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- PDB-7xrf: Crystal structaure of DgpB/C complex -

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Basic information

Entry
Database: PDB / ID: 7xrf
TitleCrystal structaure of DgpB/C complex
Components
  • AP_endonuc_2 domain-containing protein
  • DgpB
KeywordsLYASE / C-glycoside cleavage / isomerization
Function / homology
Function and homology information


lyase activity / metal ion binding
Similarity search - Function
Domain of unknown function DUF6379 / C-glycoside deglycosidase beta subunit / : / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily
Similarity search - Domain/homology
: / C-deglycosylation enzyme beta subunit / Xylose isomerase-like TIM barrel domain-containing protein
Similarity search - Component
Biological specieshuman intestinal bacterium PUE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.137 Å
AuthorsMa, M. / He, P.
Funding support China, 2items
OrganizationGrant numberCountry
Other government1000061223476 China
Other government90011451310011 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 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2May 8, 2024Group: Database references / Category: 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

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Assembly

Deposited unit
A: AP_endonuc_2 domain-containing protein
B: DgpB
C: AP_endonuc_2 domain-containing protein
D: DgpB
E: AP_endonuc_2 domain-containing protein
F: DgpB
G: AP_endonuc_2 domain-containing protein
H: DgpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,18912
Polymers211,9708
Non-polymers2204
Water4,288238
1
A: AP_endonuc_2 domain-containing protein
B: DgpB
E: AP_endonuc_2 domain-containing protein
F: DgpB
hetero molecules

C: AP_endonuc_2 domain-containing protein
D: DgpB
G: AP_endonuc_2 domain-containing protein
H: DgpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,18912
Polymers211,9708
Non-polymers2204
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area19940 Å2
ΔGint-111 kcal/mol
Surface area69600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.076, 159.704, 176.168
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
AP_endonuc_2 domain-containing protein


Mass: 36930.324 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) human intestinal bacterium PUE (bacteria)
Gene: dgpC / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3Q9WXL1
#2: Protein
DgpB


Mass: 16062.067 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) human intestinal bacterium PUE (bacteria)
Gene: dgpB / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3Q9WUX0
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.59 Å3/Da / Density % sol: 52.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.2 M magnesium acetate and 10% PEG 8000

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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: May 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9875 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 226255 / % possible obs: 99.9 % / Redundancy: 14.5 % / CC1/2: 0.86 / Rmerge(I) obs: 0.2 / Net I/σ(I): 6.3
Reflection shellResolution: 2.1→3.1 Å / Rmerge(I) obs: 0.86 / Num. unique obs: 689 / CC1/2: 0.85

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EXZ

7exz


Resolution: 2.137→19.836 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.82 / Phase error: 31.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.251 3784 1.67 %
Rwork0.2061 222471 -
obs0.2069 226255 96.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.81 Å2 / Biso mean: 61.4346 Å2 / Biso min: 25.46 Å2
Refinement stepCycle: final / Resolution: 2.137→19.836 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14399 0 4 238 14641
Biso mean--57.09 57.43 -
Num. residues----1830
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.137-2.16350.4611720.3869411948
2.1635-2.1920.36811350.4047784692
2.192-2.22190.39661430.396851799
2.2219-2.25360.44281440.3976847399
2.2536-2.28720.41861400.38868538100
2.2872-2.32290.42251470.37848999
2.3229-2.36090.39691450.3456853699
2.3609-2.40160.34151470.32268544100
2.4016-2.44520.35071460.3056846699
2.4452-2.49210.33421430.28438512100
2.4921-2.54290.33751480.2799853499
2.5429-2.59810.28421450.2593857999
2.5981-2.65840.33371440.246850299
2.6584-2.72470.27741430.2256847099
2.7247-2.79820.25781470.2344854899
2.7982-2.88030.27551470.2374851899
2.8803-2.97290.2941430.2263843499
2.9729-3.07880.29531420.2266844698
3.0788-3.20160.29771470.2275842498
3.2016-3.34670.25741470.2073842598
3.3467-3.52220.241450.1967833598
3.5222-3.74150.26031430.1867843498
3.7415-4.02810.27891370.1779826197
4.0281-4.42940.18121360.1627827996
4.4294-5.0610.19441360.15825096
5.061-6.34160.17971320.1761812195
6.3416-19.8360.19271400.1556787192

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