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- PDB-7xhl: Complex structure of a Glucose 6-Phosphate Dehydrogenase from Zym... -

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Basic information

Entry
Database: PDB / ID: 7xhl
TitleComplex structure of a Glucose 6-Phosphate Dehydrogenase from Zymomonas mobilis
ComponentsGlucose 6-Phosphate Dehydrogenase
KeywordsOXIDOREDUCTASE / Nicotinamide cofactor / Complex
Function / homologyBETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE
Function and homology information
Biological speciesZymomonas mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsMeng, D.D. / Liu, M.X. / Liu, W.D. / You, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21778073 China
CitationJournal: Acs Catalysis / Year: 2023
Title: Coenzyme Engineering of Glucose-6-phosphate Dehydrogenase on a Nicotinamide-Based Biomimic and Its Application as a Glucose Biosensor
Authors: Meng, D.D. / Liu, M.X. / Su, H. / Song, H.Y. / Chen, L.J. / Li, Q.Z. / Liu, Y.N. / Zhu, Z.G. / Liu, W.D. / Sheng, X. / You, C. / Zhang, Y.H.
History
DepositionApr 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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 Dehydrogenase
B: Glucose 6-Phosphate Dehydrogenase
C: Glucose 6-Phosphate Dehydrogenase
D: Glucose 6-Phosphate Dehydrogenase
E: Glucose 6-Phosphate Dehydrogenase
F: Glucose 6-Phosphate Dehydrogenase
G: Glucose 6-Phosphate Dehydrogenase
H: Glucose 6-Phosphate Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)434,56112
Polymers433,2208
Non-polymers1,3414
Water00
1
A: Glucose 6-Phosphate Dehydrogenase
B: Glucose 6-Phosphate Dehydrogenase
C: Glucose 6-Phosphate Dehydrogenase
D: Glucose 6-Phosphate Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,2816
Polymers216,6104
Non-polymers6702
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14840 Å2
ΔGint-105 kcal/mol
Surface area72470 Å2
MethodPISA
2
E: Glucose 6-Phosphate Dehydrogenase
F: Glucose 6-Phosphate Dehydrogenase
G: Glucose 6-Phosphate Dehydrogenase
H: Glucose 6-Phosphate Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,2816
Polymers216,6104
Non-polymers6702
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14980 Å2
ΔGint-106 kcal/mol
Surface area69840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.316, 342.335, 103.355
Angle α, β, γ (deg.)90.00, 92.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glucose 6-Phosphate Dehydrogenase


Mass: 54152.527 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-NMN / BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / NICOTINAMIDE MONONUCLEOTIDE


Mass: 335.227 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H16N2O8P / 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: 3.28 Å3/Da / Density % sol: 62.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M di-Ammonium hydrogen Phosphate, 0.1 M Tris Hydrochloride pH 8.5, 14% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.2
ReflectionResolution: 3.25→88.41 Å / Num. obs: 86216 / % possible obs: 98.9 % / Redundancy: 3.1 % / CC1/2: 0.976 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.1 / Rrim(I) all: 0.18 / Net I/σ(I): 6.4 / Num. measured all: 269015 / Scaling rejects: 80
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.25-3.313.10.6661420245740.5230.450.8071.899.4
17.2-88.412.30.09311655040.930.0770.1221282.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimless0.7.7data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 600000000 / Resolution: 3.25→78.11 Å / Cross valid method: THROUGHOUT / σ(F): 205.17 / Phase error: 38.73 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.297 4464 5.18 %
Rwork0.237 --
obs0.248 86147 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.42 Å2
Refinement stepCycle: LAST / Resolution: 3.25→78.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28288 0 88 0 28376
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11A10472X-RAY DIFFRACTIONPOSITIONAL
12B10472X-RAY DIFFRACTIONPOSITIONAL
13C10472X-RAY DIFFRACTIONPOSITIONAL
14D10472X-RAY DIFFRACTIONPOSITIONAL
15E10472X-RAY DIFFRACTIONPOSITIONAL
16F10472X-RAY DIFFRACTIONPOSITIONAL
17G10472X-RAY DIFFRACTIONPOSITIONAL
18H10472X-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-3.310.38552330.32764066X-RAY DIFFRACTION94
3.31-3.370.37051980.31474152X-RAY DIFFRACTION95
3.37-3.430.38492160.30824076X-RAY DIFFRACTION94
3.43-3.50.31782020.29884129X-RAY DIFFRACTION95
3.5-3.580.3752270.29054052X-RAY DIFFRACTION93
3.58-3.660.36072070.28294153X-RAY DIFFRACTION95
3.66-3.750.34332240.27554098X-RAY DIFFRACTION95
3.75-3.850.32562170.27314127X-RAY DIFFRACTION95
3.85-3.970.31932170.26064146X-RAY DIFFRACTION95
3.97-4.090.2992070.25134083X-RAY DIFFRACTION95
4.09-4.240.31222140.24614152X-RAY DIFFRACTION94
4.24-4.410.27792170.23034071X-RAY DIFFRACTION94
4.41-4.610.28492130.21414091X-RAY DIFFRACTION94
4.61-4.850.25762190.22344092X-RAY DIFFRACTION94
4.85-5.160.27922090.22844100X-RAY DIFFRACTION94
5.16-5.560.29152140.23894111X-RAY DIFFRACTION94
5.56-6.120.32592150.25434096X-RAY DIFFRACTION93
6.12-70.32542110.23674053X-RAY DIFFRACTION93
7-8.820.26462260.20494042X-RAY DIFFRACTION92
8.82-78.110.26462080.20323963X-RAY DIFFRACTION90

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