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- PDB-8jiy: A carbohydrate binding domain of a putative chondroitinase -

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Basic information

Entry
Database: PDB / ID: 8jiy
TitleA carbohydrate binding domain of a putative chondroitinase
ComponentsDUF4955 domain-containing protein
KeywordsSUGAR BINDING PROTEIN / Carbohydrate binding
Function / homologyDomain of unknown function DUF4955 / Domain of unknown function (DUF4955) / Secretion system C-terminal sorting domain / Pectate lyase superfamily protein / Pectate lyase superfamily protein / Secretion system C-terminal sorting domain / Pectin lyase fold / Pectin lyase fold/virulence factor / DUF4955 domain-containing protein
Function and homology information
Biological speciesPolaribacter haliotis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsLiu, G.C. / Chang, Y.G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Identification and structural characterization of a novel chondroitin sulfate-specific carbohydrate-binding module: The first member of a new family, CBM100.
Authors: Liu, G. / Chang, Y. / Mei, X. / Chen, G. / Zhang, Y. / Jiang, X. / Tao, W. / Xue, C.
History
DepositionMay 29, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DUF4955 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)27,1171
Polymers27,1171
Non-polymers00
Water4,864270
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.313, 56.634, 69.456
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DUF4955 domain-containing protein


Mass: 27117.342 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Polaribacter haliotis (bacteria) / Gene: H9I45_07735 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7L8AJZ3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.04 Å3/Da / Density % sol: 39.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.2 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.55→43.89 Å / Num. obs: 32725 / % possible obs: 99.4 % / Redundancy: 5.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.026 / Rrim(I) all: 0.062 / Χ2: 0.97 / Net I/σ(I): 17 / Num. measured all: 169904
Reflection shellResolution: 1.55→1.58 Å / % possible obs: 99.5 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.238 / Num. measured all: 6887 / Num. unique obs: 1596 / CC1/2: 0.937 / Rpim(I) all: 0.127 / Rrim(I) all: 0.271 / Χ2: 0.56 / Net I/σ(I) obs: 4.4

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→29.56 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2284 2010 6.15 %
Rwork0.1905 --
obs0.1928 32661 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→29.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1706 0 0 270 1976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.767
X-RAY DIFFRACTIONf_dihedral_angle_d6.059236
X-RAY DIFFRACTIONf_chiral_restr0.056266
X-RAY DIFFRACTIONf_plane_restr0.005315
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.28371410.25612145X-RAY DIFFRACTION99
1.59-1.630.30331420.252168X-RAY DIFFRACTION99
1.63-1.680.29411400.24122154X-RAY DIFFRACTION99
1.68-1.730.26431380.23132171X-RAY DIFFRACTION100
1.73-1.80.25541420.21912165X-RAY DIFFRACTION99
1.8-1.870.24681440.21752162X-RAY DIFFRACTION99
1.87-1.950.26391420.20682187X-RAY DIFFRACTION99
1.95-2.060.20351440.18312143X-RAY DIFFRACTION99
2.06-2.180.21051370.18792191X-RAY DIFFRACTION99
2.18-2.350.23241460.1892174X-RAY DIFFRACTION98
2.35-2.590.24571420.19272188X-RAY DIFFRACTION99
2.59-2.960.20541470.18982221X-RAY DIFFRACTION100
2.96-3.730.20321470.17792233X-RAY DIFFRACTION99

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