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- PDB-1x99: X-ray crystal structure of Xerocomus chrysenteron lectin XCL at 1... -

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Basic information

Entry
Database: PDB / ID: 1x99
TitleX-ray crystal structure of Xerocomus chrysenteron lectin XCL at 1.4 Angstroms resolution, mutated at Q46M, V54M, L58M
Componentslectin
KeywordsSUGAR BINDING PROTEIN / fungal lectin
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 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 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
DepositionAug 20, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: lectin
B: lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,21210
Polymers32,5452
Non-polymers6678
Water2,954164
1
A: lectin
B: lectin
hetero molecules

A: lectin
B: lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,42320
Polymers65,0904
Non-polymers1,33316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area9190 Å2
ΔGint-126 kcal/mol
Surface area22030 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)59.153, 59.153, 149.663
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operation: x, -y, -z+1/3

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Components

#1: Protein lectin / XCL lectin


Mass: 16272.558 Da / Num. of mol.: 2 / Mutation: Q48M, V56M, L60M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xerocomus chrysenteron (fungus) / Plasmid: modified pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q8WZC9
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.3 Å3/Da / Density % sol: 47 %
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: SLS / Beamline: X06SA / Wavelength: 0.9184, 0.9791
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 5, 2003
RadiationMonochromator: Si 111 monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91841
20.97911
ReflectionResolution: 1.4→51.3 Å / Num. all: 60727 / Num. obs: 60727 / % possible obs: 99.97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 15.6 % / Biso Wilson estimate: 14.2 Å2 / Rsym value: 0.077 / Net I/σ(I): 15.6
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 12.1 % / Mean I/σ(I) obs: 7.3 / Rsym value: 0.265 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.4→51.3 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.526 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.065 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18743 3075 5.1 %RANDOM
Rwork0.17378 ---
all0.17447 57615 --
obs0.17447 57615 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.845 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å20 Å2
2--0.12 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.4→51.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2218 0 37 164 2419
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222306
X-RAY DIFFRACTIONr_bond_other_d0.0010.022035
X-RAY DIFFRACTIONr_angle_refined_deg1.2721.923125
X-RAY DIFFRACTIONr_angle_other_deg1.73634702
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.075286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.23723.168101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.13315363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1011515
X-RAY DIFFRACTIONr_chiral_restr0.110.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022571
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02498
X-RAY DIFFRACTIONr_nbd_refined0.1760.2350
X-RAY DIFFRACTIONr_nbd_other0.1850.22002
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21120
X-RAY DIFFRACTIONr_nbtor_other0.0850.21334
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0960.2100
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.20.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.25
X-RAY DIFFRACTIONr_mcbond_it1.081.51698
X-RAY DIFFRACTIONr_mcbond_other0.3561.5607
X-RAY DIFFRACTIONr_mcangle_it1.3622271
X-RAY DIFFRACTIONr_scbond_it1.96831052
X-RAY DIFFRACTIONr_scangle_it2.454.5854
X-RAY DIFFRACTIONr_rigid_bond_restr0.93235196
X-RAY DIFFRACTIONr_sphericity_free4.1653164
X-RAY DIFFRACTIONr_sphericity_bonded1.59134302
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.173 223 -
Rwork0.144 4177 -
obs--100 %

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