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- PDB-8wc1: A carbohydrate binding domain of a putative pectate lyase -

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Basic information

Entry
Database: PDB / ID: 8wc1
TitleA carbohydrate binding domain of a putative pectate lyase
ComponentsPectate lyase family 9
KeywordsLYASE / Carbohydrate binding
Function / homology: / Right handed beta helix domain / Right handed beta helix region / Pectin lyase fold / Pectin lyase fold/virulence factor / lyase activity / extracellular region / Pectate lyase family 9
Function and homology information
Biological speciesMonoglobus pectinilyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 1.30 Angstroms resolution
Authors: Liu, G.C. / Chang, Y.G.
History
DepositionSep 11, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pectate lyase family 9


Theoretical massNumber of molelcules
Total (without water)19,2361
Polymers19,2361
Non-polymers00
Water4,882271
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.957, 52.190, 71.023
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 Pectate lyase family 9


Mass: 19236.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monoglobus pectinilyticus (bacteria) / Gene: B9O19_00428 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2K9P019
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 1.92 Å3/Da / Density % sol: 36.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 28% w/v PEG MME 2000, 0.1M Bis-Tris pH6.5

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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: Jul 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.3→42.06 Å / Num. obs: 37307 / % possible obs: 99.9 % / Redundancy: 6.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.026 / Rrim(I) all: 0.067 / Χ2: 0.97 / Net I/σ(I): 18.1 / Num. measured all: 230563
Reflection shellResolution: 1.3→1.32 Å / % possible obs: 100 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.297 / Num. measured all: 10763 / Num. unique obs: 1819 / CC1/2: 0.947 / Rpim(I) all: 0.137 / Rrim(I) all: 0.328 / Χ2: 1.09 / Net I/σ(I) obs: 5.6

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→34.82 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 17.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1837 2000 5.37 %
Rwork0.171 --
obs0.1717 37241 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→34.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1127 0 0 271 1398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005
X-RAY DIFFRACTIONf_angle_d0.897
X-RAY DIFFRACTIONf_dihedral_angle_d6.39161
X-RAY DIFFRACTIONf_chiral_restr0.083184
X-RAY DIFFRACTIONf_plane_restr0.006200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.330.26171410.22062495X-RAY DIFFRACTION100
1.33-1.370.20391420.20222483X-RAY DIFFRACTION100
1.37-1.410.1961400.18572470X-RAY DIFFRACTION100
1.41-1.450.18961400.18232474X-RAY DIFFRACTION100
1.45-1.510.19511420.17742494X-RAY DIFFRACTION100
1.51-1.570.22081400.17372476X-RAY DIFFRACTION100
1.57-1.640.17261420.16512499X-RAY DIFFRACTION100
1.64-1.720.17011420.16782501X-RAY DIFFRACTION100
1.72-1.830.20741420.17352505X-RAY DIFFRACTION100
1.83-1.970.16551420.16812515X-RAY DIFFRACTION100
1.97-2.170.16811440.16152527X-RAY DIFFRACTION100
2.17-2.490.17991450.17222554X-RAY DIFFRACTION100
2.49-3.130.17811450.18982559X-RAY DIFFRACTION100
3.13-34.820.18321530.15332689X-RAY DIFFRACTION100

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