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Yorodumi- PDB-3zs4: CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS PHOSPHORIBOSYL IS... -
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-Basic information
Entry | Database: PDB / ID: 3zs4 | ||||||
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Title | CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS PHOSPHORIBOSYL ISOMERASE WITH BOUND PRFAR | ||||||
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: 1.9 Å | ||||||
Authors | Due, A.V. / Kuper, J. / Geerlof, A. / Wilmanns, M. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Mycobacterium Tuberculosis Phosphoribosyl Isomerase with Bound Prfar Authors: Due, A.V. / Kuper, J. / Geerlof, A. / 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 | 3zs4.cif.gz | 66.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zs4.ent.gz | 47.2 KB | Display | PDB format |
PDBx/mmJSON format | 3zs4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zs/3zs4 ftp://data.pdbj.org/pub/pdb/validation_reports/zs/3zs4 | HTTPS FTP |
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-Related structure data
Related structure data | 2bnt 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
#1: Protein | Mass: 25658.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL References: UniProt: P60578, UniProt: P9WMM5*PLUS, 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase, phosphoribosylanthranilate isomerase |
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#2: Chemical | ChemComp-1PR / |
#3: 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: 2.6 Å3/Da / Density % sol: 52.5 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 0.1 M TRIS-HCL PH 8.5, 2.4 M DI-AMMONIUM HYDROGEN PHOSPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 23, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→57.35 Å / Num. obs: 22159 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.63 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 4.5 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BNT 2bnt Resolution: 1.9→57.35 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.825 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.131 / 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: 18.117 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→57.35 Å
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