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- PDB-7xre: Crystal structure of DgpA -

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Basic information

Entry
Database: PDB / ID: 7xre
TitleCrystal structure of DgpA
ComponentsDgpA
KeywordsOXIDOREDUCTASE / C-glycoside cleavage and isomerization / oxidation
Function / homologyGfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / NAD(P)-binding domain superfamily / nucleotide binding / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Oxidoreductase
Function and homology information
Biological specieshuman intestinal bacterium PUE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.76 Å
AuthorsMa, W. / He, P.
Funding support China, 2items
OrganizationGrant numberCountry
Other government90011451310011 China
Other government1000061223476 China
CitationJournal: Acta Pharm Sin B / Year: 2023
Title: Structural mechanism of a dual-functional enzyme DgpA/B/C as both a C -glycoside cleaving enzyme and an O - to C -glycoside isomerase.
Authors: He, P. / Wang, S. / Li, S. / Liu, S. / Zhou, S. / Wang, J. / Tao, J. / Wang, D. / Wang, R. / Ma, W.
History
DepositionMay 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed ..._citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DgpA
B: DgpA
C: DgpA
D: DgpA
E: DgpA
F: DgpA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,60512
Polymers243,6256
Non-polymers3,9816
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29860 Å2
ΔGint-116 kcal/mol
Surface area76150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.790, 130.760, 206.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
DgpA


Mass: 40604.152 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) human intestinal bacterium PUE (bacteria)
Gene: dgpA / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3Q9WWX8
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.84 Å3/Da / Density % sol: 56.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.2 M magnesium formate and 20% PEG 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9875 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Oct 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9875 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 65488 / % possible obs: 98.2 % / Redundancy: 11.5 % / CC1/2: 0.75 / Rmerge(I) obs: 0.182 / Net I/σ(I): 10.6
Reflection shellResolution: 2.7→3.7 Å / Num. unique obs: 1013 / CC1/2: 0.8

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-3000data reduction
HKL-3000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.76→17.076 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2942 3311 5.06 %
Rwork0.2347 62177 -
obs0.2377 65488 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 204.71 Å2 / Biso mean: 73.0667 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.76→17.076 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16250 0 264 38 16552
Biso mean--84.93 61.21 -
Num. residues----2151
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.76-2.79930.35531180.3186227487
2.7993-2.84090.37951390.3198234290
2.8409-2.88510.38131430.3111239493
2.8851-2.93220.40281340.302245796
2.9322-2.98250.33861420.3034260199
2.9825-3.03640.3691250.30012592100
3.0364-3.09450.36031370.29572612100
3.0945-3.15720.34791340.28772611100
3.1572-3.22550.31671330.27672589100
3.2255-3.30.40641410.27332613100
3.3-3.38190.31151300.26482608100
3.3819-3.47260.29341510.27072599100
3.4726-3.57380.31451500.25242587100
3.5738-3.68810.30671420.26232638100
3.6881-3.81850.32081510.25192610100
3.8185-3.96950.31141370.2262634100
3.9695-4.14770.27521320.22162634100
4.1477-4.3630.23851440.20612636100
4.363-4.63120.24521350.18762638100
4.6312-4.98050.24921320.19622660100
4.9805-5.46680.27241450.21412651100
5.4668-6.2240.26261470.23232677100
6.224-7.71910.29361310.23472727100
7.7191-17.0760.26551380.19072793100

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