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- PDB-8w01: Crystal structure of DUF1735 domain-containing protein (GH18-like... -

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Basic information

Entry
Database: PDB / ID: 8w01
TitleCrystal structure of DUF1735 domain-containing protein (GH18-like) from Bacteroides faecium at 2.7 A resolution (Space group C2)
ComponentsDUF1735 domain-containing protein
KeywordsSUGAR BINDING PROTEIN / DUF1735 domain-containing protein / inactive endoglycosidase / GH18-like / Bacteroides faecium / gut microbiome
Function / homologyDomain of unknown function DUF1735 / BT_3987-like, N-terminal domain / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily / carbohydrate metabolic process / DUF1735 domain-containing protein
Function and homology information
Biological speciesBacteroides faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsSastre, D.E. / Navarro, M.V.A.S. / Sultana, N. / Sundberg, E.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM148075 United States
CitationJournal: Nat Commun / Year: 2024
Title: Human gut microbes express functionally distinct endoglycosidases to metabolize the same N-glycan substrate.
Authors: Sastre, D.E. / Sultana, N. / V A S Navarro, M. / Huliciak, M. / Du, J. / Cifuente, J.O. / Flowers, M. / Liu, X. / Lollar, P. / Trastoy, B. / Guerin, M.E. / Sundberg, E.J.
History
DepositionFeb 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DUF1735 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)57,3491
Polymers57,3491
Non-polymers00
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)138.388, 57.600, 74.430
Angle α, β, γ (deg.)90.00, 92.63, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein DUF1735 domain-containing protein


Mass: 57349.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides faecium (bacteria) / Gene: BacF7301_21000 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6H0KVH8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.58 Å3/Da / Density % sol: 52.39 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium bromide, 0.1 M Bis Tris propane pH 7.5, 20% (w/v) PEG 3350 (PACT 2-26(G2))

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Sep 21, 2022
Details: 0.25 degrees, 1.50 sec, detector distance 271.00 mm
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.67→50 Å / Num. obs: 16875 / % possible obs: 99.9 % / Redundancy: 7.3 % / CC1/2: 0.958 / CC star: 0.989 / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.073 / Rrim(I) all: 0.198 / Rsym value: 0.184 / Χ2: 2.063 / Net I/σ(I): 14.635
Reflection shellResolution: 2.67→2.72 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 2.121 / Num. unique obs: 1591 / CC1/2: 0.77 / CC star: 0.933 / Rpim(I) all: 0.261 / Rrim(I) all: 0.627 / Rsym value: 0.568 / Χ2: 0.691 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.67→37.18 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2299 851 5.04 %
Rwork0.1802 --
obs0.1827 16872 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.67→37.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3545 0 0 134 3679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043617
X-RAY DIFFRACTIONf_angle_d0.6434917
X-RAY DIFFRACTIONf_dihedral_angle_d14.3081305
X-RAY DIFFRACTIONf_chiral_restr0.046552
X-RAY DIFFRACTIONf_plane_restr0.005635
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.67-2.830.31691350.23482553X-RAY DIFFRACTION96
2.83-3.050.30611450.22142667X-RAY DIFFRACTION100
3.05-3.350.26441400.20972670X-RAY DIFFRACTION100
3.35-3.840.20781350.16972688X-RAY DIFFRACTION100
3.84-4.840.1941440.14752691X-RAY DIFFRACTION100
4.84-37.180.20321520.17092752X-RAY DIFFRACTION100

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