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- PDB-6va7: Crystal structure of glucose-6-phosphate dehydrogenase P396L muta... -

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Basic information

Entry
Database: PDB / ID: 6va7
TitleCrystal structure of glucose-6-phosphate dehydrogenase P396L mutant in complex with catalytic NADP+
ComponentsGlucose-6-phosphate 1-dehydrogenase
KeywordsOXIDOREDUCTASE / Dehydrogenase / NADP+ / Rossmann-fold
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 / Resolution: 3.07 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 17, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,0922
Polymers59,3491
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)120,1844
Polymers118,6972
Non-polymers1,4872
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)157.354, 157.354, 113.616
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 59348.625 Da / Num. of mol.: 1 / Mutation: P396L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: G6PD / Plasmid: pET28 / 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

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 5.9 Å3/Da / Density % sol: 79.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: MES, magnesium chloride, PEG3350, NADP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.07→49.76 Å / Num. obs: 27090 / % possible obs: 99.8 % / Redundancy: 13.284 % / Biso Wilson estimate: 86.158 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.114 / Rrim(I) all: 0.119 / Χ2: 1.116 / Net I/σ(I): 21.94 / Num. measured all: 359866
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
3.07-3.2613.6371.5961.6158092428942600.6471.65899.3
3.26-3.4813.6340.7863.5255149404540450.8920.816100
3.48-3.7612.490.3757.247073377437690.9710.39199.9
3.76-4.1214.0910.18315.1649334350135010.9940.19100
4.12-4.613.7490.09926.4143679317731770.9980.103100
4.6-5.312.9960.07334.7436767283028290.9990.076100
5.3-6.4812.9190.0683731239242524180.9990.07199.7
6.48-9.0812.9890.0457.21249381920192010.042100
9.08-49.7611.610.02195.2135951185117110.02298.8

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 600000000 / Resolution: 3.07→49.76 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2247 1354 5 %
Rwork0.2025 25730 -
obs0.2036 27084 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 206.36 Å2 / Biso mean: 93.9035 Å2 / Biso min: 60.96 Å2
Refinement stepCycle: final / Resolution: 3.07→49.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3493 0 48 0 3541
Biso mean--81.27 --
Num. residues----432
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.07-3.180.28871320.30722507263999
3.18-3.310.30141320.299425082640100
3.31-3.460.31651340.26925452679100
3.46-3.640.27561340.250725372671100
3.64-3.870.23371330.221225362669100
3.87-4.170.2331350.205125562691100
4.17-4.590.19331350.17525812716100
4.59-5.250.20111370.166825902727100
5.25-6.610.20731370.201626122749100
6.62-49.760.20981450.180927582903100
Refinement TLS params.Method: refined / Origin x: 24.1864 Å / Origin y: 95.3026 Å / Origin z: 30.1281 Å
111213212223313233
T0.7738 Å2-0.0624 Å20.0323 Å2-0.6272 Å20.0361 Å2--0.7324 Å2
L1.9482 °20.5982 °20.1658 °2-1.1696 °20.4323 °2--1.6408 °2
S0.0669 Å °-0.0918 Å °0.1058 Å °-0.0911 Å °-0.0397 Å °-0.1905 Å °-0.158 Å °0.0209 Å °-0.0257 Å °
Refinement TLS groupSelection details: all

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