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- PDB-6gxr: Crystal structure of BP39L lectin from Burkholderia pseudomallei ... -

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Basic information

Entry
Database: PDB / ID: 6gxr
TitleCrystal structure of BP39L lectin from Burkholderia pseudomallei at 1.7 A resolution
ComponentsBP39L lectin
KeywordsSUGAR BINDING PROTEIN / Lectin
Function / homologyUncharacterized protein / Uncharacterized protein
Function and homology information
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsSykorova, P. / Novotna, J. / Demo, G. / Pompidor, G. / Dubska, E. / Komarek, J. / Fujdiarova, E. / Haronikova, L. / Varrot, A. / Imberty, A. ...Sykorova, P. / Novotna, J. / Demo, G. / Pompidor, G. / Dubska, E. / Komarek, J. / Fujdiarova, E. / Haronikova, L. / Varrot, A. / Imberty, A. / Shilova, N. / Bovin, N. / Pokorna, M. / Wimmerova, M.
Funding support Czech Republic, 2items
OrganizationGrant numberCountry
Czech Science Foundation13-25401S Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicCEITEC 2020 (LQ1601) Czech Republic
CitationJournal: Int.J.Biol.Macromol. / Year: 2020
Title: Characterization of novel lectins from Burkholderia pseudomallei and Chromobacterium violaceum with seven-bladed beta-propeller fold.
Authors: Sykorova, P. / Novotna, J. / Demo, G. / Pompidor, G. / Dubska, E. / Komarek, J. / Fujdiarova, E. / Houser, J. / Haronikova, L. / Varrot, A. / Shilova, N. / Imberty, A. / Bovin, N. / Pokorna, M. / Wimmerova, M.
History
DepositionJun 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BP39L lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9452
Polymers37,8491
Non-polymers961
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-12 kcal/mol
Surface area13120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.076, 87.549, 159.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-688-

HOH

21A-812-

HOH

31A-815-

HOH

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Components

#1: Protein BP39L lectin


Mass: 37848.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: CXQ84_12580, DP46_150, ERS012350_01657 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A069B727, UniProt: Q63TL0*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 1.93 Å3/Da / Density meas: 641794.75 Mg/m3 / Density % sol: 36.22 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES, 15% PEG 5000 MME, 0.2 M ammonium sulphate, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 31, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→79.55 Å / Num. obs: 33933 / % possible obs: 94.7 % / Redundancy: 14 % / CC1/2: 1 / Rmerge(I) obs: 0.071 / Net I/σ(I): 25.1
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 6.2 / Num. unique obs: 4942 / CC1/2: 0.924 / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→79.55 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.509 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.022 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19609 1701 5 %RANDOM
Rwork0.15737 ---
obs0.1593 32232 94.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.887 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å2-0 Å2-0 Å2
2--4.57 Å20 Å2
3----4.89 Å2
Refinement stepCycle: 1 / Resolution: 1.7→79.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2596 0 5 317 2918
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0192695
X-RAY DIFFRACTIONr_bond_other_d0.0070.022351
X-RAY DIFFRACTIONr_angle_refined_deg2.0991.93718
X-RAY DIFFRACTIONr_angle_other_deg1.10835449
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.795363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.39425.221113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66715303
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.741158
X-RAY DIFFRACTIONr_chiral_restr0.1390.2408
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213150
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02558
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8121.5181443
X-RAY DIFFRACTIONr_mcbond_other1.811.5181442
X-RAY DIFFRACTIONr_mcangle_it2.5232.2711803
X-RAY DIFFRACTIONr_mcangle_other2.5222.2721804
X-RAY DIFFRACTIONr_scbond_it2.6941.7821252
X-RAY DIFFRACTIONr_scbond_other2.6821.7731248
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0632.5551907
X-RAY DIFFRACTIONr_long_range_B_refined5.78419.7882991
X-RAY DIFFRACTIONr_long_range_B_other5.65519.2962919
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 127 -
Rwork0.234 2355 -
obs--95.54 %

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