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Yorodumi- PDB-2bhl: X-RAY STRUCTURE OF HUMAN GLUCOSE-6-PHOSPHATE DEHYDROGENASE (DELET... -
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-Basic information
Entry | Database: PDB / ID: 2bhl | ||||||
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Title | X-RAY STRUCTURE OF HUMAN GLUCOSE-6-PHOSPHATE DEHYDROGENASE (DELETION VARIANT) COMPLEXED WITH GLUCOSE-6-PHOSPHATE | ||||||
Components | GLUCOSE-6-PHOSPHATE 1-DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / OXIDOREDUCTASE (CHOH(D)-NADP) / GLUCOSE METABOLISM | ||||||
Function / homology | Function and homology information negative regulation of protein glutathionylation / pentose biosynthetic process / ribose phosphate biosynthetic process / glucose-6-phosphate dehydrogenase (NADP+) / positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / pentose-phosphate shunt, oxidative branch / glucose-6-phosphate dehydrogenase activity / response to iron(III) ion / Pentose phosphate pathway / NADPH regeneration ...negative regulation of protein glutathionylation / pentose biosynthetic process / ribose phosphate biosynthetic process / glucose-6-phosphate dehydrogenase (NADP+) / positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / pentose-phosphate shunt, oxidative branch / glucose-6-phosphate dehydrogenase activity / response to iron(III) ion / Pentose phosphate pathway / NADPH regeneration / negative regulation of cell growth involved in cardiac muscle cell development / glucose 6-phosphate metabolic process / NADP metabolic process / pentose-phosphate shunt / glucose binding / NFE2L2 regulates pentose phosphate pathway genes / response to food / cholesterol biosynthetic process / erythrocyte maturation / centriolar satellite / negative regulation of reactive oxygen species metabolic process / glutathione metabolic process / regulation of neuron apoptotic process / substantia nigra development / TP53 Regulates Metabolic Genes / lipid metabolic process / cytoplasmic side of plasma membrane / response to organic cyclic compound / glucose metabolic process / cellular response to oxidative stress / NADP binding / response to ethanol / intracellular membrane-bounded organelle / protein homodimerization activity / extracellular exosome / membrane / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Kotaka, M. / Gover, S. / Lam, V.M.S. / Adams, M.J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Structural Studies of Glucose-6-Phosphate and Nadp+ Binding to Human Glucose-6-Phosphate Dehydrogenase Authors: Kotaka, M. / Gover, S. / Vandeputte-Rutten, L. / Au, S.W.N. / Lam, V.M.S. / Adams, M.J. #1: Journal: Structure / Year: 2000 Title: Human Glucose-6-Phosphate Dehydrogenase: The Crystal Structure Reveals a Structural Nadp Molecule and Provides Insights Into Enzyme Deficiency Authors: Au, S.W.N. / Gover, S. / Lam, V.M.S. / Adams, M.J. #2: Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Solution of the Structure of Tetrameric Human Glucose 6-Phosphate Dehydrogenase by Molecular Replacement Authors: Au, S.W.N. / Naylor, C.E. / Gover, S. / Vandeputte-Rutten, L. / Scopes, D.A. / Mason, P.J. / Luzzatto, L. / Lam, V.M.S. / Adams, M.J. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: PROCHECK, WITH IDENTIFICATION CORRESPONDING TO THE 2.0A LEUCONOSTOC ... HELIX DETERMINATION METHOD: PROCHECK, WITH IDENTIFICATION CORRESPONDING TO THE 2.0A LEUCONOSTOC MESENTERODES STRUCTURE, 1DPG. THE BEND AT LYS 47 IN HELIX A IS A CONSEQUENCE OF THE CONSERVED PRO 50. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: PROCHECK WITH EXTENSION TAKEN WHERE HYDROGEN BONDING INDICATES THAT ... SHEET DETERMINATION METHOD: PROCHECK WITH EXTENSION TAKEN WHERE HYDROGEN BONDING INDICATES THAT THIS IS APPROPRIATE |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bhl.cif.gz | 204.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bhl.ent.gz | 163.8 KB | Display | PDB format |
PDBx/mmJSON format | 2bhl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bh/2bhl ftp://data.pdbj.org/pub/pdb/validation_reports/bh/2bhl | HTTPS FTP |
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-Related structure data
Related structure data | 2bh9C 1qkiS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.99911, -0.00678, -0.04166), Vector: |
-Components
#1: Protein | Mass: 56397.258 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Details: THE 25 N-TERMINAL RESIDUES HAVE BEEN REMOVED AND THE FIRST RESIDUE IS VALINE, NOT HISTIDINE Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PTRC99A/DG6PD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DF213 References: UniProt: P11413, glucose-6-phosphate dehydrogenase (NADP+) #2: Chemical | ChemComp-GOL / #3: Sugar | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 59.8 % |
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Crystal grow | pH: 8.5 Details: 0.1M TRIS, PH 8.5; 0.2M MGCL2; 12% PEG 4000; 5% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 27, 2002 / Details: MIRRORS |
Radiation | Monochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→69 Å / Num. obs: 32261 / % possible obs: 98.9 % / Observed criterion σ(I): -4 / Redundancy: 6.8 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 2.9→3.07 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2 / % possible all: 92.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QKI CHAIN A, B Resolution: 2.9→69 Å / Cross valid method: FREE R-VALUE / σ(F): 0 Details: RESIDUES 506 TO 515 WERE DISORDERED AND NOT INCLUDED
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Refinement step | Cycle: LAST / Resolution: 2.9→69 Å
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Refine LS restraints |
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