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Yorodumi- PDB-4bnd: Structure of an atypical alpha-phosphoglucomutase similar to euka... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bnd | |||||||||
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Title | Structure of an atypical alpha-phosphoglucomutase similar to eukaryotic phosphomannomutases | |||||||||
Components | (ALPHA-PHOSPHOGLUCOMUTASE) x 2 | |||||||||
Keywords | ISOMERASE / SUBSTRATE SPECIFICITY / PHOSPHOGLUCOSE INTERCONVERSION | |||||||||
Function / homology | Function and homology information phosphomannomutase / phosphomannomutase activity / GDP-mannose biosynthetic process / mannose metabolic process / protein N-linked glycosylation / phosphatase activity / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | LACTOCOCCUS LACTIS SUBSP. CREMORIS MG1363 (lactic acid bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | |||||||||
Authors | Nogly, P. / Matias, P.M. / De Rosa, M. / Castro, R. / Santos, H. / Neves, A.R. / Archer, M. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: High-Resolution Structure of an Atypical [Alpha]-Phosphoglucomutase Related to Eukaryotic Phosphomannomutases Authors: Nogly, P. / Matias, P.M. / De Rosa, M. / Castro, R. / Santos, H. / Neves, A.R. / Archer, M. #1: Journal: J.Biol.Chem. / Year: 2006 Title: The Alpha-Phosphoglucomutase of Lactococcus Lactis is Unrelated to the Alpha-D-Phosphohexomutase Superfamily and is Encoded by the Essential Gene Pgmh. Authors: Neves, A.R. / Pool, W.A. / Castro, R. / Mingote, A. / Santos, F. / Kok, J. / Kuipers, O.P. / Santos, H. #2: Journal: Acta Crystallogr.,Sect.F / Year: 2012 Title: Production and Crystallization of Alpha-Phosphoglucomutase from Lactococcus Lactis. Authors: Nogly, P. / Castro, R. / De Rosa, M. / Neves, A.R. / Santos, H. / Archer, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bnd.cif.gz | 409.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bnd.ent.gz | 344.1 KB | Display | PDB format |
PDBx/mmJSON format | 4bnd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bnd_validation.pdf.gz | 453.1 KB | Display | wwPDB validaton report |
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Full document | 4bnd_full_validation.pdf.gz | 455.2 KB | Display | |
Data in XML | 4bnd_validation.xml.gz | 27.1 KB | Display | |
Data in CIF | 4bnd_validation.cif.gz | 41.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/4bnd ftp://data.pdbj.org/pub/pdb/validation_reports/bn/4bnd | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.8786, -0.1906, 0.4379), Vector: |
-Components
#1: Protein | Mass: 28429.162 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LACTOCOCCUS LACTIS SUBSP. CREMORIS MG1363 (lactic acid bacteria) Plasmid: PNZ8048 Production host: LACTOCOCCUS LACTIS SUBSP. CREMORIS NZ9000 (lactic acid bacteria) References: UniProt: Q00G41, UniProt: A2RIP9*PLUS, phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) | ||||
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#2: Protein | Mass: 28371.061 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LACTOCOCCUS LACTIS SUBSP. CREMORIS MG1363 (lactic acid bacteria) Plasmid: PNZ8048 Production host: LACTOCOCCUS LACTIS SUBSP. CREMORIS NZ9000 (lactic acid bacteria) References: UniProt: Q00G41, UniProt: A2RIP9*PLUS, phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) | ||||
#3: Chemical | ChemComp-GOL / #4: Chemical | #5: 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: 2.3 Å3/Da / Density % sol: 46 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: SEEDING, 2.0 M AMMONIUM SULFATE, 0.1 M HEPES PH 7.5, 2% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9334 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 12, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→33 Å / Num. obs: 89350 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 8.3 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 3.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.5→30.05 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.329 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.064 / ESU R Free: 0.065 / 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 / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.501 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→30.05 Å
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