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- PDB-6vaq: Crystal structure of glucose-6-phosphate dehydrogenase V394L muta... -

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Basic information

Entry
Database: PDB / ID: 6vaq
TitleCrystal structure of glucose-6-phosphate dehydrogenase V394L 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 / glucose-6-phosphate dehydrogenase activity / response to iron(III) ion / pentose-phosphate shunt, oxidative branch / 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 / glucose-6-phosphate dehydrogenase activity / response to iron(III) ion / pentose-phosphate shunt, oxidative branch / 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 / D-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 / regulation of neuron apoptotic process / glutathione metabolic process / substantia nigra development / TP53 Regulates Metabolic Genes / lipid metabolic process / 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 / 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: 2.95 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)60,0902
Polymers59,3471
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)120,1804
Polymers118,6932
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)158.973, 158.973, 113.186
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: 59346.609 Da / Num. of mol.: 1 / Mutation: V394L
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 Å3/Da / Density % sol: 79.49 %
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: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.95→39.74 Å / Num. obs: 30866 / % possible obs: 99.7 % / Redundancy: 13.167 % / Biso Wilson estimate: 77.664 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.108 / Rrim(I) all: 0.113 / Χ2: 1.2 / Net I/σ(I): 19.29 / Num. measured all: 406400
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
2.95-3.1313.591.1022.1165411489248130.8141.14598.4
3.13-3.3513.6670.5694.5663225462646260.9510.591100
3.35-3.6213.150.2968.9556663430943090.9850.308100
3.62-3.9613.0790.14717.0752030397839780.9960.153100
3.96-4.4213.6930.09626.2849787363636360.9970.1100
4.42-5.113.0370.07334.241889321332130.9980.076100
5.1-6.2312.4050.07333.0634325276727670.9980.076100
6.23-8.7312.8220.05741.3828131219421940.9990.06100
8.73-39.7411.2320.04252.5814939134213300.9990.04499.1

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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: 2.95→39.74 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2223 1543 5 %
Rwork0.2092 29299 -
obs0.2099 30842 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.98 Å2 / Biso mean: 80.5336 Å2 / Biso min: 50.74 Å2
Refinement stepCycle: final / Resolution: 2.95→39.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3485 0 48 0 3533
Biso mean--68.51 --
Num. residues----431
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.95-3.050.40161350.38452550268597
3.05-3.160.34111370.304526142751100
3.16-3.290.24821380.274226102748100
3.29-3.440.28981390.254926452784100
3.44-3.620.28471390.253926452784100
3.62-3.840.23291390.211826452784100
3.84-4.140.20681400.194626492789100
4.14-4.550.20251410.183926802821100
4.56-5.210.16991410.178126782819100
5.21-6.560.26291430.204327222865100
6.56-39.740.17441510.184128613012100
Refinement TLS params.Method: refined / Origin x: 24.2069 Å / Origin y: 96.4276 Å / Origin z: 29.9509 Å
111213212223313233
T0.5744 Å2-0.0495 Å20.0333 Å2-0.458 Å20.0435 Å2--0.4798 Å2
L2.1679 °20.756 °20.2855 °2-1.3447 °20.4309 °2--1.8006 °2
S0.0783 Å °-0.1126 Å °0.1199 Å °-0.0089 Å °-0.0662 Å °-0.0904 Å °-0.1907 Å °0.0983 Å °-0.0061 Å °
Refinement TLS groupSelection details: all

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