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- PDB-8x8h: A carbohydrate binding domain of a putative pectate lyase -

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Basic information

Entry
Database: PDB / ID: 8x8h
TitleA carbohydrate binding domain of a putative pectate lyase
ComponentsPectate disaccharide-lyase
KeywordsSUGAR BINDING PROTEIN / Carbohydrate binding
Function / homology
Function and homology information


carbon-oxygen lyase activity, acting on polysaccharides / extracellular region
Similarity search - Function
: / Pel9A-like, right handed beta helix region / : / Parallel beta-helix repeat / Parallel beta-helix repeats / Pectin lyase fold / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
Pel9A-like right handed beta-helix region domain-containing protein
Similarity search - Component
Biological speciesLachnoclostridium phytofermentans
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLiu, G.C. / Chang, Y.G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of a carbohydrate binding domain at 2.00 Angstroms resolution
Authors: Liu, G.C. / Chang, Y.G.
History
DepositionNov 27, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pectate disaccharide-lyase
B: Pectate disaccharide-lyase
C: Pectate disaccharide-lyase
D: Pectate disaccharide-lyase


Theoretical massNumber of molelcules
Total (without water)74,7504
Polymers74,7504
Non-polymers00
Water13,511750
1
A: Pectate disaccharide-lyase


Theoretical massNumber of molelcules
Total (without water)18,6881
Polymers18,6881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pectate disaccharide-lyase


Theoretical massNumber of molelcules
Total (without water)18,6881
Polymers18,6881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Pectate disaccharide-lyase


Theoretical massNumber of molelcules
Total (without water)18,6881
Polymers18,6881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Pectate disaccharide-lyase


Theoretical massNumber of molelcules
Total (without water)18,6881
Polymers18,6881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.100, 81.100, 251.942
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Pectate disaccharide-lyase


Mass: 18687.584 Da / Num. of mol.: 4 / Fragment: Carbohydrate binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lachnoclostridium phytofermentans (strain ATCC 700394 / DSM 18823 / ISDg) (bacteria)
Gene: Cphy_1888 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9KT46
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 750 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.77 Å3/Da / Density % sol: 55.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20% w/v PEG 6000, 0.1M Citric acid pH4.0, 1M Lithium chloride

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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→49.75 Å / Num. obs: 58037 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.02 / Rrim(I) all: 0.071 / Χ2: 1.01 / Net I/σ(I): 23.7 / Num. measured all: 747451
Reflection shellResolution: 2→2.05 Å / % possible obs: 100 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.472 / Num. measured all: 53996 / Num. unique obs: 4239 / CC1/2: 0.987 / Rpim(I) all: 0.137 / Rrim(I) all: 0.492 / Χ2: 0.97 / Net I/σ(I) obs: 5.1

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→32.9 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2085 1998 3.46 %
Rwork0.1619 --
obs0.1634 57806 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→32.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4332 0 0 750 5082
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011
X-RAY DIFFRACTIONf_angle_d0.942
X-RAY DIFFRACTIONf_dihedral_angle_d6.228624
X-RAY DIFFRACTIONf_chiral_restr0.072692
X-RAY DIFFRACTIONf_plane_restr0.007760
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.25551400.21263916X-RAY DIFFRACTION100
2.05-2.110.22591400.17563864X-RAY DIFFRACTION100
2.11-2.170.20211400.16673917X-RAY DIFFRACTION99
2.17-2.240.18251390.16323920X-RAY DIFFRACTION100
2.24-2.320.24581420.16013939X-RAY DIFFRACTION100
2.32-2.410.23411390.16413912X-RAY DIFFRACTION100
2.41-2.520.21611420.16963968X-RAY DIFFRACTION100
2.52-2.650.18931410.17713946X-RAY DIFFRACTION100
2.65-2.820.26861430.1893961X-RAY DIFFRACTION100
2.82-3.040.25041420.18123989X-RAY DIFFRACTION100
3.04-3.340.23361440.17534011X-RAY DIFFRACTION100
3.34-3.820.19871440.14624054X-RAY DIFFRACTION100
3.82-4.820.16551470.13344086X-RAY DIFFRACTION100
4.82-32.90.19361550.15954325X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -1.9301 Å / Origin y: 27.9086 Å / Origin z: 15.4087 Å
111213212223313233
T0.0511 Å2-0.052 Å2-0.0276 Å2-0.157 Å2-0.0046 Å2--0.1288 Å2
L0.2459 °2-0.0991 °2-0.0777 °2-0.4496 °20.2306 °2--1.0299 °2
S0.0123 Å °-0.0303 Å °-0.0068 Å °0.0054 Å °-0.0368 Å °0.0276 Å °0.0092 Å °-0.1644 Å °-0.0135 Å °
Refinement TLS groupSelection details: all

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