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Yorodumi- PDB-4lgl: Crystal Structure of Glycine Decarboxylase P-protein from Synecho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lgl | ||||||
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Title | Crystal Structure of Glycine Decarboxylase P-protein from Synechocystis sp. PCC 6803, apo form | ||||||
Components | Glycine dehydrogenase [decarboxylating] | ||||||
Keywords | OXIDOREDUCTASE / alpha(2) homodimeric / dehydrogenase (decarboxylating) / S / S-(2-hydroxyethyl)thiocysteine | ||||||
Function / homology | Function and homology information glycine dehydrogenase (aminomethyl-transferring) / glycine dehydrogenase (decarboxylating) activity / glycine cleavage complex / glycine decarboxylation via glycine cleavage system / glycine binding / pyridoxal phosphate binding / cytosol Similarity search - Function | ||||||
Biological species | Synechocystis sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.0004 Å | ||||||
Authors | Hasse, D. / Andersson, E. / Carlsson, G. / Masloboy, A. / Hagemann, M. / Bauwe, H. / Andersson, I. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Structure of the Homodimeric Glycine Decarboxylase P-protein from Synechocystis sp. PCC 6803 Suggests a Mechanism for Redox Regulation. Authors: Hasse, D. / Andersson, E. / Carlsson, G. / Masloboy, A. / Hagemann, M. / Bauwe, H. / Andersson, I. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2010 Title: Crystallization and preliminary X-ray diffraction analyses of the homodimeric glycine decarboxylase (P-protein) from the cyanobacterium Synechocystis sp. PCC 6803. Authors: Hasse, D. / Hagemann, M. / Andersson, I. / Bauwe, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lgl.cif.gz | 742.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lgl.ent.gz | 612.6 KB | Display | PDB format |
PDBx/mmJSON format | 4lgl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lgl_validation.pdf.gz | 458 KB | Display | wwPDB validaton report |
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Full document | 4lgl_full_validation.pdf.gz | 472.5 KB | Display | |
Data in XML | 4lgl_validation.xml.gz | 70.2 KB | Display | |
Data in CIF | 4lgl_validation.cif.gz | 101.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lg/4lgl ftp://data.pdbj.org/pub/pdb/validation_reports/lg/4lgl | HTTPS FTP |
-Related structure data
Related structure data | 4lhcC 4lhdC 1wytS C: citing same article (ref.) 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: 107573.289 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Kazusa / Gene: gcvP, slr0293 / Plasmid: pBAD-slr0293 / Production host: Escherichia coli (E. coli) / Strain (production host): LMG194 References: UniProt: P74416, glycine dehydrogenase (aminomethyl-transferring) #2: Chemical | #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: 2.72 Å3/Da / Density % sol: 54.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.75 Details: 100 mM Tris-HCl pH 7.75, 17% PEG 3350, 0.25 M LiCl and 10 mM 2-mercaptoethanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 29, 2008 |
Radiation | Monochromator: na / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2→54.11 Å / Num. all: 158584 / Num. obs: 158314 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 32.9 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 26.88 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 3.53 / Num. unique all: 15696 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1WYT heterodimer Resolution: 2.0004→54.107 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.84 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.935 Å2 / ksol: 0.338 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.0004→54.107 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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