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- PDB-7sei: Glucose-6-phosphate 1-dehydrogenase (K403Q) -

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Basic information

Entry
Database: PDB / ID: 7sei
TitleGlucose-6-phosphate 1-dehydrogenase (K403Q)
ComponentsGlucose-6-phosphate 1-dehydrogenase
KeywordsOXIDOREDUCTASE / Glucose-6-phosphate 1-dehydrogenase / K403Q
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 pathway / pentose-phosphate shunt, oxidative branch / 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 pathway / pentose-phosphate shunt, oxidative branch / 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 / erythrocyte maturation / cholesterol biosynthetic process / centriolar satellite / negative regulation of reactive oxygen species metabolic process / regulation of neuron apoptotic process / substantia nigra development / glutathione metabolic process / TP53 Regulates Metabolic Genes / response to organic cyclic compound / lipid metabolic process / 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: 3.65 Å
AuthorsMathews, I.I. / Garcia, A.A. / Wakatsuki, S. / Mochly-Rosen, D.
Funding support United States, 5items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)HD084422 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM133894 United States
National Science Foundation (NSF, United States)1656518 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5T32GM113854 United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Stabilization of glucose-6-phosphate dehydrogenase oligomers enhances catalytic activity and stability of clinical variants.
Authors: Garcia, A.A. / Mathews, I.I. / Horikoshi, N. / Matsui, T. / Kaur, M. / Wakatsuki, S. / Mochly-Rosen, D.
History
DepositionSep 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)60,0752
Polymers59,3321
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)120,1504
Polymers118,6632
Non-polymers1,4872
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)157.730, 157.730, 113.820
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: 59331.531 Da / Num. of mol.: 1 / Mutation: K403Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: G6PD / Plasmid: pET-28a (+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43
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: 5.96 Å3/Da / Density % sol: 79.38 %
Crystal growTemperature: 295 K / Method: vapor diffusion / Details: PEG8K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 26, 2021 / Details: Flat side-deflecting, Rh-coated Si mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.65→39.43 Å / Num. obs: 16483 / % possible obs: 99.9 % / Redundancy: 26.588 % / Biso Wilson estimate: 120.317 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.213 / Rrim(I) all: 0.217 / Χ2: 0.75 / Net I/σ(I): 15.3 / Num. measured all: 438256 / Scaling rejects: 16
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
3.65-3.7427.3752.7451.6533233121412140.6322.796100
3.74-3.8526.9462.1082.1531204115911580.7082.14899.9
3.85-3.9626.5221.6342.729784112311230.8461.666100
3.96-4.0825.8131.2993.4928265109510950.8821.325100
4.08-4.2123.1560.9884.324823107210720.9121.011100
4.21-4.3626.1130.7625.8927027103510350.9540.777100
4.36-4.5328.5170.5798.0428802101010100.9730.589100
4.53-4.7128.6550.43810.36275669629620.9860.446100
4.71-4.9228.3670.3712.04263259289280.9890.377100
4.92-5.1628.2820.35812.24251148888880.990.365100
5.16-5.4427.9830.32913.02243178698690.9910.335100
5.44-5.7727.6810.2815.16220067957950.9910.285100
5.77-6.1727.2330.26715.52206707597590.9940.272100
6.17-6.6626.6920.19419.54191387177170.9980.197100
6.66-7.325.680.14524.55169496606600.9980.148100
7.3-8.1622.6960.09731.71138226106090.9990.09999.8
8.16-9.4224.6030.05551.83132615395390.9990.056100
9.42-11.5426.3590.04270.241233646846810.043100
11.54-16.3224.6680.0476.61920137337310.041100
16.32-39.4321.1150.03976.32441322820910.0491.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6va8

6va8


Resolution: 3.65→39.43 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.906 / WRfactor Rfree: 0.2128 / WRfactor Rwork: 0.1739 / FOM work R set: 0.8223 / SU B: 19.787 / SU ML: 0.268 / SU R Cruickshank DPI: 1.0147 / SU Rfree: 0.4123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.015 / ESU R Free: 0.412 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2352 825 5 %RANDOM
Rwork0.1913 ---
obs0.1935 15658 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 276.49 Å2 / Biso mean: 138.286 Å2 / Biso min: 96.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å2-0 Å2
2--0.03 Å2-0 Å2
3----0.07 Å2
Refinement stepCycle: final / Resolution: 3.65→39.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3439 0 48 0 3487
Biso mean--136.09 --
Num. residues----426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133568
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153370
X-RAY DIFFRACTIONr_angle_refined_deg1.7331.6474834
X-RAY DIFFRACTIONr_angle_other_deg1.2221.5827739
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7355423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.15321.401207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.19315612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9591531
X-RAY DIFFRACTIONr_chiral_restr0.0760.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024017
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02868
LS refinement shellResolution: 3.65→3.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 61 -
Rwork0.351 1145 -
all-1206 -
obs--100 %

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