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Yorodumi- PDB-4x58: Anthranilate phosphoribosyl transferase variant N138A from Mycoba... -
+Open data
-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 | ||||||
Components | Anthranilate phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / Anthranilate Phosphoribosyltransferase / Anthranilic Acids / Mycobacterium tuberculosis / Magnesium / Tryptophan / mutation / Magnesium binding / Phosphoribosyl pyrophosphate | ||||||
Function / homology | Function and homology information anthranilate phosphoribosyltransferase / anthranilate phosphoribosyltransferase activity / tryptophan biosynthetic process / magnesium ion binding / extracellular region / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Cookson, T.V.M. / Evans, G.L. / Parker, E.J. / Lott, J.S. | ||||||
Citation | Journal: Biochemistry / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4x58.cif.gz | 263.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4x58.ent.gz | 211.8 KB | Display | PDB format |
PDBx/mmJSON format | 4x58.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4x58_validation.pdf.gz | 835.7 KB | Display | wwPDB validaton report |
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Full document | 4x58_full_validation.pdf.gz | 838.3 KB | Display | |
Data in XML | 4x58_validation.xml.gz | 27.2 KB | Display | |
Data in CIF | 4x58_validation.cif.gz | 39.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x5/4x58 ftp://data.pdbj.org/pub/pdb/validation_reports/x5/4x58 | HTTPS FTP |
-Related structure data
Related structure data | 4x59C 4x5aC 4x5bC 4x5cC 4x5dC 4x5eC 3qr9S C: citing same article (ref.) 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 on special symmetry positions |
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-Components
-Protein / Sugars , 2 types, 3 molecules AB
#1: Protein | Mass: 38805.859 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: trpD / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A5U4M0, UniProt: P9WFX5*PLUS, anthranilate phosphoribosyltransferase #4: Sugar | ChemComp-PRP / | |
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-Non-polymers , 5 types, 282 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95369 Å | |||||||||||||||||||||||||||
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
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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