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Yorodumi- PDB-2y85: CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS PHOSPHORIBOSYL IS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2y85 | ||||||
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Title | CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS PHOSPHORIBOSYL ISOMERASE WITH BOUND RCDRP | ||||||
Components | PHOSPHORIBOSYL ISOMERASE A | ||||||
Keywords | ISOMERASE / BIFUNCTIONAL ENZYME / TRYPTOPHAN BIOSYNTHESIS / HISTIDINE BIOSYNTHESIS / TIM-BARREL / AROMATIC AMINO ACID 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 / L-histidine biosynthetic process / tryptophan biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | 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 | 2y85.cif.gz | 360.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y85.ent.gz | 293.4 KB | Display | PDB format |
PDBx/mmJSON format | 2y85.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2y85_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 2y85_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 2y85_validation.xml.gz | 36.9 KB | Display | |
Data in CIF | 2y85_validation.cif.gz | 50 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/2y85 ftp://data.pdbj.org/pub/pdb/validation_reports/y8/2y85 | HTTPS FTP |
-Related structure data
Related structure data | 2y88C 2y89C 1vzwS 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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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 25658.766 Da / Num. of mol.: 4 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 #2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-137 / #5: 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: 2.23 Å3/Da / Density % sol: 44.29 % / Description: NONE |
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Crystal grow | pH: 5.7 Details: 32% PEG 6000, 0.1M SODIUM CITRATE PH 5.7, 5MM RCDRP. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.978 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 13, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. obs: 34306 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 4.9 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.1 / % possible all: 95.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1VZW Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.866 / SU B: 24.641 / SU ML: 0.29 / Cross valid method: THROUGHOUT / ESU R: 0.719 / ESU R Free: 0.33 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.899 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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Refine LS restraints |
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