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- PDB-5idb: Crystal structure of CGL1 from Crassostrea gigas, mannose-bound f... -

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Basic information

Entry
Database: PDB / ID: 5idb
TitleCrystal structure of CGL1 from Crassostrea gigas, mannose-bound form (CGL1/MAN2)
ComponentsNatterin-3
KeywordsSUGAR BINDING PROTEIN / CGL1 / lectin / Crassostrea gigas / N-type / mannose
Function / homologyDM9 repeat / DM9 repeat / Repeats found in Drosophila proteins. / metal ion binding / beta-D-mannopyranose / alpha-D-mannopyranose / Natterin-3
Function and homology information
Biological speciesCrassostrea gigas (Pacific oyster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1 Å
AuthorsUnno, H.
CitationJournal: Sci Rep / Year: 2016
Title: Identification, Characterization, and X-ray Crystallographic Analysis of a Novel Type of Mannose-Specific Lectin CGL1 from the Pacific Oyster Crassostrea gigas.
Authors: Unno, H. / Matsuyama, K. / Tsuji, Y. / Goda, S. / Hiemori, K. / Tateno, H. / Hirabayashi, J. / Hatakeyama, T.
History
DepositionFeb 24, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2016Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Derived calculations / Category: chem_comp / diffrn_source / pdbx_struct_oper_list
Item: _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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
B: Natterin-3
A: Natterin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0999
Polymers30,8112
Non-polymers1,2887
Water8,737485
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-8 kcal/mol
Surface area12250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.320, 57.930, 80.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Natterin-3


Mass: 15405.501 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crassostrea gigas (Pacific oyster) / Gene: CGI_10011001, CGI_10018577 / Production host: Escherichia coli (E. coli) / References: UniProt: K1QRB6
#2: Sugar
ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsBMA A 1001 AND MAN A 1002 ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER. BMA B 1001 AND MAN B 1002 ...BMA A 1001 AND MAN A 1002 ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER. BMA B 1001 AND MAN B 1002 ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER.

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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: 41.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 9.5 / Details: 30% PEG 3000, 100mM CHES

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jan 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1→23.5 Å / Num. obs: 131088 / % possible obs: 89 % / Redundancy: 7.6 % / Net I/σ(I): 16.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 1→22.39 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.573 / SU ML: 0.014 / Cross valid method: THROUGHOUT / ESU R: 0.021 / ESU R Free: 0.023 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.144 6598 5 %RANDOM
Rwork0.12228 ---
obs0.12338 124314 90.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 10.103 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1→22.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2246 0 13 496 2755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0192313
X-RAY DIFFRACTIONr_bond_other_d0.0020.022170
X-RAY DIFFRACTIONr_angle_refined_deg2.0531.9823143
X-RAY DIFFRACTIONr_angle_other_deg1.14535012
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.4250.2360
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212561
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02517
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_it0.9460.7141134
X-RAY DIFFRACTIONr_mcbond_other0.9470.7141133
X-RAY DIFFRACTIONr_mcangle_it1.1241.0831414
X-RAY DIFFRACTIONr_mcangle_other1.1231.0831415
X-RAY DIFFRACTIONr_scbond_it2.6860.9281179
X-RAY DIFFRACTIONr_scbond_other2.6850.9291180
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0631.3141730
X-RAY DIFFRACTIONr_long_range_B_refined4.90310.8542449
X-RAY DIFFRACTIONr_long_range_B_other3.5259.1652040
X-RAY DIFFRACTIONr_rigid_bond_restr6.75134483
X-RAY DIFFRACTIONr_sphericity_free40.088566
X-RAY DIFFRACTIONr_sphericity_bonded10.66354859
LS refinement shellResolution: 1→1.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 273 -
Rwork0.234 5014 -
obs--50.14 %

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