyltransferase 2 (17130499) from Nostoc sp. at 1.85 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vqu.cif.gz | 140 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vqu.ent.gz | 108 KB | Display | PDB format |
PDBx/mmJSON format | 1vqu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vq/1vqu ftp://data.pdbj.org/pub/pdb/validation_reports/vq/1vqu | HTTPS FTP |
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-Related structure data
Related structure data | 1kgzS S: Starting model for refinement |
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Similar structure data | |
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: 39319.656 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7120 / Gene: trpD2 / Production host: Escherichia coli (E. coli) References: UniProt: Q8YXQ9, anthranilate phosphoribosyltransferase #2: Chemical | #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 | Density Matthews: 2.23 Å3/Da / Density % sol: 44.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop Details: 20.025% PEG 3350, 0.2M Acetate_Na, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 |
Detector | Type: ADSC / Detector: CCD / Date: Oct 19, 2003 |
Radiation | Monochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→99.05 Å / Num. obs: 52559 / % possible obs: 98.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 41.56 Å2 / Rsym value: 0.063 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.85→1.9 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.3 / Num. unique all: 3920 / Rsym value: 0.749 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1kgz Resolution: 1.85→99.05 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 7.948 / SU ML: 0.115 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.133 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.689 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→99.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 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 | Refine-ID: X-RAY DIFFRACTION / Selection: ALL
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