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- PDB-7zvd: K89 acetylated glucose-6-phosphate dehydrogenase (G6PD) in a comp... -

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Basic information

Entry
Database: PDB / ID: 7zvd
TitleK89 acetylated glucose-6-phosphate dehydrogenase (G6PD) in a complex with structural NADP+
ComponentsGlucose-6-phosphate 1-dehydrogenase
KeywordsOXIDOREDUCTASE / Lysine acetylation / metabolic regulation / post-translational modification / genetic code expansion
Function / homology
Function and homology information


negative regulation of protein glutathionylation / pentose biosynthetic process / ribose phosphate biosynthetic process / positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / glucose-6-phosphate dehydrogenase (NADP+) / 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 / positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / glucose-6-phosphate dehydrogenase (NADP+) / 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 / cholesterol biosynthetic process / erythrocyte maturation / negative regulation of reactive oxygen species metabolic process / regulation of neuron apoptotic process / substantia nigra development / glutathione metabolic process / TP53 Regulates Metabolic Genes / centriolar satellite / : / 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 / 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: 2.46 Å
AuthorsWu, F. / Muskat, N.H. / Nudelman, H. / Shahar, A. / Arbely, E.
Funding supportEuropean Union, Israel, 2items
OrganizationGrant numberCountry
European Research Council (ERC)678461European Union
Israel Science Foundation1769/20 Israel
CitationJournal: Nat Commun / Year: 2023
Title: Acetylation-dependent coupling between G6PD activity and apoptotic signaling.
Authors: Wu, F. / Muskat, N.H. / Dvilansky, I. / Koren, O. / Shahar, A. / Gazit, R. / Elia, N. / Arbely, E.
History
DepositionMay 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.2Feb 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Feb 28, 2024Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,6052
Polymers55,8621
Non-polymers7431
Water82946
1
N: Glucose-6-phosphate 1-dehydrogenase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)113,2104
Polymers111,7232
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_455-x-1/2,y,-z+1/21
Buried area8090 Å2
ΔGint-23 kcal/mol
Surface area38430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.220, 172.220, 216.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

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


Mass: 55861.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: G6PD / Production host: Escherichia coli (E. coli)
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.48 Å3/Da / Density % sol: 50.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1M Hepes pH 7.2, 0.2M L-Proline, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.46→54.98 Å / Num. obs: 20737 / % possible obs: 99.9 % / Redundancy: 2 % / Rmerge(I) obs: 0.03291 / Rpim(I) all: 0.03291 / Rrim(I) all: 0.04654 / Net I/σ(I): 13.21
Reflection shellResolution: 2.46→2.54 Å / Num. unique obs: 2315 / CC1/2: 0.588 / Rpim(I) all: 0.684

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Processing

Software
NameVersionClassification
REFMAC5.8.0350refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 600000000 / Resolution: 2.46→54.98 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.883 / SU B: 31.565 / SU ML: 0.31 / Cross valid method: THROUGHOUT / ESU R: 0.55 / ESU R Free: 0.327 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28934 1036 5 %RANDOM
Rwork0.20766 ---
obs0.21178 19700 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.226 Å2
Baniso -1Baniso -2Baniso -3
1-2.59 Å2-0 Å20 Å2
2--2.52 Å2-0 Å2
3----5.11 Å2
Refinement stepCycle: 1 / Resolution: 2.46→54.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3980 0 0 46 4026
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0124078
X-RAY DIFFRACTIONr_bond_other_d0.0080.0163661
X-RAY DIFFRACTIONr_angle_refined_deg2.031.6465525
X-RAY DIFFRACTIONr_angle_other_deg0.7771.5548539
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.4395483
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.7699.84833
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.51510697
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1030.2588
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024644
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02845
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.865.1981935
X-RAY DIFFRACTIONr_mcbond_other5.8395.1991935
X-RAY DIFFRACTIONr_mcangle_it7.8087.7952417
X-RAY DIFFRACTIONr_mcangle_other7.8097.7982418
X-RAY DIFFRACTIONr_scbond_it6.895.8362143
X-RAY DIFFRACTIONr_scbond_other6.8865.8342141
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.648.5253109
X-RAY DIFFRACTIONr_long_range_B_refined11.38962.4714420
X-RAY DIFFRACTIONr_long_range_B_other11.38862.4694421
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.46→2.524 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 83 -
Rwork0.359 1451 -
obs--99.93 %
Refinement TLS params.Method: refined / Origin x: -24.1087 Å / Origin y: -21.5859 Å / Origin z: 29.5129 Å
111213212223313233
T0.0798 Å20.0252 Å2-0.0026 Å2-0.0122 Å20.0039 Å2--0.1005 Å2
L0.6677 °20.1621 °2-0.3903 °2-0.5189 °2-0.5332 °2--0.7653 °2
S0.0279 Å °0.0166 Å °0.1694 Å °0.1716 Å °0.0603 Å °0.1075 Å °-0.2144 Å °-0.0841 Å °-0.0883 Å °

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