+Open data
-Basic information
Entry | Database: PDB / ID: 4w9t | ||||||
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Title | Crystal structure of HisAP from Streptomyces sp. Mg1 | ||||||
Components | Phosphoribosyl isomerase A | ||||||
Keywords | ISOMERASE / TIM-BARREL / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG | ||||||
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 | Streptomyces sp. Mg1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å | ||||||
Authors | MICHALSKA, K. / VERDUZCO-CASTRO, E.A. / ENDRES, M. / BARONA-GOMEZ, F. / JOACHIMIAK, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochem. J. / Year: 2016 Title: Co-occurrence of analogous enzymes determines evolution of a novel ( beta alpha )8-isomerase sub-family after non-conserved mutations in flexible loop. Authors: Verduzco-Castro, E.A. / Michalska, K. / Endres, M. / Juarez-Vazquez, A.L. / Noda-Garcia, L. / Chang, C. / Henry, C.S. / Babnigg, G. / Joachimiak, A. / Barona-Gomez, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4w9t.cif.gz | 108.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4w9t.ent.gz | 81.3 KB | Display | PDB format |
PDBx/mmJSON format | 4w9t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w9/4w9t ftp://data.pdbj.org/pub/pdb/validation_reports/w9/4w9t | HTTPS FTP |
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-Related structure data
Related structure data | 4tx9C 4u28C 4wuiC 4x9sC 5dn1C 1vzwS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25330.543 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. Mg1 (bacteria) / Gene: priA, hisA, SSAG_02214 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold / References: UniProt: B4V386 | ||
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#2: Chemical | ChemComp-SO4 / #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: 3.01 Å3/Da / Density % sol: 59.15 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 2 M (NH4)2SO4, 0.1 M Bis/Tris, protein 10 mg/ml, pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 20, 2013 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→30 Å / Num. all: 43584 / Num. obs: 43584 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 11.7 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 34.9 |
Reflection shell | Resolution: 1.57→1.6 Å / Redundancy: 8.1 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 2.1 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VZW Resolution: 1.57→27.859 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 18.66 / Stereochemistry target values: ML / Details: HYDROGEN ATOMS HAVE BEEN ADDED IN RIDING POSITIONS
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.57→27.859 Å
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Refine LS restraints |
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LS refinement shell |
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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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