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- PDB-3zdf: Structure of GAPDH with CP12 peptide from Thermosynechococcus elo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3zdf | ||||||
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Title | Structure of GAPDH with CP12 peptide from Thermosynechococcus elongatus | ||||||
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![]() | OXIDOREDUCTASE / CALVIN CYCLE / PHOTOSYNTHESIS | ||||||
Function / homology | ![]() negative regulation of reductive pentose-phosphate cycle / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / apoplast / 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 | ![]() | 287.2 KB | Display | ![]() |
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PDB format | ![]() | 235.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3zcxSC ![]() 4boyC 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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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
NCS oper:
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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: Protein/peptide | Mass: 2737.865 Da / Num. of mol.: 2 / Fragment: C-TERMINAL, RESIDUES 53-75 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.18 % / Description: NONE |
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Crystal grow | Details: 0.1 M BICINE PH 9, 10 % W/V PEG 20,000/ 2% V/V DIOXANE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 3, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 2.34→63.26 Å / Num. obs: 33680 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.61 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 5.38 |
Reflection shell | Resolution: 2.34→2.4 Å / Redundancy: 6.53 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.18 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3ZCX Resolution: 2.34→63.26 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.926 / SU B: 11.922 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.332 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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: 29.036 Å2
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Refinement step | Cycle: LAST / Resolution: 2.34→63.26 Å
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Refine LS restraints |
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