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- PDB-1xi0: X-ray crystal structure of wild-type Xerocomus chrysenteron lectin XCL -

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Basic information

Entry
Database: PDB / ID: 1xi0
TitleX-ray crystal structure of wild-type Xerocomus chrysenteron lectin XCL
Componentslectin
KeywordsSUGAR BINDING PROTEIN / beta sandwich / greek key motif
Function / homologyFungal fruit body lectin / Fungal fruit body lectin / Cytolysin/lectin / Cytolysin/lectin / Mutm (Fpg) Protein; Chain: A, domain 2 / Sandwich / Mainly Beta / Lectin
Function and homology information
Biological speciesXerocomus chrysenteron (red-cracking bolete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBirck, C. / Damian, L. / Marty-Detraves, C. / Lougarre, A. / Schulze-Briese, C. / Koehl, P. / Fournier, D. / Paquereau, L. / Samama, J.P.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: A new lectin family with structure similarity to actinoporins revealed by the crystal structure of Xerocomus chrysenteron lectin XCL
Authors: Birck, C. / Damian, L. / Marty-Detraves, C. / Lougarre, A. / Schulze-Briese, C. / Koehl, P. / Fournier, D. / Paquereau, L. / Samama, J.P.
History
DepositionSep 21, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 30, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: lectin
B: lectin


Theoretical massNumber of molelcules
Total (without water)32,0642
Polymers32,0642
Non-polymers00
Water1,17165
1
A: lectin
B: lectin

A: lectin
B: lectin


Theoretical massNumber of molelcules
Total (without water)64,1274
Polymers64,1274
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)84.084, 84.084, 71.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11B-175-

HOH

Detailsthe biological assembly is a tetramer generated from the dimer in the asymetric unit by the operation: -x, -y, z

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Components

#1: Protein lectin / XCL lectin


Mass: 16031.808 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xerocomus chrysenteron (red-cracking bolete)
Plasmid: modified pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8WZC9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.3 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: ammonium sulfate, MES, zinc chloride, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 14, 2002
RadiationMonochromator: Diamond (111), Ge (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. all: 89122 / Num. obs: 20047 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 27.9 Å2 / Rsym value: 0.062 / Net I/σ(I): 17.3
Reflection shellResolution: 1.98→2.05 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 6.2 / Num. unique all: 2010 / Rsym value: 0.272 / % possible all: 99.1

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1x99

1x99


Resolution: 2→50 Å / Isotropic thermal model: anisotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 952 -RANDOM
Rwork0.21 ---
all0.215 19176 --
obs0.215 18955 97.3 %-
Refine analyzeLuzzati coordinate error obs: 0.27 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2111 0 0 65 2176
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0074
X-RAY DIFFRACTIONc_angle_deg1.34
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.009
RfactorNum. reflection
Rfree0.288 79
Rwork0.318 -
obs-1684

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