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- PDB-4x5c: Anthranilate phosphoribosyltransferase variant R193L from Mycobac... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4x5c | ||||||
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Title | Anthranilate phosphoribosyltransferase variant R193L from Mycobacterium tuberculosis with pyrophosphate/PRPP and Mg2+ bound | ||||||
![]() | 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. / 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 | ![]() | 256.7 KB | Display | ![]() |
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PDB format | ![]() | 206.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4x58C ![]() 4x59C ![]() 4x5aC ![]() 4x5bC ![]() 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
#1: Protein | Mass: 38804.848 Da / Num. of mol.: 2 / Mutation: R193L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A5U4M0, UniProt: P9WFX5*PLUS, anthranilate phosphoribosyltransferase #2: Sugar | ChemComp-PRP / | #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-POP / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.45 % |
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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: Dec 3, 2012 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.33→94.12 Å / Num. obs: 29405 / % possible obs: 100 % / Redundancy: 7.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.182 / Rpim(I) all: 0.072 / Net I/σ(I): 10.2 / Num. measured all: 216139 / Scaling rejects: 2 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3QR9 Resolution: 2.33→94.12 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.917 / SU B: 19.716 / SU ML: 0.205 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.376 / ESU R Free: 0.258 / 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: 89.03 Å2 / Biso mean: 40.194 Å2 / Biso min: 19.3 Å2
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Refinement step | Cycle: final / Resolution: 2.33→94.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.33→2.391 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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