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Yorodumi- PDB-4lhc: Crystal structure of Synechocystis sp. PCC 6803 glycine decarboxy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lhc | ||||||
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Title | Crystal structure of Synechocystis sp. PCC 6803 glycine decarboxylase (P-protein), holo form with pyridoxal-5'-phosphate and glycine | ||||||
Components | Glycine dehydrogenase [decarboxylating] | ||||||
Keywords | OXIDOREDUCTASE / alpha(2) homodimer / dehydrogenase (decarboxylating) / cofactor pyridoxal 5'-phosphate | ||||||
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: 1.899 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 | 4lhc.cif.gz | 752.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lhc.ent.gz | 616.4 KB | Display | PDB format |
PDBx/mmJSON format | 4lhc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lhc_validation.pdf.gz | 518.1 KB | Display | wwPDB validaton report |
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Full document | 4lhc_full_validation.pdf.gz | 531.4 KB | Display | |
Data in XML | 4lhc_validation.xml.gz | 78 KB | Display | |
Data in CIF | 4lhc_validation.cif.gz | 116.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lh/4lhc ftp://data.pdbj.org/pub/pdb/validation_reports/lh/4lhc | HTTPS FTP |
-Related structure data
Related structure data | 4lglSC 4lhdC 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 107649.172 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) |
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-Non-polymers , 6 types, 1425 molecules
#2: Chemical | ChemComp-GLY / #3: Chemical | #4: Chemical | ChemComp-PO4 / #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-BCN / | #7: 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: 2.74 Å3/Da / Density % sol: 55.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5 Details: 100 mM Bicine pH 9, 1.6 M (NH4)3PO4, 5 mM TCEP and 0.2 mM PLP, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 1, 2011 / Details: multilayer mirror |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 1.899→99 Å / Num. all: 185699 / Num. obs: 185454 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 1.899→1.97 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 4.3 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4LGL Resolution: 1.899→49.783 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 17.31 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.894 Å2 / ksol: 0.38 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.899→49.783 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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