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- PDB-7e6i: Glucose-6-phosphate dehydrogenase in complex with its substrate g... -

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Basic information

Entry
Database: PDB / ID: 7e6i
TitleGlucose-6-phosphate dehydrogenase in complex with its substrate glucose-6-phosphate
ComponentsGlucose-6-phosphate 1-dehydrogenase
KeywordsOXIDOREDUCTASE / Glucose-6-phosphate / dehydrogenase / pentose phosphate pathway / Kluyveromyces lactis
Function / homology
Function and homology information


glucose-6-phosphate dehydrogenase (NADP+) / glucose-6-phosphate dehydrogenase activity / pentose-phosphate shunt / glucose metabolic process / NADP binding
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
Chem-7PE / 6-O-phosphono-beta-D-glucopyranose / Glucose-6-phosphate 1-dehydrogenase
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsVu, H.H. / Chang, J.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2019R1A2C4069796 Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Structural basis for substrate recognition of glucose-6-phosphate dehydrogenase from Kluyveromyces lactis.
Authors: Vu, H.H. / Jin, C. / Chang, J.H.
History
DepositionFeb 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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)57,3364
Polymers56,6431
Non-polymers6933
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint-2 kcal/mol
Surface area22280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.254, 120.254, 214.980
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-634-

HOH

21A-812-

HOH

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Components

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


Mass: 56643.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: ZWF, KLLA0D19855g / Production host: Escherichia coli (E. coli)
References: UniProt: P48828, glucose-6-phosphate dehydrogenase (NADP+)
#2: Sugar ChemComp-BG6 / 6-O-phosphono-beta-D-glucopyranose / BETA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13O9P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
b-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-7PE / 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL / POLYETHYLENE GLYCOL FRAGMENT / Polyethylene glycol


Mass: 310.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O7
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
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: 3.96 Å3/Da / Density % sol: 68.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.4 M sodium malonate dibasic pH 5.5 and 24% (w/v) PEG 3350, 20 mM G6P

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 9, 2020
RadiationMonochromator: Synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. obs: 37034 / % possible obs: 99.9 % / Redundancy: 29.1 % / Biso Wilson estimate: 34.37 Å2 / CC1/2: 0.996 / Net I/σ(I): 45.5
Reflection shellResolution: 2.39→2.49 Å / Num. unique obs: 3601 / CC1/2: 0.853

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BH9

2bh9


Resolution: 2.39→34.97 Å / SU ML: 0.2317 / Cross valid method: FREE R-VALUE / σ(F): 1.55 / Phase error: 19.4265
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2237 2000 5.41 %
Rwork0.1891 34980 -
obs0.191 36980 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.68 Å2
Refinement stepCycle: LAST / Resolution: 2.39→34.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3885 0 40 212 4137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00774012
X-RAY DIFFRACTIONf_angle_d0.9715422
X-RAY DIFFRACTIONf_chiral_restr0.0592586
X-RAY DIFFRACTIONf_plane_restr0.0056702
X-RAY DIFFRACTIONf_dihedral_angle_d7.6293540
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.450.29521390.27322427X-RAY DIFFRACTION99
2.45-2.520.28361390.25192435X-RAY DIFFRACTION100
2.52-2.590.29211400.23682445X-RAY DIFFRACTION100
2.59-2.680.26361410.22582475X-RAY DIFFRACTION100
2.68-2.770.26021390.20962434X-RAY DIFFRACTION100
2.77-2.880.2391420.20752466X-RAY DIFFRACTION100
2.88-3.010.24591400.20482472X-RAY DIFFRACTION100
3.01-3.170.25111430.19572481X-RAY DIFFRACTION100
3.17-3.370.22831410.18972479X-RAY DIFFRACTION100
3.37-3.630.21291430.18062502X-RAY DIFFRACTION99.96
3.63-40.1881440.16772515X-RAY DIFFRACTION100
4-4.570.15621450.15092526X-RAY DIFFRACTION100
4.57-5.760.21171480.16722584X-RAY DIFFRACTION100
5.76-34.970.23831560.18572739X-RAY DIFFRACTION99.93
Refinement TLS params.Method: refined / Origin x: 32.6743138445 Å / Origin y: 78.6182892352 Å / Origin z: 117.478078261 Å
111213212223313233
T0.280308648888 Å2-0.0487356657497 Å20.0319065997649 Å2-0.145067863541 Å20.0315680687214 Å2--0.21831272145 Å2
L0.0580466593649 °20.155689176052 °2-0.0579960713665 °2-0.831697277255 °2-0.374192410894 °2--0.59000133756 °2
S-0.0106313271589 Å °-0.085077241081 Å °-0.00211897769968 Å °0.0507041585831 Å °-0.000329865503091 Å °0.131815770879 Å °0.166641268564 Å °-0.0680922894805 Å °-0.0364784872754 Å °
Refinement TLS groupSelection details: all

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