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- PDB-4x58: Anthranilate phosphoribosyl transferase variant N138A from Mycoba... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4x58 | ||||||
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Title | Anthranilate phosphoribosyl transferase variant N138A from Mycobacterium tuberculosis in complex with PRPP and Mg | ||||||
![]() | Anthranilate phosphoribosyltransferase | ||||||
![]() | TRANSFERASE / Anthranilate Phosphoribosyltransferase / Anthranilic Acids / Mycobacterium tuberculosis / Magnesium / Tryptophan / mutation / Magnesium binding / Phosphoribosyl pyrophosphate | ||||||
Function / homology | ![]() anthranilate phosphoribosyltransferase / anthranilate phosphoribosyltransferase activity / tryptophan biosynthetic process / magnesium ion binding / extracellular region / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cookson, T.V.M. / Evans, G.L. / Parker, E.J. / Lott, J.S. | ||||||
![]() | ![]() Title: Structures of Mycobacterium tuberculosis Anthranilate Phosphoribosyltransferase Variants Reveal the Conformational Changes That Facilitate Delivery of the Substrate to the Active Site. Authors: Cookson, T.V. / Evans, G.L. / Castell, A. / Baker, E.N. / Lott, J.S. / Parker, E.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 263.2 KB | Display | ![]() |
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PDB format | ![]() | 211.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 835.7 KB | Display | ![]() |
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Full document | ![]() | 838.3 KB | Display | |
Data in XML | ![]() | 27.2 KB | Display | |
Data in CIF | ![]() | 39.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4x59C ![]() 4x5aC ![]() 4x5bC ![]() 4x5cC ![]() 4x5dC ![]() 4x5eC ![]() 3qr9S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein / Sugars , 2 types, 3 molecules AB![](data/chem/img/PRP.gif)
![](data/chem/img/PRP.gif)
#1: Protein | Mass: 38805.859 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A5U4M0, UniProt: P9WFX5*PLUS, anthranilate phosphoribosyltransferase #4: Sugar | ChemComp-PRP / | |
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-Non-polymers , 5 types, 282 molecules ![](data/chem/img/MLT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MLT / | ||||||
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#3: Chemical | ChemComp-GOL / #5: Chemical | #6: Chemical | ChemComp-IMD / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: imidazole malate, PEG 4000 |
-Data collection
Diffraction | Mean temperature: 110 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 18, 2011 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.95369 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.75→94.41 Å / Num. obs: 69172 / % possible obs: 99.8 % / Redundancy: 9.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.045 / Net I/σ(I): 12.7 / Num. measured all: 671321 / Scaling rejects: 18 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3QR9 Resolution: 1.75→94.41 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.779 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 58.77 Å2 / Biso mean: 20.536 Å2 / Biso min: 9.01 Å2
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Refinement step | Cycle: final / Resolution: 1.75→94.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 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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