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Yorodumi- PDB-1c47: BINDING DRIVEN STRUCTURAL CHANGES IN CRYSTALINE PHOSPHOGLUCOMUTAS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c47 | ||||||
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Title | BINDING DRIVEN STRUCTURAL CHANGES IN CRYSTALINE PHOSPHOGLUCOMUTASE ASSOCIATED WITH CHEMICAL REACTION | ||||||
Components | ALPHA-D-GLUCOSE 1,6-BISPHOSPHATE PHOSPHOTRANSFERASE | ||||||
Keywords | TRANSFERASE / PHOSPHOGLUCOMUTASE / PHOSPHOTRANSFERASE WITH BOUND REACTION INTERMEDIATE | ||||||
Function / homology | Function and homology information phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) / phosphoglucomutase activity / sarcoplasmic reticulum / glucose metabolic process / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Baranidharan, S. / Ray Jr., W.J. | ||||||
Citation | Journal: To be Published Title: Binding Driven Structural Changes in Crystaline Phosphoglucomutase Associated with Chemical Reaction Authors: Baranidharan, S. / Ray Jr., W.J. / Liu, Y. #1: Journal: Biochemistry / Year: 1993 Title: Structural Changes at the Metal Ion Binding Site During the Phosphoglucomutase Reaction Authors: Ray Jr., W.J. / Post, C.B. / Liu, Y. / Rhyu, G.I. #2: Journal: J.Biol.Chem. / Year: 1992 Title: The Crystal Structure of Phosphoglucomutase Refined at 2.7 A Resolution Authors: Dai, J.B. / Liu, Y. / Ray, W.J. / Konno, M. #3: Journal: J.Biol.Chem. / Year: 1986 Title: The Catalytic Activity of Muscle Phosphoglucomutase in the Crystalline Phase Authors: Ray Jr., W.J. #4: Journal: J.Biol.Chem. / Year: 1986 Title: The Structure of Rabbit Muscle Phosphoglucomutase at Intermediate Resolution Authors: Lin, Z.-J. / Konno, M. / Abad-Zapatero, C. / Murthy, R.W.M.R.N. / Ray Jr., W.J. / Rossmann, M.G. #5: Journal: Acta Crystallogr.,Sect.D / Year: 1997 Title: Structure of Rabbit Muscle Phosphoglucomutase at 2.4 A Resolution Authors: Liu, Y.W. / Ray Jr., W.J. / Baranidharan, S. #6: Journal: Acta Crystallogr.,Sect.D / Year: 1997 Title: ENHANCED DIFFRACTIVITY OF PHOSPHOGLUCOMUTASE CRYSTALS - USE OF AN ALTERNATE CRYOCRYSTALLOGRAPHIC PROCEDURE Authors: Ray Jr., W.R. / Baranidharan, S. / Liu, Y.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c47.cif.gz | 225.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c47.ent.gz | 180.1 KB | Display | PDB format |
PDBx/mmJSON format | 1c47.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1c47_validation.pdf.gz | 836.8 KB | Display | wwPDB validaton report |
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Full document | 1c47_full_validation.pdf.gz | 860.6 KB | Display | |
Data in XML | 1c47_validation.xml.gz | 25.7 KB | Display | |
Data in CIF | 1c47_validation.cif.gz | 39 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/1c47 ftp://data.pdbj.org/pub/pdb/validation_reports/c4/1c47 | HTTPS FTP |
-Related structure data
Related structure data | 3pmgS S: Starting model for refinement |
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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
#1: Protein | Mass: 61499.926 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Organ: MUSCLE / References: UniProt: P00949, EC: 2.7.5.1 #2: Sugar | ChemComp-G16 / | #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: 3.12 Å3/Da / Density % sol: 60.63 % / Description: PDB ENTRY 3PMG HAS RELATED INFORMATION |
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-Data collection
Diffraction | Mean temperature: 289 K |
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Diffraction source | Wavelength: 1.54 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Apr 1, 1996 / Details: NI FILTER |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. obs: 46085 / % possible obs: 96.5 % / Observed criterion σ(I): 1 / Redundancy: 2.2 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.082 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3PMG Resolution: 2.7→6 Å / σ(F): 1
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Displacement parameters | Biso mean: 22.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.7 Å / Total num. of bins used: 20
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Xplor file | Serial no: 1 / Param file: PARAM19 / Topol file: TOPH19.PRO |