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Yorodumi- PDB-2y89: CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS PHOSPHORIBOSYL IS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2y89 | ||||||
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Title | CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS PHOSPHORIBOSYL ISOMERASE A (VARIANT D11N) | ||||||
Components | PHOSPHORIBOSYL ISOMERASE A | ||||||
Keywords | ISOMERASE / AROMATIC AMINO ACID BIOSYNTHESIS / TRYPTOPHAN BIOSYNTHESIS / TIM BARREL / HISTIDINE BIOSYNTHESIS | ||||||
Function / homology | Function and homology information phosphoribosylanthranilate isomerase / 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase / 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase activity / phosphoribosylanthranilate isomerase activity / histidine biosynthetic process / tryptophan biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Due, A.V. / Kuper, J. / Geerlof, A. / Wilmanns, M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Bisubstrate Specificity in Histidine/Tryptophan Biosynthesis Isomerase from Mycobacterium Tuberculosis by Active Site Metamorphosis. Authors: Due, A.V. / Kuper, J. / Geerlof, A. / Kries, J.P. / Wilmanns, M. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y89.cif.gz | 56 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y89.ent.gz | 44.2 KB | Display | PDB format |
PDBx/mmJSON format | 2y89.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/2y89 ftp://data.pdbj.org/pub/pdb/validation_reports/y8/2y89 | HTTPS FTP |
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-Related 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
#1: Protein | Mass: 25657.781 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PETM11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: P60578, UniProt: P9WMM5*PLUS, phosphoribosylanthranilate isomerase, 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase | ||||
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#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.6 Å3/Da / Density % sol: 73.3 % / Description: NONE |
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Crystal grow | Details: 0.1 M BIS-TRIS PH 7.5, 2.0M AMMONIUM SULFATE. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.801 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 3, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.801 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→57.74 Å / Num. obs: 17377 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 14.14 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 23.86 |
Reflection shell | Resolution: 2.5→2.52 Å / Redundancy: 14.44 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 3.12 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→100 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.901 / SU B: 11.371 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES G144-T147 WERE NOT MODELED OWING TO INSUFFICIENT ELECTRON DENSITY. THE SIDECHAINS OF D135, R141, K174, D175, T177, AND L178 ARE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES G144-T147 WERE NOT MODELED OWING TO INSUFFICIENT ELECTRON DENSITY. THE SIDECHAINS OF D135, R141, K174, D175, T177, AND L178 ARE ALSO POORLY DEFINED IN THE ELECTRON DENSITY MAP AND FOR THAT REASON WERE NOT MODELED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.264 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→100 Å
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