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Yorodumi- PDB-5hki: Crystal structure of Mycobacterium tuberculosis H37Rv orotate pho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hki | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis H37Rv orotate phosphoribosyltransferase in complex with Fe(III) dicitrate | ||||||
Components | Orotate phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / OPRT / de novo pyrimidine nucleotide synthesis / ferric dicitrate complex | ||||||
Function / homology | Function and homology information UMP biosynthetic process / orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / pyrimidine nucleobase biosynthetic process / 'de novo' UMP biosynthetic process / magnesium ion binding Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Donini, S. / Ferraris, D.M. / Bolognesi, G. / Rizzi, M. | ||||||
Funding support | Italy, 1items
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Citation | Journal: Sci Rep / Year: 2017 Title: Structural investigations on orotate phosphoribosyltransferase from Mycobacterium tuberculosis, a key enzyme of the de novo pyrimidine biosynthesis. Authors: Donini, S. / Ferraris, D.M. / Miggiano, R. / Massarotti, A. / Rizzi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hki.cif.gz | 140.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hki.ent.gz | 111.1 KB | Display | PDB format |
PDBx/mmJSON format | 5hki.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hki_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 5hki_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 5hki_validation.xml.gz | 27.4 KB | Display | |
Data in CIF | 5hki_validation.cif.gz | 37.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hk/5hki ftp://data.pdbj.org/pub/pdb/validation_reports/hk/5hki | HTTPS FTP |
-Related structure data
Related structure data | 5hkfC 5hklC 2p1zS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 20202.830 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: No His-tag was traced in this case. The overall electron density presents a gaps between the residues 1-3, numbered from the N-terminal methionine. Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Gene: pyrE, umpA, Rv0382c, MTV036.17c / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P9WHK9, orotate phosphoribosyltransferase #2: Chemical | #3: 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: 2.67 Å3/Da / Density % sol: 54.04 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 0.01M Iron(III) chloride hexahydrate, 0.1M Sodium citrate tribasic dihydrate pH 6.1, 10% (v/v) Jeffamine M-600 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→42.17 Å / Num. obs: 18336 / % possible obs: 95.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.74 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.78 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2P1Z Resolution: 2.4→64.99 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.89 / SU B: 9.45 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.443 / ESU R Free: 0.283 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.789 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→64.99 Å
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Refine LS restraints |
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