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Yorodumi- PDB-6i34: Crystal structure of Neanderthal glycine decarboxylase (P-protein) -
+Open data
-Basic information
Entry | Database: PDB / ID: 6i34 | ||||||
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Title | Crystal structure of Neanderthal glycine decarboxylase (P-protein) | ||||||
Components | Neanderthal Glycine decarboxylase | ||||||
Keywords | OXIDOREDUCTASE / mitochondrial / glycine decarboxylase / glycine cleavage system P-protein | ||||||
Function / homology | Function and homology information response to methylamine / response to lipoic acid / glycine dehydrogenase (aminomethyl-transferring) / pyridoxal binding / glycine dehydrogenase (decarboxylating) activity / glycine catabolic process / Glycine degradation / glycine cleavage complex / glycine decarboxylation via glycine cleavage system / glycine binding ...response to methylamine / response to lipoic acid / glycine dehydrogenase (aminomethyl-transferring) / pyridoxal binding / glycine dehydrogenase (decarboxylating) activity / glycine catabolic process / Glycine degradation / glycine cleavage complex / glycine decarboxylation via glycine cleavage system / glycine binding / cellular response to leukemia inhibitory factor / pyridoxal phosphate binding / electron transfer activity / lyase activity / mitochondrial matrix / protein homodimerization activity / mitochondrion / nucleoplasm / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens neanderthalensis (Neandertal) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Van Laer, B. / Kapp, U. / Leonard, G. / Mueller-Dieckmann, C. | ||||||
Citation | Journal: To Be Published Title: Structural insights in human glycine decarboxylase and comparison with the Neanderthal variant Authors: Van Laer, B. / Kapp, U. / Signor, L. / Leonard, G. / Mueller-Dieckmann, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6i34.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6i34.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 6i34.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6i34_validation.pdf.gz | 519.6 KB | Display | wwPDB validaton report |
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Full document | 6i34_full_validation.pdf.gz | 548.6 KB | Display | |
Data in XML | 6i34_validation.xml.gz | 138.9 KB | Display | |
Data in CIF | 6i34_validation.cif.gz | 196.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i3/6i34 ftp://data.pdbj.org/pub/pdb/validation_reports/i3/6i34 | HTTPS FTP |
-Related structure data
Related structure data | 6i33SC 6i35C 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 109546.219 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens neanderthalensis (Neandertal) Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P23378*PLUS, glycine dehydrogenase (aminomethyl-transferring) |
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-Non-polymers , 5 types, 1384 molecules
#2: Chemical | ChemComp-PLP / #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-PEG / #5: Chemical | ChemComp-GOL / #6: 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: 2.32 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M HEPES pH 7, 6 % PEG3350, 10 mM DTT |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 23, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→47.9 Å / Num. obs: 245944 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 5.1 % / CC1/2: 0.993 / Rrim(I) all: 0.192 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 1.2 / CC1/2: 0.64 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6I33 Resolution: 2.1→47.9 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / Cross valid method: THROUGHOUT / ESU R: 0.248 / ESU R Free: 0.19 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.11 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→47.9 Å
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Refine LS restraints |
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