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- PDB-8zqf: Crystal structure of a novel alginate-binding carbohydrate bindin... -

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Basic information

Entry
Database: PDB / ID: 8zqf
TitleCrystal structure of a novel alginate-binding carbohydrate binding module
ComponentsAlginate lyase
KeywordsSUGAR BINDING PROTEIN / A novel alginate-binding carbohydrate binding module
Function / homologyPL-6 family / Chondroitinase B / Pectin lyase fold / Pectin lyase fold/virulence factor / Prokaryotic membrane lipoprotein lipid attachment site profile. / lyase activity / Alginate lyase
Function and homology information
Biological speciesVibrio breoganii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMei, X.W. / Tao, W.W. / Chang, Y.G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of a novel alginate-binding carbohydrate binding module
Authors: Mei, X.W. / Tao, W.W. / Chang, Y.G.
History
DepositionJun 2, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alginate lyase


Theoretical massNumber of molelcules
Total (without water)23,4551
Polymers23,4551
Non-polymers00
Water7,368409
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.950, 64.360, 41.440
Angle α, β, γ (deg.)90.00, 110.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alginate lyase / A novel alginate-binding carbohydrate binding module


Mass: 23455.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio breoganii (bacteria) / Gene: A6E01_07505 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A193KCC3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.07 Å3/Da / Density % sol: 40.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 2.1 M DL-Malic acid pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97907 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 21, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 1.5→19.37 Å / Num. obs: 30419 / % possible obs: 99.3 % / Redundancy: 6.5 % / CC1/2: 0.989 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.051 / Rrim(I) all: 0.129 / Χ2: 1.03 / Net I/σ(I): 13.5 / Num. measured all: 196600
Reflection shellResolution: 1.5→1.53 Å / % possible obs: 98.7 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.231 / Num. measured all: 9936 / Num. unique obs: 1471 / CC1/2: 0.966 / Rpim(I) all: 0.096 / Rrim(I) all: 0.251 / Χ2: 1.01 / Net I/σ(I) obs: 9.7

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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: 1.5→19.37 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.214 2005 6.6 %
Rwork0.1809 --
obs0.1831 30389 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→19.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1510 0 0 409 1919
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.877
X-RAY DIFFRACTIONf_dihedral_angle_d6.846214
X-RAY DIFFRACTIONf_chiral_restr0.058234
X-RAY DIFFRACTIONf_plane_restr0.006286
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.27051450.2072001X-RAY DIFFRACTION98
1.54-1.580.24721360.19452002X-RAY DIFFRACTION99
1.58-1.630.23921330.1862018X-RAY DIFFRACTION99
1.63-1.680.23251350.18031986X-RAY DIFFRACTION98
1.68-1.740.22611620.18322026X-RAY DIFFRACTION99
1.74-1.810.23081350.18842022X-RAY DIFFRACTION99
1.81-1.890.22471360.18492017X-RAY DIFFRACTION99
1.89-1.990.23411560.18992029X-RAY DIFFRACTION99
1.99-2.110.21891390.18222014X-RAY DIFFRACTION99
2.11-2.280.17591340.17992057X-RAY DIFFRACTION100
2.28-2.510.1931530.17512021X-RAY DIFFRACTION100
2.51-2.870.21450.17982051X-RAY DIFFRACTION100
2.87-3.610.19011440.17092062X-RAY DIFFRACTION100
3.61-19.370.21661520.1742078X-RAY DIFFRACTION100

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