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- PDB-8wab: Crystal structure of a chondroitin sulfate-binding carbohydrate b... -

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Basic information

Entry
Database: PDB / ID: 8wab
TitleCrystal structure of a chondroitin sulfate-binding carbohydrate binding module of a chondroitinase
ComponentsDNRLRE domain-containing protein
KeywordsSUGAR BINDING PROTEIN / Chondroitin sulfate-binding carbohydrate binding module
Function / homology
Function and homology information


carbohydrate binding / carbohydrate metabolic process / lyase activity / extracellular region
Similarity search - Function
Secretion system C-terminal sorting domain / Polysaccharide lyase 8 / Polysaccharide lyase 8, N-terminal alpha-helical / Polysaccharide lyase family 8, N terminal alpha-helical domain / Polysaccharide lyase family 8, C-terminal / Polysaccharide lyase family 8, C-terminal beta-sandwich domain / Polysaccharide lyase family 8, central domain / Polysaccharide lyase family 8, super-sandwich domain / Secretion system C-terminal sorting domain / Polysaccharide lyase family 8-like, C-terminal ...Secretion system C-terminal sorting domain / Polysaccharide lyase 8 / Polysaccharide lyase 8, N-terminal alpha-helical / Polysaccharide lyase family 8, N terminal alpha-helical domain / Polysaccharide lyase family 8, C-terminal / Polysaccharide lyase family 8, C-terminal beta-sandwich domain / Polysaccharide lyase family 8, central domain / Polysaccharide lyase family 8, super-sandwich domain / Secretion system C-terminal sorting domain / Polysaccharide lyase family 8-like, C-terminal / Chondroitin AC/alginate lyase / Glycoside hydrolase-type carbohydrate-binding / Galactose mutarotase-like domain superfamily
Similarity search - Domain/homology
DNRLRE domain-containing protein
Similarity search - Component
Biological speciesDysgonomonas sp. HDW5A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLiu, G.C. / Chang, Y.G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of a carbohydrate binding module at 2.2 Angstroms resolution
Authors: Liu, G.C. / Chang, Y.G.
History
DepositionSep 7, 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: DNRLRE domain-containing protein
B: DNRLRE domain-containing protein


Theoretical massNumber of molelcules
Total (without water)45,5962
Polymers45,5962
Non-polymers00
Water6,467359
1
A: DNRLRE domain-containing protein


Theoretical massNumber of molelcules
Total (without water)22,7981
Polymers22,7981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNRLRE domain-containing protein


Theoretical massNumber of molelcules
Total (without water)22,7981
Polymers22,7981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-6 kcal/mol
Surface area14910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.401, 45.717, 56.421
Angle α, β, γ (deg.)102.28, 96.00, 113.21
Int Tables number1
Space group name H-MP1

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Components

#1: Protein DNRLRE domain-containing protein


Mass: 22798.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dysgonomonas sp. HDW5A (bacteria) / Gene: G7050_17395 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6G7XAP5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.01 Å3/Da / Density % sol: 38.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 27% PEG 4000, 0.1M Sodium cacodylate

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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: 2.2→40.36 Å / Num. obs: 17339 / % possible obs: 96.2 % / Redundancy: 1.8 % / CC1/2: 0.96 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.085 / Rrim(I) all: 0.12 / Χ2: 0.54 / Net I/σ(I): 5.3 / Num. measured all: 31219
Reflection shellResolution: 2.2→2.27 Å / % possible obs: 95.8 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.216 / Num. measured all: 2779 / Num. unique obs: 1533 / CC1/2: 0.837 / Rpim(I) all: 0.216 / Rrim(I) all: 0.306 / Χ2: 0.54 / Net I/σ(I) obs: 2.7

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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: 2.2→27.55 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 23.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2234 1731 9.99 %
Rwork0.1684 --
obs0.1739 17323 96.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→27.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2791 0 0 359 3150
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.828
X-RAY DIFFRACTIONf_dihedral_angle_d6.32381
X-RAY DIFFRACTIONf_chiral_restr0.056442
X-RAY DIFFRACTIONf_plane_restr0.006496
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.30981470.22851322X-RAY DIFFRACTION96
2.26-2.340.2941390.20881259X-RAY DIFFRACTION95
2.34-2.420.32541440.18971288X-RAY DIFFRACTION95
2.42-2.520.24451440.19591298X-RAY DIFFRACTION96
2.52-2.630.22231420.17541278X-RAY DIFFRACTION96
2.63-2.770.23921430.17391289X-RAY DIFFRACTION96
2.77-2.940.25111480.18071319X-RAY DIFFRACTION97
2.94-3.170.24131450.17271308X-RAY DIFFRACTION97
3.17-3.490.20991440.15971296X-RAY DIFFRACTION97
3.49-3.990.19231460.15121322X-RAY DIFFRACTION97
3.99-5.030.17171450.13461301X-RAY DIFFRACTION97

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