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- PDB-2dpg: COMPLEX OF INACTIVE MUTANT (H240->N) OF GLUCOSE 6-PHOSPHATE DEHYD... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2dpg | |||||||||
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Title | COMPLEX OF INACTIVE MUTANT (H240->N) OF GLUCOSE 6-PHOSPHATE DEHYDROGENASE FROM LEUCONOSTOC MESENTEROIDES WITH NADP+ | |||||||||
![]() | GLUCOSE 6-PHOSPHATE DEHYDROGENASE | |||||||||
![]() | OXIDOREDUCTASE / CHOH(D) - NAD(P) / NADP/NAD / GLUCOSE METABOLISM | |||||||||
Function / homology | ![]() glucose-6-phosphate dehydrogenase [NAD(P)+] / glucose-6-phosphate dehydrogenase activity / pentose-phosphate shunt, oxidative branch / glucose metabolic process / NADP binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Adams, M.J. / Naylor, C.E. / Paludin, S. / Gover, S. | |||||||||
![]() | ![]() Title: On the mechanism of the reaction catalyzed by glucose 6-phosphate dehydrogenase. Authors: Cosgrove, M.S. / Naylor, C. / Paludan, S. / Adams, M.J. / Levy, H.R. #1: ![]() Title: The Three-Dimensional Structure of Glucose 6-Phosphate Dehydrogenase from Leuconostoc Mesenteroides Refined at 2.0 A Resolution Authors: Rowland, P. / Basak, A.K. / Gover, S. / Levy, H.R. / Adams, M.J. #2: ![]() Title: Site-Directed Mutagenesis to Facilitate X-Ray Structural Studies of Leuconostoc Mesenteroides Glucose 6-Phosphate Dehydrogenase Authors: Adams, M.J. / Basak, A.K. / Gover, S. / Rowland, P. / Levy, H.R. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 109.4 KB | Display | ![]() |
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PDB format | ![]() | 84.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 723.1 KB | Display | ![]() |
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Full document | ![]() | 725.1 KB | Display | |
Data in XML | ![]() | 19 KB | Display | |
Data in CIF | ![]() | 26.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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Components on special symmetry positions |
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Components
#1: Protein | Mass: 54345.602 Da / Num. of mol.: 1 / Mutation: H240N Source method: isolated from a genetically manipulated source Details: THE MUTANT IS INACTIVE, LACKING THE CATALYTIC BASE. THE STRUCTURE CONTAINS A PARTIAL NADP BOUND TO NUCLEOTIDE BINDING DOMAIN. Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P11411, glucose-6-phosphate dehydrogenase (NADP+) |
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#2: Chemical | ChemComp-NAP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 60 % Description: MERGE OF 2.5 ANGSTROM SRS DATA (EXPT 1) WITH 3.5 ANGSTROM IN-HOUSE DATA (EXPT 2). FOR DETAILS, SEE JRNL REFERENCE. | |||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: HANGING DROP VAPOR DIFFUSION. 2+2 MICROLITER DROPS. IN THE WELL 2.27M UNBUFFERED AMMONIUM SULFATE. THE PROTEIN AT 4.8MG/ML IN 0.1M TRIS-HCL AT PH 7.5 WITH 0.5MM NADP+ AND 25MM G6P., vapor ...Details: HANGING DROP VAPOR DIFFUSION. 2+2 MICROLITER DROPS. IN THE WELL 2.27M UNBUFFERED AMMONIUM SULFATE. THE PROTEIN AT 4.8MG/ML IN 0.1M TRIS-HCL AT PH 7.5 WITH 0.5MM NADP+ AND 25MM G6P., vapor diffusion - hanging drop | |||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1994 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.876 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 16263 / % possible obs: 68.4 % / Observed criterion σ(I): -3 / Redundancy: 1.3 % / Biso Wilson estimate: 41.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.5→2.6 Å / Mean I/σ(I) obs: 2.2 / Rsym value: 0.411 / % possible all: 0.548 |
Reflection | *PLUS Num. measured all: 21142 |
Reflection shell | *PLUS Rmerge(I) obs: 0.125 |
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Processing
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Refinement | Method to determine structure: RIGID-BODY, DIFFERENCE FOURIER Starting model: INCOMPLETE REFINED STRUCTURE OF NATIVE PROTEIN CONTAINING NADP Resolution: 2.5→25 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / Cross valid method: FREE R / σ(F): 0 Details: FOR DETAILS OF THE BULK SOLVENT MODELLING, SEE JRNL REFERENCE.
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Displacement parameters | Biso mean: 30.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 25 Å / Luzzati sigma a obs: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.35 |