+Open data
-Basic information
Entry | Database: PDB / ID: 1mjw | ||||||
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Title | STRUCTURE OF INORGANIC PYROPHOSPHATASE MUTANT D42N | ||||||
Components | INORGANIC PYROPHOSPHATASE | ||||||
Keywords | HYDROLASE / ACID ANHYDRIDE HYDROLASE / MUTATION | ||||||
Function / homology | Function and homology information inorganic triphosphate phosphatase activity / inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / magnesium ion binding / zinc ion binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.95 Å | ||||||
Authors | Oganesyan, V. / Harutyunyan, E.H. / Avaeva, S.M. / Samygina, V.R. / Huber, R. | ||||||
Citation | Journal: Biochemistry Mosc. / Year: 1998 Title: Three-dimensional structures of mutant forms of E. coli inorganic pyrophosphatase with Asp-->Asn single substitution in positions 42, 65, 70, and 97. Authors: Avaeva, S.M. / Rodina, E.V. / Vorobyeva, N.N. / Kurilova, S.A. / Nazarova, T.I. / Sklyankina, V.A. / Oganessyan, V.Y. / Samygina, V.R. / Harutyunyan, E.H. #1: Journal: FEBS Lett. / Year: 1994 Title: X-Ray Crystallographic Studies of Recombinant Inorganic Pyrophosphatase from Escherichia Coli Authors: Oganessyan, V.Yu. / Kurilova, S.A. / Vorobyeva, N.N. / Nazarova, T.I. / Popov, A.N. / Lebedev, A.A. / Avaeva, S.M. / Harutyunyan, E.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mjw.cif.gz | 82.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mjw.ent.gz | 63.5 KB | Display | PDB format |
PDBx/mmJSON format | 1mjw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mjw_validation.pdf.gz | 382.6 KB | Display | wwPDB validaton report |
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Full document | 1mjw_full_validation.pdf.gz | 390 KB | Display | |
Data in XML | 1mjw_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 1mjw_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mj/1mjw ftp://data.pdbj.org/pub/pdb/validation_reports/mj/1mjw | 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.504235, -0.862655, 0.039672), Vector: |
-Components
#1: Protein | Mass: 19596.348 Da / Num. of mol.: 2 / Mutation: D42N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: JM109 / Plasmid: PUC19 Gene (production host): PYROPHOSPHATASE FROM ESCHERICHIA COLI Production host: Escherichia coli (E. coli) / References: UniProt: P0A7A9, inorganic diphosphatase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 40 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Avaeva, S., (1997) FEBS Lett., 410, 502. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 25910 / % possible obs: 97.5 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.08 |
Reflection | *PLUS Highest resolution: 1.95 Å / Lowest resolution: 15 Å / Num. obs: 259100 / Num. measured all: 2581560 / Rmerge(I) obs: 0.057 |
-Processing
Software | Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.95→15 Å / σ(F): 1 Details: ESTIMATED COORD. ERROR 0.25 ANGSTROMS FINAL RMS COORD. SHIFT 0.002 ANGSTROMS
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Displacement parameters | Biso mean: 34.25 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→15 Å
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Refine LS restraints |
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Refinement | *PLUS Num. reflection obs: 259100 / Rfactor obs: 0.191 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |