[English] 日本語
Yorodumi
- PDB-6va0: Crystal structure of glucose-6-phosphate dehydrogenase W509A muta... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6va0
TitleCrystal structure of glucose-6-phosphate dehydrogenase W509A mutant in complex with catalytic NADP+
ComponentsGlucose-6-phosphate 1-dehydrogenase
KeywordsOXIDOREDUCTASE / Dehydrogenase / NADP+
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 / NAD(P)-binding domain superfamily
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 / molecular replacement / Resolution: 3.1 Å
AuthorsHorikoshi, N. / Mochly-Rosen, D. / Wakatsuki, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Long-range structural defects by pathogenic mutations in most severe glucose-6-phosphate dehydrogenase deficiency.
Authors: Horikoshi, N. / Hwang, S. / Gati, C. / Matsui, T. / Castillo-Orellana, C. / Raub, A.G. / Garcia, A.A. / Jabbarpour, F. / Batyuk, A. / Broweleit, J. / Xiang, X. / Chiang, A. / Broweleit, R. / ...Authors: Horikoshi, N. / Hwang, S. / Gati, C. / Matsui, T. / Castillo-Orellana, C. / Raub, A.G. / Garcia, A.A. / Jabbarpour, F. / Batyuk, A. / Broweleit, J. / Xiang, X. / Chiang, A. / Broweleit, R. / Vohringer-Martinez, E. / Mochly-Rosen, D. / Wakatsuki, S.
History
DepositionDec 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
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)59,9612
Polymers59,2171
Non-polymers7431
Water00
1
A: Glucose-6-phosphate 1-dehydrogenase
hetero molecules

A: Glucose-6-phosphate 1-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,9224
Polymers118,4352
Non-polymers1,4872
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area3710 Å2
ΔGint-18 kcal/mol
Surface area36510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.364, 157.364, 113.566
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw

-
Components

#1: Protein Glucose-6-phosphate 1-dehydrogenase / G6PD


Mass: 59217.453 Da / Num. of mol.: 1 / Mutation: W509A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: G6PD / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
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.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.91 Å3/Da / Density % sol: 79.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: MES, PEG4000, Magnesium chloride, AG1

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 3.1→47.62 Å / Num. obs: 25692 / % possible obs: 97.2 % / Redundancy: 42.341 % / Biso Wilson estimate: 93.78 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.143 / Rrim(I) all: 0.145 / Χ2: 1.072 / Net I/σ(I): 34.75 / Num. measured all: 1087829
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.1-3.2944.6271.7722.59186855419541870.851.79399.8
3.29-3.5142.8330.9774.9167564391339120.9420.989100
3.51-3.7939.5660.5589.99123366368231180.9850.56584.7
3.79-4.1542.6080.28319.18138561339232520.9940.28695.9
4.15-4.6442.9390.1336.75133239310731030.9990.13299.9
4.64-5.3544.1260.0952.24120950274127410.9990.091100
5.35-6.5342.9110.0859.361011832358235810.081100
6.53-9.1540.0810.04199.54751121874187410.042100
9.15-47.6235.7450.023161.69409991159114710.02399

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A08

6a08


Resolution: 3.1→47.62 Å / SU ML: 0.3364 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.0013
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2396 1285 5 %
Rwork0.2317 24397 -
obs0.2321 25682 97.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 94.46 Å2
Refinement stepCycle: LAST / Resolution: 3.1→47.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3505 0 48 0 3553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00383637
X-RAY DIFFRACTIONf_angle_d0.80174927
X-RAY DIFFRACTIONf_chiral_restr0.0501529
X-RAY DIFFRACTIONf_plane_restr0.0055635
X-RAY DIFFRACTIONf_dihedral_angle_d14.4773486
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.230.3281430.3072727X-RAY DIFFRACTION99.76
3.23-3.370.33451440.29392730X-RAY DIFFRACTION99.93
3.37-3.550.29661450.28962745X-RAY DIFFRACTION99.86
3.55-3.770.48621160.41372208X-RAY DIFFRACTION80.36
3.77-4.060.29611380.26392624X-RAY DIFFRACTION95.18
4.06-4.470.24631460.21742768X-RAY DIFFRACTION99.9
4.47-5.120.15931470.1812798X-RAY DIFFRACTION99.93
5.12-6.450.22391490.20562823X-RAY DIFFRACTION100
6.45-47.620.17921570.19072974X-RAY DIFFRACTION99.9
Refinement TLS params.Method: refined / Origin x: 24.2464109505 Å / Origin y: 95.359487288 Å / Origin z: 30.1231071187 Å
111213212223313233
T0.60474445895 Å2-0.0585430846554 Å20.0560507764829 Å2-0.389915093097 Å20.0279907943593 Å2--0.518616636643 Å2
L3.08955745559 °20.743352224372 °20.57138766696 °2-1.51390003069 °20.390649216778 °2--2.41934650111 °2
S0.110562299741 Å °-0.0994280338666 Å °0.159407283192 Å °-0.0371879568625 Å °-0.100290236278 Å °-0.23319679701 Å °-0.148327715121 Å °0.0564434393248 Å °-0.000742199713551 Å °
Refinement TLS groupSelection details: all

+
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