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Yorodumi- PDB-5eq8: Crystal structure of Medicago truncatula Histidinol-Phosphate Pho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5eq8 | ||||||
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Title | Crystal structure of Medicago truncatula Histidinol-Phosphate Phosphatase (MtHPP) in complex with L-histidinol | ||||||
Components | Inositol monophosphatase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / histidine biosynthesis / metabolic pathways / dimer / plant | ||||||
Function / homology | Function and homology information histidinol-phosphatase / histidinol-phosphatase activity / L-histidine biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | Medicago truncatula (barrel medic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Ruszkowski, M. / Dauter, Z. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Structural Studies of Medicago truncatula Histidinol Phosphate Phosphatase from Inositol Monophosphatase Superfamily Reveal Details of Penultimate Step of Histidine Biosynthesis in Plants. Authors: Ruszkowski, M. / Dauter, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5eq8.cif.gz | 127.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eq8.ent.gz | 103.3 KB | Display | PDB format |
PDBx/mmJSON format | 5eq8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5eq8_validation.pdf.gz | 444.6 KB | Display | wwPDB validaton report |
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Full document | 5eq8_full_validation.pdf.gz | 446 KB | Display | |
Data in XML | 5eq8_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 5eq8_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/5eq8 ftp://data.pdbj.org/pub/pdb/validation_reports/eq/5eq8 | HTTPS FTP |
-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: 30422.305 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: MTR_3g117220 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold / References: UniProt: G7J7Q5 |
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#2: Chemical | ChemComp-HSO / |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.38 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30% PEG 3350, 0.1 M Bis-Tris pH 6.5, 0.2 M ammonium acetate, 10 mM magnesium acetate. Crystals were incubated for 8 min with 5 mM histidinol-phosphate and flash-frozen in Paraton-N |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.7999 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Oct 21, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7999 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→40 Å / Num. obs: 59314 / % possible obs: 99.6 % / Redundancy: 16 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 26.5 |
Reflection shell | Resolution: 1.3→1.38 Å / Redundancy: 15.4 % / Rmerge(I) obs: 1.359 / Mean I/σ(I) obs: 2.1 / % possible all: 97.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→39.04 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.887 / SU ML: 0.034 / Cross valid method: FREE R-VALUE / ESU R: 0.04 / ESU R Free: 0.041 / 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: 22.073 Å2
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Refinement step | Cycle: 1 / Resolution: 1.3→39.04 Å
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