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Yorodumi- PDB-1e77: COMPLEX OF ACTIVE MUTANT (Q365->C) OF GLUCOSE 6-PHOSPHATE DEHYDRO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1.0E+77 | ||||||
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Title | COMPLEX OF ACTIVE MUTANT (Q365->C) OF GLUCOSE 6-PHOSPHATE DEHYDROGENASE FROM LEUCONOSTOC MESENTEROIDES WITH SUBSTRATE | ||||||
Components | GLUCOSE 6-PHOSPHATE 1-DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / OXIDOREDUCTASE (CHOH(D) - NAD(P)) / GLUCOSE METABOLISM | ||||||
Function / homology | Function and homology information 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 | LEUCONOSTOC MESENTEROIDES (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å | ||||||
Authors | Adams, M.J. / Vandeputte-Rutten, L. / Gover, S. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: An Examination of the Role of Asp-177 in the His-Asp Catalytic Dyad of Leuconostoc Mesenteroides Glucose 6-Phosphate Dehydrogenase: X-Ray Structure and Ph Dependence of Kinetic Parameters of ...Title: An Examination of the Role of Asp-177 in the His-Asp Catalytic Dyad of Leuconostoc Mesenteroides Glucose 6-Phosphate Dehydrogenase: X-Ray Structure and Ph Dependence of Kinetic Parameters of the D177N Mutant Enzyme Authors: Cosgrove, M.S. / Gover, S. / Naylor, C.E. / Vandeputte-Rutten, L. / Adams, M.J. / Levy, H.R. #1: Journal: Structure / Year: 1994 Title: The Three-Dimensional Structure of Glucose 6-Phosphate Dehydrogenase from Leuconostoc Mesenteroides Refined at 2 Angstroms Resolution Authors: Rowland, P. / Basak, A.K. / Gover, S. / Levy, H.R. / Adams, M.J. #2: Journal: Protein Sci. / Year: 1993 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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Remark 650 | HELIX DETERMINATION METHOD: PROCHECK, WITH IDENTIFICATION CORRESPONDING TO 2.0A L. MESENTEROIDES ... HELIX DETERMINATION METHOD: PROCHECK, WITH IDENTIFICATION CORRESPONDING TO 2.0A L. MESENTEROIDES STRUCTURE, 1DPG. HELIX_ID: A,BEND AT K21 IS CONSEQUENCE OF CONSERVED P24. HELIX_ID: B,THE LAST TURN IS 3_10 (CLASS 5). HELIX_ID: C,THE FIRST TURN IS 3_10 (CLASS 5). HELIX_ID: D,THE FIRST TURN IS 3_10 (CLASS 5). HELIX_ID: F,THE FIRST TURN IS 3_10 (CLASS 5). HELIX_ID: H,G231 BRIDGES H & I' SO IS NOT HELICAL. HELIX_ID: I',PART OF HELIX I IN 1DPG. RESIDUES 235-239 DISTORTED BY SIDECHAIN INTERACTION OF N239 WITH D235. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: INITIAL AND TERMINAL RESIDUES ARE AS DEFINED BY PROCHECK. REGISTRATION ... SHEET DETERMINATION METHOD: INITIAL AND TERMINAL RESIDUES ARE AS DEFINED BY PROCHECK. REGISTRATION IS AS GIVEN BY HYDROGEN BONDS AND IN THE CASE OF SHEET COE INVOLVES RESIDUES THAT IMMEDIATELY PRECEDE EACH SHEET ELEMENT. THIS IS DONE TO PRESERVE OBSERVED CONSISTENCY WITH NATIVE STRUCTURE 1DPG. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e77.cif.gz | 110.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e77.ent.gz | 84.8 KB | Display | PDB format |
PDBx/mmJSON format | 1e77.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e7/1e77 ftp://data.pdbj.org/pub/pdb/validation_reports/e7/1e77 | HTTPS FTP |
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-Related structure data
-Links
-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: 54344.660 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) LEUCONOSTOC MESENTEROIDES (bacteria) / Description: SITE DIRECTED MUTAGENESIS / Gene: G6PD / Plasmid: PLMZ / Gene (production host): G6PD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SU294 References: UniProt: P11411, glucose-6-phosphate dehydrogenase (NADP+) |
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#2: Sugar | ChemComp-BG6 / |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
Compound details | CHAIN A ENGINEERED MUTATION GLN365CYS BETA-D-GLUCOSE 6-PHOSPHATE + NADP(+) = D-GLUCONO-DELTA- ...CHAIN A ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 41.3 % Description: MOLECULE LOCATED BY DIFFERENCE FOURIER AND RIGID-BODY REFINEMENT | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.8 Details: HANGING DROP VAPOUR DIFFUSION, 2+2 MICROLITER DROPS. THE WELL BUFFER: 21% W/V PEG 400 IN 0.1M HEPES-NAOH, PH 7.8 WITH 0.2M CALCIUM CHLORIDE. THE PROTEIN AT 7MG/ML, WITH 20MM GLUCOSE 6- ...Details: HANGING DROP VAPOUR DIFFUSION, 2+2 MICROLITER DROPS. THE WELL BUFFER: 21% W/V PEG 400 IN 0.1M HEPES-NAOH, PH 7.8 WITH 0.2M CALCIUM CHLORIDE. THE PROTEIN AT 7MG/ML, WITH 20MM GLUCOSE 6-PHOSPHATE AND 10MM BENZAMIDE ADENINE DINUCLEOTIDE (BAD). | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.88 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 22, 1996 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.88 Å / Relative weight: 1 |
Reflection | Resolution: 2.69→24.9 Å / Num. obs: 13462 / % possible obs: 94.6 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Rsym value: 0.112 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.69→2.79 Å / Mean I/σ(I) obs: 3.3 / Rsym value: 0.331 / % possible all: 93.1 |
Reflection | *PLUS Num. measured all: 38922 / Rmerge(I) obs: 0.112 |
Reflection shell | *PLUS % possible obs: 93.1 % / Rmerge(I) obs: 0.331 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: REFINED COORDINATES OF APO-ENZYME IN THE SAME SPACEGROUP Resolution: 2.69→25 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / Cross valid method: FREE R-VALUE / σ(F): 0 / Details: BULK SOLVENT WAS MODELLED
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Displacement parameters | Biso mean: 19.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 25 Å / Luzzati sigma a obs: 0.27 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.69→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.69→2.79 Å / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 12817 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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