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- PDB-8xmz: Crystal structure of a novel porphyran-binding carbohydrate bindi... -

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Basic information

Entry
Database: PDB / ID: 8xmz
TitleCrystal structure of a novel porphyran-binding carbohydrate binding module
ComponentsT9SS C-terminal target domain-containing protein
KeywordsSUGAR BINDING PROTEIN / A novel porphyran-binding carbohydrate binding module
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Secretion system C-terminal sorting domain / Secretion system C-terminal sorting domain / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Galactose-binding-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
T9SS C-terminal target domain-containing protein
Similarity search - Component
Biological speciesAquimarina sp. BL5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMei, X.W. / Chang, Y.G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of a novel porphyran-binding carbohydrate binding module
Authors: Mei, X.W. / Chang, Y.G.
History
DepositionDec 28, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T9SS C-terminal target domain-containing protein
B: T9SS C-terminal target domain-containing protein


Theoretical massNumber of molelcules
Total (without water)36,6402
Polymers36,6402
Non-polymers00
Water82946
1
A: T9SS C-terminal target domain-containing protein


Theoretical massNumber of molelcules
Total (without water)18,3201
Polymers18,3201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: T9SS C-terminal target domain-containing protein


Theoretical massNumber of molelcules
Total (without water)18,3201
Polymers18,3201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.614, 95.614, 215.531
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein T9SS C-terminal target domain-containing protein


Mass: 18319.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Carbohydrate binding module / Source: (gene. exp.) Aquimarina sp. BL5 (bacteria) / Gene: D1818_19300 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3A9W2N2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 3.88 Å3/Da / Density % sol: 68.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 30% w/v Polyethylene glycol monomethyl ether 5,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.5→47.81 Å / Num. obs: 21013 / % possible obs: 99.9 % / Redundancy: 19 % / CC1/2: 1 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.021 / Rrim(I) all: 0.094 / Χ2: 0.99 / Net I/σ(I): 26.3 / Num. measured all: 398629
Reflection shellResolution: 2.5→2.6 Å / % possible obs: 99.8 % / Redundancy: 19.8 % / Rmerge(I) obs: 1.158 / Num. measured all: 45470 / Num. unique obs: 2302 / CC1/2: 0.979 / Rpim(I) all: 0.264 / Rrim(I) all: 1.188 / Χ2: 0.96 / Net I/σ(I) obs: 3.5

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→32.95 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2994 1980 9.54 %
Rwork0.2599 --
obs0.2635 20752 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→32.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2023 0 0 46 2069
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.653
X-RAY DIFFRACTIONf_dihedral_angle_d6.189291
X-RAY DIFFRACTIONf_chiral_restr0.047315
X-RAY DIFFRACTIONf_plane_restr0.003372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.44021360.36111287X-RAY DIFFRACTION97
2.56-2.630.44991350.34041286X-RAY DIFFRACTION98
2.63-2.710.32141350.31411290X-RAY DIFFRACTION98
2.71-2.80.37661350.30191297X-RAY DIFFRACTION98
2.8-2.90.35711400.29931312X-RAY DIFFRACTION99
2.9-3.010.32331400.30661309X-RAY DIFFRACTION99
3.01-3.150.42811380.29021309X-RAY DIFFRACTION100
3.15-3.320.37331440.29291352X-RAY DIFFRACTION99
3.32-3.520.29441400.2731336X-RAY DIFFRACTION100
3.52-3.790.31031420.26121343X-RAY DIFFRACTION100
3.79-4.180.30951450.25111365X-RAY DIFFRACTION100
4.18-4.780.20671450.20381376X-RAY DIFFRACTION100
4.78-6.010.27231490.22291406X-RAY DIFFRACTION100
6.02-32.950.27061560.25911504X-RAY DIFFRACTION99

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