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- PDB-6e08: Crystal structure of G6PD in complex with structural NADP -

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Basic information

Entry
Database: PDB / ID: 600000000
TitleCrystal structure of G6PD in complex with structural NADP
ComponentsGlucose-6-phosphate 1-dehydrogenase
KeywordsOXIDOREDUCTASE / G6PD / NADP
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 / glucose 6-phosphate metabolic process ...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 / glucose 6-phosphate metabolic process / NADP+ metabolic process / pentose-phosphate shunt / D-glucose binding / NFE2L2 regulates pentose phosphate pathway genes / Oxidoreductases / cholesterol biosynthetic process / response to food / erythrocyte maturation / negative regulation of reactive oxygen species metabolic process / substantia nigra development / regulation of neuron apoptotic process / TP53 Regulates Metabolic Genes / lipid metabolic process / glutathione metabolic process / cytoplasmic side of plasma membrane / glucose metabolic process / centriolar satellite / NADP binding / cellular response to oxidative stress / response to ethanol / protein homodimerization activity / extracellular exosome / membrane / identical protein binding / 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 / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain ...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 / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
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: 1.9 Å
AuthorsRahighi, S. / Mochly Rosen, D. / Wakatsuki, S.
CitationJournal: Nat Commun / Year: 2018
Title: Correcting glucose-6-phosphate dehydrogenase deficiency with a small-molecule activator.
Authors: Hwang, S. / Mruk, K. / Rahighi, S. / Raub, A.G. / Chen, C.H. / Dorn, L.E. / Horikoshi, N. / Wakatsuki, S. / Chen, J.K. / Mochly-Rosen, D.
History
DepositionJul 6, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionJul 25, 2018ID: 5VFL
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / 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 1.2Oct 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
L: Glucose-6-phosphate 1-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5367
Polymers59,3331
Non-polymers1,2046
Water7,314406
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.580, 173.410, 215.909
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11L-836-

HOH

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Components

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


Mass: 59332.586 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 K-12 (bacteria)
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
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: 20% w/v PEG 3350, 0.2 M potassium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 40413 / % possible obs: 95.3 % / Redundancy: 5.7 % / CC1/2: 1 / Rmerge(I) obs: 0.79 / Net I/σ(I): 11
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 3 / Num. unique obs: 5400 / CC1/2: 0.82 / % possible all: 91.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BHL

2bhl


Resolution: 1.9→18.28 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 8.127 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.139 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21258 2171 5.1 %RANDOM
Rwork0.17182 ---
obs0.17402 40413 94.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.422 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 1.9→18.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3946 0 78 406 4430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0144119
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173639
X-RAY DIFFRACTIONr_angle_refined_deg1.7861.6825571
X-RAY DIFFRACTIONr_angle_other_deg1.071.658543
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8525485
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.71221.849238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.46415702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9621532
X-RAY DIFFRACTIONr_chiral_restr0.0990.2518
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024586
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02787
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_it1.4271.8141943
X-RAY DIFFRACTIONr_mcbond_other1.4261.8121942
X-RAY DIFFRACTIONr_mcangle_it2.1472.712427
X-RAY DIFFRACTIONr_mcangle_other2.1462.7122428
X-RAY DIFFRACTIONr_scbond_it2.4532.2012176
X-RAY DIFFRACTIONr_scbond_other2.4532.2012176
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9063.1643145
X-RAY DIFFRACTIONr_long_range_B_refined5.46422.4734740
X-RAY DIFFRACTIONr_long_range_B_other5.38222.0924648
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 166 -
Rwork0.274 2782 -
obs--89.82 %
Refinement TLS params.Method: refined / Origin x: 24.2895 Å / Origin y: 21.7716 Å / Origin z: 29.5292 Å
111213212223313233
T0.0232 Å20.006 Å20.0025 Å2-0.0108 Å2-0.0068 Å2--0.0083 Å2
L0.3748 °20.0909 °20.0861 °2-0.2768 °20.1612 °2--0.4916 °2
S-0.0005 Å °0.0132 Å °-0.0235 Å °-0.0084 Å °0.0447 Å °-0.0377 Å °0.0458 Å °0.0458 Å °-0.0442 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L28 - 513
2X-RAY DIFFRACTION1L601 - 606
3X-RAY DIFFRACTION1L701 - 1106

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