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- PDB-7e6h: glucose-6-phosphate dehydrogenase from Kluyveromyces lactis -

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Basic information

Entry
Database: PDB / ID: 7e6h
Titleglucose-6-phosphate dehydrogenase from Kluyveromyces lactis
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, oxidative branch / glucose metabolic process / NADP binding / 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
Chem-7PE / Glucose-6-phosphate 1-dehydrogenase
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHa, V.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)57,0763
Polymers56,6431
Non-polymers4332
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area320 Å2
ΔGint-1 kcal/mol
Surface area22200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.670, 120.670, 213.711
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
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-601-

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: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


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


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


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 4.07 Å3/Da / Density % sol: 69.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium malonate dibasic at pH 5.5 and 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 26093 / % possible obs: 100 % / Redundancy: 21.3 % / Biso Wilson estimate: 53.6 Å2 / CC1/2: 0.997 / Net I/σ(I): 31.8
Reflection shellResolution: 2.7→2.8 Å / Num. unique obs: 2543 / CC1/2: 0.947

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Processing

Software
NameVersionClassification
PHENIX(1.18_3845: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BH9

2bh9


Resolution: 2.7→46.94 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2368 2000 7.68 %
Rwork0.1868 --
obs0.1906 26035 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→46.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3889 0 24 61 3974
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083999
X-RAY DIFFRACTIONf_angle_d0.955402
X-RAY DIFFRACTIONf_dihedral_angle_d10.859538
X-RAY DIFFRACTIONf_chiral_restr0.057581
X-RAY DIFFRACTIONf_plane_restr0.006702
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.29151390.23181682X-RAY DIFFRACTION100
2.77-2.840.28781380.21441650X-RAY DIFFRACTION100
2.84-2.920.27181410.21731693X-RAY DIFFRACTION100
2.92-3.020.2761410.2121686X-RAY DIFFRACTION100
3.02-3.130.26931390.19971677X-RAY DIFFRACTION100
3.13-3.250.24431410.2051694X-RAY DIFFRACTION100
3.25-3.40.25211410.20591694X-RAY DIFFRACTION100
3.4-3.580.30221400.19851691X-RAY DIFFRACTION100
3.58-3.80.24151420.1851713X-RAY DIFFRACTION100
3.8-4.10.21011430.17341713X-RAY DIFFRACTION100
4.1-4.510.21761440.16181719X-RAY DIFFRACTION100
4.51-5.160.19231450.15941749X-RAY DIFFRACTION100
5.16-6.50.26841470.20141776X-RAY DIFFRACTION100
6.5-46.940.20231590.181898X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 32.4984 Å / Origin y: 79.2426 Å / Origin z: 116.7739 Å
111213212223313233
T0.3562 Å2-0.0723 Å20.0629 Å2-0.2991 Å20.0283 Å2--0.3758 Å2
L0.8169 °20.578 °2-0.1859 °2-4.1952 °2-0.9479 °2--2.0779 °2
S0.0366 Å °-0.1174 Å °-0.1217 Å °0.0707 Å °-0.0543 Å °0.4546 Å °0.341 Å °-0.2661 Å °0.0405 Å °
Refinement TLS groupSelection details: all

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