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- PDB-6va8: Crystal structure of glucose-6-phosphate dehydrogenase F381L muta... -

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Basic information

Entry
Database: PDB / ID: 6va8
TitleCrystal structure of glucose-6-phosphate dehydrogenase F381L mutant in complex with catalytic NADP+
ComponentsGlucose-6-phosphate 1-dehydrogenase
KeywordsOXIDOREDUCTASE / Dehydrogenase / NADP+ / Rossmann-fold
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
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: 3.95 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)60,0422
Polymers59,2991
Non-polymers7431
Water0
1
A: Glucose-6-phosphate 1-dehydrogenase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)120,0844
Polymers118,5972
Non-polymers1,4872
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)158.620, 158.620, 113.910
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: 59298.570 Da / Num. of mol.: 1 / Mutation: F381L
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 / Nicotinamide adenine dinucleotide phosphate


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: 6.01 Å3/Da / Density % sol: 79.54 %
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: Jul 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.95→47.96 Å / Num. obs: 13187 / % possible obs: 99.6 % / Redundancy: 10.16 % / CC1/2: 0.995 / Net I/σ(I): 8.31
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
3.95-4.1910.8081.5911.5522350208520680.6011.67199.2
4.19-4.4810.7060.9112.720834194719460.7960.95899.9
4.48-4.8310.4920.5684.319179183018280.8970.59899.9
4.83-5.299.7270.5224.4816536170017000.9230.551100
5.29-5.919.720.445.4215017154815450.9320.46599.8
5.91-6.810.580.37.8814579137813780.980.315100
6.8-8.2910.2030.15214.4512019117811780.9940.16100
8.29-11.558.9480.05431.9484749539470.9990.05799.4
11.55-47.968.4340.04132.4449766085900.9990.04497

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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: 3.95→47.96 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2238 656 4.99 %
Rwork0.2059 12500 -
obs0.2068 13156 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 255.9 Å2 / Biso mean: 122.7511 Å2 / Biso min: 76.87 Å2
Refinement stepCycle: final / Resolution: 3.95→47.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3447 0 48 0 3495
Biso mean--118.88 --
Num. residues----426
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.95-4.260.30971280.27662440256899
4.26-4.690.26181290.2124532582100
4.69-5.360.24181300.199324762606100
5.36-6.750.23511330.22225152648100
6.76-47.960.17731360.17892616275299
Refinement TLS params.Method: refined / Origin x: 16.8198 Å / Origin y: 55.4568 Å / Origin z: 1.5662 Å
111213212223313233
T0.8967 Å20.0522 Å20.0207 Å2-1.0721 Å20.0086 Å2--0.9746 Å2
L1.8513 °2-0.9466 °20.5959 °2-1.9393 °2-0.0039 °2--2.2434 °2
S-0.0176 Å °0.0184 Å °-0.1377 Å °0.1971 Å °0.0728 Å °-0.0792 Å °0.0428 Å °0.1705 Å °-0.0398 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA29 - 502
2X-RAY DIFFRACTION1allA799

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