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Yorodumi- PDB-8hmn: Crystal structure of GAPDH complexed with arsenate from Lactiplan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8hmn | ||||||
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Title | Crystal structure of GAPDH complexed with arsenate from Lactiplantibacillus plantarum | ||||||
Components | Glyceraldehyde-3-phosphate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / GAPDH / arsenate / Lactiplantibacillus plantarum | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / glucose metabolic process / NAD binding / NADP binding Similarity search - Function | ||||||
Biological species | Lactiplantibacillus plantarum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å | ||||||
Authors | Yoneda, K. / Kinoshita, H. | ||||||
Funding support | Japan, 1items
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Citation | Journal: To Be Published Title: Crystal structure of GAPDH complexed with arsenate from Lactiplantibacillus plantarum Authors: Yoneda, K. / Kinoshita, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hmn.cif.gz | 281.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hmn.ent.gz | 225.3 KB | Display | PDB format |
PDBx/mmJSON format | 8hmn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hmn_validation.pdf.gz | 3.2 MB | Display | wwPDB validaton report |
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Full document | 8hmn_full_validation.pdf.gz | 3.2 MB | Display | |
Data in XML | 8hmn_validation.xml.gz | 61.5 KB | Display | |
Data in CIF | 8hmn_validation.cif.gz | 86.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hm/8hmn ftp://data.pdbj.org/pub/pdb/validation_reports/hm/8hmn | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 38647.348 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactiplantibacillus plantarum (bacteria) Gene: gap / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIPL / References: UniProt: Q88YH6 |
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-Non-polymers , 5 types, 850 molecules
#2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-ART / #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-TRS / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.22 Å3/Da / Density % sol: 44.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 25%(w/v) PEG 1500, 0.1 M MIB buffer |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Cryo / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: May 31, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→48.49 Å / Num. obs: 69658 / % possible obs: 99.8 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.056 / Rrim(I) all: 0.104 / Χ2: 1.12 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.87→1.9 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.908 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5267 / CC1/2: 0.762 / Rpim(I) all: 0.574 / Χ2: 0.96 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.16→45.59 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.91 / SU B: 6.931 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.353 / ESU R Free: 0.239 / 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 / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.668 Å2
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Refinement step | Cycle: 1 / Resolution: 2.16→45.59 Å
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