[English] 日本語
Yorodumi
- PDB-2bh9: X-RAY STRUCTURE OF A DELETION VARIANT OF HUMAN GLUCOSE 6-PHOSPHAT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2bh9
TitleX-RAY STRUCTURE OF A DELETION VARIANT OF HUMAN GLUCOSE 6-PHOSPHATE DEHYDROGENASE COMPLEXED WITH STRUCTURAL AND COENZYME NADP
ComponentsGLUCOSE-6-PHOSPHATE 1-DEHYDROGENASE
KeywordsOXIDOREDUCTASE / OXIDOREDUCTASE (CHOH(D)-NADP) / CARBOHYDRATE METABOLISM / GLUCOSE METABOLISM
Function / homology
Function and homology information


pentose biosynthetic process / ribose phosphate biosynthetic process / response to iron(III) ion / positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / glucose-6-phosphate dehydrogenase (NADP+) / glucose-6-phosphate dehydrogenase activity / Pentose phosphate pathway / pentose-phosphate shunt, oxidative branch / negative regulation of cell growth involved in cardiac muscle cell development / NADPH regeneration ...pentose biosynthetic process / ribose phosphate biosynthetic process / response to iron(III) ion / positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / glucose-6-phosphate dehydrogenase (NADP+) / glucose-6-phosphate dehydrogenase activity / Pentose phosphate pathway / pentose-phosphate shunt, oxidative branch / negative regulation of cell growth involved in cardiac muscle cell development / NADPH regeneration / 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 / negative regulation of reactive oxygen species metabolic process / regulation of neuron apoptotic process / glutathione metabolic process / substantia nigra development / TP53 Regulates Metabolic Genes / lipid metabolic process / centriolar satellite / 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
Glucose-6-phosphate dehydrogenase, active site / Glucose-6-phosphate dehydrogenase active site. / Glucose-6-phosphate dehydrogenase / Glucose-6-phosphate dehydrogenase, NAD-binding / Glucose-6-phosphate dehydrogenase, C-terminal / Glucose-6-phosphate dehydrogenase, NAD binding domain / Glucose-6-phosphate dehydrogenase, C-terminal domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain ...Glucose-6-phosphate dehydrogenase, active site / Glucose-6-phosphate dehydrogenase active site. / Glucose-6-phosphate dehydrogenase / Glucose-6-phosphate dehydrogenase, NAD-binding / Glucose-6-phosphate dehydrogenase, C-terminal / Glucose-6-phosphate dehydrogenase, NAD binding domain / Glucose-6-phosphate dehydrogenase, C-terminal domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Glucose-6-phosphate 1-dehydrogenase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGover, S. / Vandeputte-Rutten, L. / Au, S.W.N. / 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
DepositionJan 8, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 25, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GLUCOSE-6-PHOSPHATE 1-DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0685
Polymers56,3971
Non-polymers1,6714
Water2,918162
1
A: GLUCOSE-6-PHOSPHATE 1-DEHYDROGENASE
hetero molecules

A: GLUCOSE-6-PHOSPHATE 1-DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,13710
Polymers112,7952
Non-polymers3,3428
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)60.760, 172.480, 217.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-2007-

HOH

21A-2010-

HOH

31A-2011-

HOH

41A-2033-

HOH

51A-2042-

HOH

61A-2045-

HOH

71A-2101-

HOH

-
Components

#1: Protein GLUCOSE-6-PHOSPHATE 1-DEHYDROGENASE / G6PD


Mass: 56397.258 Da / Num. of mol.: 1 / Fragment: RESIDUES 26-514
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PKKG6PD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DR612
References: UniProt: P11413, glucose-6-phosphate dehydrogenase (NADP+)
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE HIS 26 VAL
Sequence detailsTHE G6PD USED IN THIS WORK IS AN ENGINEERED VARIANT IN WHICH THE 25 N-TERMINAL RESIDUES HAVE BEEN ...THE G6PD USED IN THIS WORK IS AN ENGINEERED VARIANT IN WHICH THE 25 N-TERMINAL RESIDUES HAVE BEEN REMOVED AND THE FIRST RESIDUE IS VALINE, NOT HISTIDINE.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.4 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: HANGING DROP VAPOUR DIFFUSION. 1-PLUS-1 MICROLITRE DROPS IN THE WELL 0.1M TRIS-HCL,PH 7.5-8.2, 10-16% PEG 4000. PROTEIN CONCENTRATION 5MG/ML.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 21, 1996 / Details: MIRRORS
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.5→29.7 Å / Num. obs: 14581 / % possible obs: 73.3 % / Observed criterion σ(I): -4 / Redundancy: 2.5 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.6
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.4 / % possible all: 59.3

-
Processing

Software
NameClassification
BUSTER-TNTrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PARTIALLY-REFINED MONOMER OF HUMAN G6PD, CANTON VARIANT

Resolution: 2.5→29.7 Å / Cross valid method: FREE THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.296 726 5 %RANDOM
Rwork0.196 ---
obs0.201 14548 73 %-
Refinement stepCycle: LAST / Resolution: 2.5→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3971 0 108 162 4241

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more