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- PDB-2vuv: Crystal structure of Codakine at 1.3A resolution -

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Basic information

Entry
Database: PDB / ID: 2vuv
TitleCrystal structure of Codakine at 1.3A resolution
ComponentsCODAKINE
KeywordsSUGAR BINDING PROTEIN / SUGAR-BINDING PROTEIN / C-TYPE / LECTIN / MANNOSE / CODAKINE / INVERTEBRATE
Function / homology
Function and homology information


: / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily ...: / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Codakine
Similarity search - Component
Biological speciesCODAKIA ORBICULARIS (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsGourdine, J.P. / Cioci, G.C. / Miguet, L. / Unverzagt, C. / Varrot, A. / Gauthier, C. / Smith-Ravin, E.J. / Imberty, A.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: High Affinity Interaction between a Bivalve C-Type Lectin and a Biantennary Complex-Type N-Glycan Revealed by Crystallography and Microcalorimetry.
Authors: Gourdine, J.P. / Cioci, G.C. / Miguet, L. / Unverzagt, C. / Silva, D.V. / Varrot, A. / Gautier, C. / Smith-Ravin, E.J. / Imberty, A.
History
DepositionMay 30, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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.pdbx_leaving_atom_flag / _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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CODAKINE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6045
Polymers14,1871
Non-polymers4164
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)82.908, 30.395, 67.088
Angle α, β, γ (deg.)90.00, 133.86, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2015-

HOH

21A-2151-

HOH

31A-2172-

HOH

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Components

#1: Protein CODAKINE


Mass: 14187.471 Da / Num. of mol.: 1 / Fragment: RESIDUES 20-148 / Source method: isolated from a natural source / Source: (natural) CODAKIA ORBICULARIS (invertebrata) / References: UniProt: Q3KVL7
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.1 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal growDetails: 0.2 M DI-AMMONIUM CITRATE PH 5, 20% W/V PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.931
DetectorType: ADSC CCD / Detector: CCD / Details: MIRRORS
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.3→33.11 Å / Num. obs: 26746 / % possible obs: 89.7 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 10.39 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 12.1
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.1 / % possible all: 52.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
ACORNphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HOMOLOGY MODEL

Resolution: 1.3→27.63 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.641 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.049 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.161 1370 5.12 %RANDOM
Rwork0.144 ---
obs0.145 26746 89.2 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 8.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.943 Å20 Å20.552 Å2
2---0.306 Å20 Å2
3---0.129 Å2
Refinement stepCycle: LAST / Resolution: 1.3→27.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms992 0 26 174 1192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0211122
X-RAY DIFFRACTIONr_bond_other_d0.0020.02724
X-RAY DIFFRACTIONr_angle_refined_deg1.7241.9241541
X-RAY DIFFRACTIONr_angle_other_deg0.9553.0071749
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3615145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.21525.35756
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.51715150
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.083153
X-RAY DIFFRACTIONr_chiral_restr0.1180.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021350
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02237
X-RAY DIFFRACTIONr_nbd_refined0.2260.2238
X-RAY DIFFRACTIONr_nbd_other0.1870.2787
X-RAY DIFFRACTIONr_nbtor_refined0.1920.2564
X-RAY DIFFRACTIONr_nbtor_other0.0890.2535
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2116
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5540.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.360.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1871.5704
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.66421089
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4213513
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5184.5452
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: 1.3→1.34 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.23 58
Rwork0.22 945

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