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- PDB-6gxs: Crystal structure of CV39L lectin from Chromobacterium violaceum ... -

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Basic information

Entry
Database: PDB / ID: 6gxs
TitleCrystal structure of CV39L lectin from Chromobacterium violaceum at 1.8 A resolution
ComponentsCV39L lectin
KeywordsSUGAR BINDING PROTEIN / Lectin
Function / homologyDI(HYDROXYETHYL)ETHER / Uncharacterized protein
Function and homology information
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 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.title / _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

Downloads & links

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Assembly

Deposited unit
A: CV39L lectin
B: CV39L lectin
C: CV39L lectin
D: CV39L lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,98221
Polymers159,2454
Non-polymers1,73717
Water22,9691275
1
A: CV39L lectin
D: CV39L lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0697
Polymers79,6222
Non-polymers4465
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-65 kcal/mol
Surface area24860 Å2
MethodPISA
2
B: CV39L lectin
C: CV39L lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,91414
Polymers79,6222
Non-polymers1,29112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-65 kcal/mol
Surface area24770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.709, 123.781, 180.935
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
CV39L lectin


Mass: 39811.203 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757) (bacteria)
Gene: CV_1052 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7NZ70

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Non-polymers , 5 types, 1292 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1275 / 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: 2.18 Å3/Da / Density meas: 1471639.375 Mg/m3 / Density % sol: 43.6 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M sodium acetate, 25% PEG 4000, 0.2M ammonium sulphate, pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.967 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: 0.967 Å / Relative weight: 1
ReflectionResolution: 1.8→80.93 Å / Num. obs: 137285 / % possible obs: 100 % / Redundancy: 7.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Net I/σ(I): 14.7
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 19822 / CC1/2: 0.953 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→73.04 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.661 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.023 / ESU R Free: 0.022 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18852 6893 5 %RANDOM
Rwork0.15279 ---
obs0.15458 130295 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 12.009 Å2
Baniso -1Baniso -2Baniso -3
1-1.64 Å20 Å20 Å2
2---1.67 Å2-0 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.8→73.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10790 0 100 1275 12165
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.01911271
X-RAY DIFFRACTIONr_bond_other_d0.0060.029284
X-RAY DIFFRACTIONr_angle_refined_deg2.0141.91715415
X-RAY DIFFRACTIONr_angle_other_deg1.115321673
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.40451456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.23225.444529
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.647151399
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.84158
X-RAY DIFFRACTIONr_chiral_restr0.1450.21522
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02113247
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022385
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_it1.2361.0735803
X-RAY DIFFRACTIONr_mcbond_other1.2341.0725802
X-RAY DIFFRACTIONr_mcangle_it1.771.6027251
X-RAY DIFFRACTIONr_mcangle_other1.771.6037252
X-RAY DIFFRACTIONr_scbond_it2.2021.2975468
X-RAY DIFFRACTIONr_scbond_other2.2021.2975468
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1321.868160
X-RAY DIFFRACTIONr_long_range_B_refined4.35413.80913037
X-RAY DIFFRACTIONr_long_range_B_other4.16813.3812689
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 470 -
Rwork0.2 9574 -
obs--99.83 %

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