[English] 日本語
Yorodumi- PDB-1qki: X-RAY STRUCTURE OF HUMAN GLUCOSE 6-PHOSPHATE DEHYDROGENASE (VARIA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qki | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | X-RAY STRUCTURE OF HUMAN GLUCOSE 6-PHOSPHATE DEHYDROGENASE (VARIANT CANTON R459L) COMPLEXED WITH STRUCTURAL NADP+ | |||||||||
Components | GLUCOSE-6-PHOSPHATE 1-DEHYDROGENASE | |||||||||
Keywords | OXIDOREDUCTASE / OXIDOREDUTASE / (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 / glucose-6-phosphate dehydrogenase activity / response to iron(III) ion / Pentose phosphate pathway / pentose-phosphate shunt, oxidative branch / 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 / glucose-6-phosphate dehydrogenase activity / response to iron(III) ion / Pentose phosphate pathway / pentose-phosphate shunt, oxidative branch / NADPH regeneration / negative regulation of cell growth involved in cardiac muscle cell development / glucose 6-phosphate metabolic process / NADP metabolic process / pentose-phosphate shunt / D-glucose binding / NFE2L2 regulates pentose phosphate pathway genes / response to food / erythrocyte maturation / cholesterol biosynthetic process / centriolar satellite / negative regulation of reactive oxygen species metabolic process / regulation of neuron apoptotic process / substantia nigra development / glutathione metabolic process / lipid metabolic process / TP53 Regulates Metabolic Genes / response to organic cyclic compound / cytoplasmic side of plasma membrane / glucose metabolic process / NADP binding / cellular response to oxidative stress / response to ethanol / intracellular membrane-bounded organelle / protein homodimerization activity / extracellular exosome / identical protein binding / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Au, S.W.N. / Gover, S. / Lam, V.M.S. / Adams, M.J. | |||||||||
Citation | 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. #1: 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 |
| |||||||||
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 OF ALL SUBUNITS 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 |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1qki.cif.gz | 768.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1qki.ent.gz | 635.2 KB | Display | PDB format |
PDBx/mmJSON format | 1qki.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qki_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1qki_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 1qki_validation.xml.gz | 142.2 KB | Display | |
Data in CIF | 1qki_validation.cif.gz | 184 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qk/1qki ftp://data.pdbj.org/pub/pdb/validation_reports/qk/1qki | HTTPS FTP |
-Related structure data
Related structure data | 1dpgS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | THERE ARE TWO TETRAMERS ABCD AND EFGH IN THE ASYMMETRICUNIT; THESE ARE RELATED BY NON-CRYSTALLOGRAPHY SYMMETRY.DUE TO THE DIFFERENCE OF HINGE ANGLE IN EVERY SUBUNIT, TWOMATRICES ARE PROVIDED TO GENERATE A WHOLE SUBUNIT - ONEFOR THE COENZYME DOMAIN (RESIDUES 31- 200) AND ANOTHER FORTHE LARGE DOMAIN (RESIDUE 201 -511). PRO 172 IS ONLY INTHE CIS CONFORMATION IN SUBUNIT E. |
-Components
#1: Protein | Mass: 59167.367 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Gene: G6PD / Plasmid: PTRC99A/G6PDR459L / Gene (production host): G6PD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DF213 References: UniProt: P11413, glucose-6-phosphate dehydrogenase (NADP+) #2: Chemical | ChemComp-NAP / #3: Chemical | ChemComp-GOA / #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Compound details | AS ALL THE EIGHT SUBUNITS ARE VERY SIMILAR, ONLY THE SALT BRIDGES WITHIN SUBUNIT A AND WITHIN ...AS ALL THE EIGHT SUBUNITS ARE VERY SIMILAR, ONLY THE SALT BRIDGES WITHIN SUBUNIT A AND WITHIN SUBUNIT E ARE GIVEN. FOR DETAILS OF RESIDUES FORMING INTERSUBUN | Source details | THE G6PD PROTEIN USED IN THIS WORK IS THE NATURAL VARIANT ARG459 -> LEU (CANTON, CLASS II, FREQUENT IN CHINA). | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
---|
-Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.5 % / Description: 3 DATA SETS WERE MERGED, SEE REFERENCE 1. | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Method: vapor diffusion, hanging drop / pH: 5.8 Details: HANGING DROP VAPOUR DIFFUSION. 1+1 MICROLITER DROPS IN THE WELL 0.1M SODIUM CITRATE, 0.05M GLYCOLIC ACID, PH 5.8. PROTEIN CONCENTRATION 10MG/ML | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: used microseeding, Au, S.W.N., (1999) Acta Crystallogr.,Sect.D, 55, 826. pH: 5.8 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.870, 1.488 | |||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1997 / Details: MIRRORS | |||||||||
Radiation | Monochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
| |||||||||
Reflection | Resolution: 3→25 Å / Num. obs: 98864 / % possible obs: 85.3 % / Observed criterion σ(I): 4 / Redundancy: 2.2 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 5.2 | |||||||||
Reflection shell | Resolution: 3→3.2 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 1.4 / Rsym value: 0.565 / % possible all: 74.7 | |||||||||
Reflection | *PLUS Num. measured all: 647973 | |||||||||
Reflection shell | *PLUS Lowest resolution: 3.05 Å / % possible obs: 72 % / Rmerge(I) obs: 0.565 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DPG Resolution: 3→25 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: FREE R-VALUE / σ(F): 0 Details: LITTLE OF THE N-TERMINAL TAIL IS SEEN IN THE ELECTRON DENSITY MAP; SEGMENTS BUILT HERE VARY IN LENGTH AND CONFORMATION IN EACH SUBUNIT AND DO NOT OBEY THE NON-CRYSTALLOGRAPHIC SYMMETRY. FOR ...Details: LITTLE OF THE N-TERMINAL TAIL IS SEEN IN THE ELECTRON DENSITY MAP; SEGMENTS BUILT HERE VARY IN LENGTH AND CONFORMATION IN EACH SUBUNIT AND DO NOT OBEY THE NON-CRYSTALLOGRAPHIC SYMMETRY. FOR DETAILS OF THE RESIDUES RESTRAINED IN NCS GROUPS 1 AND 2, SEE JRNL REFERENCE. PARAMETER FILES FOR GLYCOLATE AND GLYCEROL ARE COMBINED INTO ONE FILE. TOPOLOGY FILES FOR GLYCOLATE AND GLYCEROL ARE COMBINED INTO ONE FILE.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 25 Å / Luzzati sigma a obs: 0.57 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→25 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Rms dev Biso : 3.21 Å2 / Rms dev position: 0.84 Å / Weight Biso : 1 / Weight position: 50 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3→3.05 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.405 |