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- PDB-5eq7: Crystal structure of Medicago truncatula Histidinol-Phosphate Pho... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5eq7 | ||||||
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Title | Crystal structure of Medicago truncatula Histidinol-Phosphate Phosphatase (MtHPP) in complex with free phosphate | ||||||
![]() | Inositol monophosphatase | ||||||
![]() | BIOSYNTHETIC PROTEIN / histidine biosynthesis / metabolic pathways / dimer / plant | ||||||
Function / homology | ![]() histidinol-phosphatase / histidinol-phosphatase activity / L-histidine biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ruszkowski, M. / Dauter, Z. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 133.7 KB | Display | ![]() |
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PDB format | ![]() | 101.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.2 KB | Display | ![]() |
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Full document | ![]() | 447.1 KB | Display | |
Data in XML | ![]() | 15.2 KB | Display | |
Data in CIF | ![]() | 22.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5eq8C ![]() 5eq9C ![]() 5eqaC ![]() 4n81S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-PO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 36.03 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Protein at 19 mg/ml concentration. 15% PEG 3350, 0.2 M diammonium hydrogen phosphate, pH 8.0. Paraton-N as cryoprotectant |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Jun 26, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.992 Å / Relative weight: 1 |
Reflection | Resolution: 1.19→40 Å / Num. obs: 76240 / % possible obs: 99.9 % / Redundancy: 34.3 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 24.7 |
Reflection shell | Resolution: 1.19→1.22 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 2 / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4n81 Resolution: 1.19→38.9 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.045 / SU ML: 0.021 / Cross valid method: FREE R-VALUE / ESU R: 0.028 / ESU R Free: 0.03 / 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: 18.039 Å2
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Refinement step | Cycle: 1 / Resolution: 1.19→38.9 Å
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Refine LS restraints |
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