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Yorodumi- PDB-6cfv: Structure of Human alpha-Phosphomannomutase 1 in complex with Ino... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cfv | ||||||
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Title | Structure of Human alpha-Phosphomannomutase 1 in complex with Inosine Monophosphate | ||||||
Components | Phosphomannomutase 1 | ||||||
Keywords | ISOMERASE / phosphatase / haloalkanoate dehalogenase superfamily / mutase | ||||||
Function / homology | Function and homology information Synthesis of GDP-mannose / phosphomannomutase / phosphomannomutase activity / GDP-mannose biosynthetic process / mannose metabolic process / protein N-linked glycosylation / cellular response to leukemia inhibitory factor / neuronal cell body / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.918 Å | ||||||
Authors | Ji, T. / Dunaway-Mariano, D. / Allen, K.N. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2018 Title: Structural Basis of the Molecular Switch between Phosphatase and Mutase Functions of Human Phosphomannomutase 1 under Ischemic Conditions. Authors: Ji, T. / Zhang, C. / Zheng, L. / 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 | 6cfv.cif.gz | 74.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cfv.ent.gz | 52.2 KB | Display | PDB format |
PDBx/mmJSON format | 6cfv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cf/6cfv ftp://data.pdbj.org/pub/pdb/validation_reports/cf/6cfv | HTTPS FTP |
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-Related structure data
Related structure data | 6cfrC 6cfsC 6cftC 6cfuC 2fucS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 29786.811 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PMM1, PMMH22 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92871, phosphomannomutase | ||||
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#2: Chemical | #3: Chemical | ChemComp-IMP / | #4: 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: 2.45 Å3/Da / Density % sol: 49.79 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop Details: 20% polyethylene glycol 3350, 0.15 M DL-malate, pH 7.0, 50 mM MgCl2, and 8 mM beta-mercaptoethanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97917 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 26, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97917 Å / Relative weight: 1 |
Reflection | Resolution: 1.918→34.88 Å / Num. obs: 23377 / % possible obs: 98.2 % / Redundancy: 2 % / Net I/σ(I): 30.32 |
Reflection shell | Resolution: 1.918→1.966 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FUC Resolution: 1.918→34.88 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.64
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.918→34.88 Å
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Refine LS restraints |
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LS refinement shell |
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