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- PDB-2boi: 1.1A Structure of Chromobacterium Violaceum Lectin CV2L in Comple... -

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Basic information

Entry
Database: PDB / ID: 2boi
Title1.1A Structure of Chromobacterium Violaceum Lectin CV2L in Complex with alpha-methyl-fucoside
ComponentsCV-IIL LECTIN
KeywordsLECTIN / FUCOSE / CHROMOBACTERIUM VIOLACEUM / PSEUDOMONAS AERUGINOSA
Function / homology
Function and homology information


Lectin, sugar-binding / Calcium-mediated lectin / Calcium-mediated lectin / Calcium-mediated lectin superfamily / Fucose-binding lectin II (PA-IIL) / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
methyl alpha-L-fucopyranoside / Calcium-mediated lectin domain-containing protein
Similarity search - Component
Biological speciesCHROMOBACTERIUM VIOLACEUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsPokorna, M. / Cioci, G. / Perret, S. / Rebuffet, E. / Adam, J. / Gilboa-Garber, N. / Mitchell, E.P. / Imberty, A. / Wimmerova, M.
CitationJournal: Biochemistry / Year: 2006
Title: Unusual Entropy Driven Affinity of Chromobacter Violaceum Lectin Cv-Iil Towards Fucose and Mannose
Authors: Pokorna, M. / Cioci, G. / Perret, S. / Rebuffet, E. / Kostlanova, N. / Adam, J. / Gilboa-Garber, N. / Mitchell, E.P. / Imberty, A. / Wimmerova, M.
History
DepositionApr 12, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET DETERMIMATION METHOD: PROVIDED BY DEPOSITOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CV-IIL LECTIN
B: CV-IIL LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2138
Polymers23,6962
Non-polymers5176
Water5,999333
1
A: CV-IIL LECTIN
B: CV-IIL LECTIN
hetero molecules

A: CV-IIL LECTIN
B: CV-IIL LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,42616
Polymers47,3924
Non-polymers1,03312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.093, 89.836, 46.479
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein CV-IIL LECTIN


Mass: 11848.111 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHROMOBACTERIUM VIOLACEUM (bacteria) / Plasmid: PET25(B) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TUNER(DE3) / References: UniProt: Q7NX84
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Sugar ChemComp-MFU / methyl alpha-L-fucopyranoside / ALPHA-L-METHYL-FUCOSE / methyl 6-deoxy-alpha-L-galactopyranoside / methyl alpha-L-fucoside / methyl L-fucoside / methyl fucoside / Methyl group


Type: L-saccharide / Mass: 178.183 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C7H14O5
IdentifierTypeProgram
LFucp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-L-fucopyranoseCOMMON NAMEGMML 1.0
o1-methyl-a-L-fucoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.2 Å3/Da / Density % sol: 45 %
Description: MOLREP WAS USED WITH MODEL 1GZT TO FIND THE POSITIONS OF 4 CA ATOMS IN THE A.U. PHASING WAS PERFORMED BY ACORN STARTING FROM THE POSITIONS OF THESE CA ATOMS.
Crystal growDetails: PEG 8000 10%, 0.1 M (NH4)2SO4 PH 5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 15, 2004 / Details: MIRRORS
RadiationMonochromator: DIAMOND AND GE DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.1→34.38 Å / Num. obs: 87549 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 8.14 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 5.36
Reflection shellResolution: 1.1→1.13 Å / Redundancy: 7.04 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.34 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
ACORNphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GZT

1gzt


Resolution: 1.1→46.47 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.541 / SU ML: 0.012 / Cross valid method: THROUGHOUT / ESU R: 0.021 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.117 4389 5 %RANDOM
Rwork0.101 ---
obs0.102 83099 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 1.1→46.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1668 0 28 333 2029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221908
X-RAY DIFFRACTIONr_bond_other_d0.0010.021744
X-RAY DIFFRACTIONr_angle_refined_deg1.6341.9612639
X-RAY DIFFRACTIONr_angle_other_deg0.84434070
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8815271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.69926.15478
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.54515300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.834158
X-RAY DIFFRACTIONr_chiral_restr0.1120.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022279
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02359
X-RAY DIFFRACTIONr_nbd_refined0.2690.2334
X-RAY DIFFRACTIONr_nbd_other0.2010.21752
X-RAY DIFFRACTIONr_nbtor_refined0.1620.2998
X-RAY DIFFRACTIONr_nbtor_other0.0860.21204
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2192
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.050.217
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3310.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.290.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.241
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6061.51282
X-RAY DIFFRACTIONr_mcbond_other0.6571.5522
X-RAY DIFFRACTIONr_mcangle_it2.14322058
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7783682
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0014.5581
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.1→1.13 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.137 327 -
Rwork0.119 6038 -
obs--100 %

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