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- PDB-1rm4: Crystal structure of recombinant photosynthetic glyceraldehyde-3-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1rm4 | ||||||
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Title | Crystal structure of recombinant photosynthetic glyceraldehyde-3-phosphate dehydrogenase A4 isoform, complexed with NADP | ||||||
![]() | Glyceraldehyde 3-phosphate dehydrogenase A | ||||||
![]() | OXIDOREDUCTASE / Rossmann fold / GAPDH-NADP complex | ||||||
Function / homology | ![]() glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) activity / reductive pentose-phosphate cycle / apoplast / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / chloroplast / glucose metabolic process / NAD binding / NADP binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sparla, F. / Fermani, S. / Falini, G. / Ripamonti, A. / Sabatino, P. / Pupillo, P. / Trost, P. | ||||||
![]() | ![]() Title: Coenzyme Site-directed Mutants of Photosynthetic A(4)-GAPDH Show Selectively Reduced NADPH-dependent Catalysis, Similar to Regulatory AB-GAPDH Inhibited by Oxidized Thioredoxin Authors: Sparla, F. / Fermani, S. / Falini, G. / Zaffagnini, M. / Ripamonti, A. / Sabatino, P. / Pupillo, P. / Trost, P. #1: ![]() Title: The dual coenzyme specificity of photosynthetic glyceraldehyde-3-phosphate dehydrogenase interpreted by the crystal structure of A4 isoform complexed with NAD Authors: Falini, G. / Fermani, S. / Ripamonti, A. / Sabatino, P. / Sparla, F. / Pupillo, P. / Trost, P. #2: ![]() Title: Crystal structure of the non-regulatory A4 isoform of spinach chloroplast glyceraldehyde-3-phosphate dehydrogenase complexed with NADP Authors: Fermani, S. / Ripamonti, A. / Sabatino, P. / Zanotti, G. / Scagliarini, S. / Sparla, F. / Trost, P. / Pupillo, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 219 KB | Display | ![]() |
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PDB format | ![]() | 174.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1rm3C ![]() 1rm5C ![]() 1jn0S 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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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is a tetramer (OPQR) generated from the monomer O by the operations: monomer R -x, y, -z and translation 0, 0, 2; monomer Q x, -y, -z and translation 0, 1, 2; monomer P -x, -y, z and translation 0, 1, 0. A second tetramer is generated from dimer AB by the operations: 1/2-x, 3/2-y, z and translation 0, 0, 0. |
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Components
#1: Protein | Mass: 36256.391 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P19866, glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: ammonium sulphate, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 19, 2001 / Details: mirrors |
Radiation | Monochromator: Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→76 Å / Num. all: 94456 / Num. obs: 81938 / % possible obs: 52 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 14.2 Å2 / Rsym value: 0.038 / Net I/σ(I): 24.2 |
Reflection shell | Resolution: 2→2.07 Å / Mean I/σ(I) obs: 3.8 / Num. unique all: 7906 / Rsym value: 0.115 / % possible all: 37.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1JN0 Resolution: 2→69.95 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 4753767.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 63.3863 Å2 / ksol: 0.394412 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→69.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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