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- PDB-8w04: Crystal structure of DUF1735-domain containing protein (GH18-like... -

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Basic information

Entry
Database: PDB / ID: 8w04
TitleCrystal structure of DUF1735-domain containing protein (GH18-like) from Bacteroides faecium at 2.9 A resolution (Space group P21)
ComponentsDUF1735 domain-containing protein
KeywordsSUGAR BINDING PROTEIN / DUF1735-domain containing protein / GH18-like / inactive endoglycosidase / 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: 2.91 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
B: DUF1735 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)114,6982
Polymers114,6982
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.259, 57.537, 137.148
Angle α, β, γ (deg.)90.00, 91.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DUF1735 domain-containing protein


Mass: 57349.098 Da / Num. of mol.: 2
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

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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: 2.55 Å3/Da / Density % sol: 51.83 %
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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 25271 / % possible obs: 97.72 % / Redundancy: 7.2 % / Biso Wilson estimate: 49.6 Å2 / CC1/2: 0.972 / CC star: 0.993 / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.076 / Rrim(I) all: 0.207 / Χ2: 2.142 / Net I/σ(I): 13.39
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.773 / Mean I/σ(I) obs: 2.26 / Num. unique obs: 2050 / CC1/2: 0.814 / CC star: 0.947 / Rpim(I) all: 0.315 / Rrim(I) all: 0.836 / Χ2: 0.781 / % possible all: 79.94

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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: 2.91→37.11 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.252 2003 7.93 %
Rwork0.2013 --
obs0.2053 25250 97.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.91→37.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7106 0 0 0 7106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037234
X-RAY DIFFRACTIONf_angle_d0.519834
X-RAY DIFFRACTIONf_dihedral_angle_d16.292610
X-RAY DIFFRACTIONf_chiral_restr0.0421104
X-RAY DIFFRACTIONf_plane_restr0.0041270
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.91-2.980.3599950.2611128X-RAY DIFFRACTION66
2.98-3.060.33881550.27351651X-RAY DIFFRACTION99
3.06-3.150.32351360.26061701X-RAY DIFFRACTION100
3.15-3.250.29541460.25611691X-RAY DIFFRACTION100
3.25-3.370.37071430.24321698X-RAY DIFFRACTION100
3.37-3.50.27411490.22011675X-RAY DIFFRACTION100
3.5-3.660.28451400.22451670X-RAY DIFFRACTION100
3.66-3.850.27711420.2171710X-RAY DIFFRACTION100
3.85-4.090.27411540.19181706X-RAY DIFFRACTION100
4.09-4.410.21191470.18811708X-RAY DIFFRACTION100
4.41-4.850.18681420.15131686X-RAY DIFFRACTION100
4.85-5.550.2061520.17011709X-RAY DIFFRACTION100
5.55-6.990.25261500.19891728X-RAY DIFFRACTION100
6.99-37.110.191520.16611786X-RAY DIFFRACTION99

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