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Yorodumi- PDB-1u7p: X-ray Crystal Structure of the Hypothetical Phosphotyrosine Phosp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1u7p | ||||||
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Title | X-ray Crystal Structure of the Hypothetical Phosphotyrosine Phosphatase MDP-1 of the Haloacid Dehalogenase Superfamily | ||||||
Components | magnesium-dependent phosphatase-1 | ||||||
Keywords | HYDROLASE / HAD superfamily / phosphoryl transfer / phosphotyrosine phosphatase / aspartate nucleophile / enzyme evolution / structural enzymology / class III | ||||||
Function / homology | Function and homology information fructosamine metabolic process / acid phosphatase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Peisach, E. / Selengut, J.D. / Dunaway-Mariano, D. / Allen, K.N. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: X-ray Crystal Structure of the Hypothetical Phosphotyrosine Phosphatase MDP-1 of the Haloacid Dehalogenase Superfamily Authors: Peisach, E. / Selengut, J.D. / Dunaway-Mariano, D. / Allen, K.N. #1: Journal: Biochemistry / Year: 2000 Title: MDP-1: A novel eukaryotic magnesium-dependent phosphatase Authors: Selengut, J.D. / Levine, R.L. #2: Journal: Biochemistry / Year: 2001 Title: MDP-1 is a new and distinct member of the haloacid dehalogenase family of aspartate-dependent phosphohydrolases Authors: Selengut, J.D. #3: Journal: Biochemistry / Year: 2000 Title: The crystal structure of bacillus cereus phosphonoacetaldehyde hydrolase: insight into catalysis of phosphorus bond cleavage and catalytic diversification within the HAD enzyme superfamily Authors: Morais, M.C. / Zhang, W. / Baker, A.S. / Zhang, G. / Dunaway-Mariano, D. / Allen, K.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1u7p.cif.gz | 148 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u7p.ent.gz | 116.4 KB | Display | PDB format |
PDBx/mmJSON format | 1u7p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u7/1u7p ftp://data.pdbj.org/pub/pdb/validation_reports/u7/1u7p | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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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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Details | The biological unit is a monomer |
-Components
#1: Protein | Mass: 18605.172 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: AF230273 / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9D967 #2: Chemical | ChemComp-MG / #3: Chemical | #4: 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 Å3/Da / Density % sol: 39.5 % |
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Crystal grow | Temperature: 291 K / pH: 8 Details: PEG 3350, sodium acetate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 8.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 19, 2003 / Details: OSMIC MIRRORS |
Radiation | Monochromator: OSMIC MIRRORS, NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→76.58 Å / Num. obs: 48167 / % possible obs: 93.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 17.4 Å2 / Rsym value: 0.061 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.0485 / % possible all: 88.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: HIGH RESOLUTION MODEL OF MDP-1 WITHOUT MAGNESIUM BOUND Resolution: 1.9→76.58 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 0.5 / Data cutoff high absF: 908245.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.5318 Å2 / ksol: 0.337413 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.1 Å2
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Refine Biso |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→76.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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