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Open data
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Basic information
Entry | Database: PDB / ID: 3zcx | ||||||
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Title | Structure of GAPDH from Thermosynechococcus elongatus | ||||||
![]() | GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE / CALVIN CYCLE / PHOTOSYNTHESIS | ||||||
Function / homology | ![]() Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glucose metabolic process / NAD binding / NADP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cotton, C.A.R. / Murray, J.W. | ||||||
![]() | ![]() Title: Structure of Gapdh Authors: Cotton, C.A.R. / Murray, J.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 276.6 KB | Display | ![]() |
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PDB format | ![]() | 225.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 27.8 KB | Display | |
Data in CIF | ![]() | 39 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3zdfC ![]() 4boyC ![]() 3b1jS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: _ / Auth seq-ID: 0 - 335 / Label seq-ID: 17 - 352
NCS oper: (Code: given Matrix: (-0.9316, 0.08015, -0.3547), Vector: |
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Components
#1: Protein | Mass: 38577.766 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: Q8DIW5, glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 53 % / Description: NONE |
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Crystal grow | Details: 60 MM SODIUM CITRATE PH 5.5, 12% W/V PEG 3000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→76.06 Å / Num. obs: 40432 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.18 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 4.61 |
Reflection shell | Resolution: 2.19→2.25 Å / Redundancy: 6.21 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.06 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3B1J Resolution: 2.19→70.96 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.95 / SU B: 9.107 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.176 / 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: 44.466 Å2
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Refinement step | Cycle: LAST / Resolution: 2.19→70.96 Å
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Refine LS restraints |
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