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- PDB-8i37: Helicobacter pylori G6PDH -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8i37
TitleHelicobacter pylori G6PDH
ComponentsGlucose-6-phosphate 1-dehydrogenase
KeywordsELECTRON TRANSPORT / Hydrogen Polysulfide / G6PDH Inactivation / Helicobacter pylori / Polysulfide Transformation / Gastric-adaptive
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 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Glucose-6-phosphate 1-dehydrogenase
Similarity search - Component
Biological speciesHelicobacter pylori SS1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsZhou, N. / Gao, L.Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Inorganic polysulfide kills Helicobacter pylori by inactivating G6PDH via cysteine polysulfidation
Authors: Ning, Z. / Gao, L.Z.
History
DepositionJan 16, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucose-6-phosphate 1-dehydrogenase
B: Glucose-6-phosphate 1-dehydrogenase
C: Glucose-6-phosphate 1-dehydrogenase
D: Glucose-6-phosphate 1-dehydrogenase


Theoretical massNumber of molelcules
Total (without water)199,3884
Polymers199,3884
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint4 kcal/mol
Surface area74000 Å2
Unit cell
Length a, b, c (Å)153.871, 153.871, 250.535
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"

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Components

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


Mass: 49846.980 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori SS1 (bacteria) / Gene: zwf
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A1U9ITQ5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 4.29 Å3/Da / Density % sol: 71.36 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Potassium sodium tartrate tetrahydrate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9791 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Sep 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.75→52.083 Å / Num. obs: 89655 / % possible obs: 99.9788 % / Redundancy: 9.7 % / Biso Wilson estimate: 55.56 Å2 / Rmerge(I) obs: 0.136 / Net I/σ(I): 11
Reflection shellResolution: 2.75→2.8 Å / Num. unique obs: 4523 / CC1/2: 0.856

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.75→52.08 Å / SU ML: 0.3607 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.3568
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2538 1994 2.23 %
Rwork0.2191 87579 -
obs0.2198 89573 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.15 Å2
Refinement stepCycle: LAST / Resolution: 2.75→52.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14088 0 0 67 14155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009114408
X-RAY DIFFRACTIONf_angle_d1.148319456
X-RAY DIFFRACTIONf_chiral_restr0.08662148
X-RAY DIFFRACTIONf_plane_restr0.00562496
X-RAY DIFFRACTIONf_dihedral_angle_d17.36785400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.820.36831420.29956139X-RAY DIFFRACTION99.95
2.82-2.890.33351380.28626212X-RAY DIFFRACTION100
2.89-2.980.36281400.29756155X-RAY DIFFRACTION100
2.98-3.080.31781430.2766229X-RAY DIFFRACTION100
3.08-3.190.32181410.27866188X-RAY DIFFRACTION100
3.19-3.310.30641420.2656184X-RAY DIFFRACTION100
3.31-3.460.33741420.25686242X-RAY DIFFRACTION100
3.46-3.650.27211420.23666242X-RAY DIFFRACTION100
3.65-3.880.26891410.20896228X-RAY DIFFRACTION99.97
3.88-4.170.23131390.1926267X-RAY DIFFRACTION99.97
4.17-4.590.1911430.17156271X-RAY DIFFRACTION100
4.59-5.260.17421430.17176304X-RAY DIFFRACTION99.98
5.26-6.620.24911480.22216369X-RAY DIFFRACTION100
6.62-52.080.21921500.19916549X-RAY DIFFRACTION99.45

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