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- PDB-6m5m: SPL-1 - GlcNAc complex -

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Basic information

Entry
Database: PDB / ID: 6m5m
TitleSPL-1 - GlcNAc complex
Components(N-acetylglucosamine-specific lectin) x 2
KeywordsSUGAR BINDING PROTEIN / Lectin / GlcNAc / SPL-1
Function / homology
Function and homology information


carbohydrate binding / metal ion binding
Similarity search - Function
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
Similarity search - Domain/homology
N-acetylglucosamine-specific lectin / N-acetylglucosamine-specific lectin
Similarity search - Component
Biological speciesSaxidomus purpuratus (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsUnno, H. / Hatakeyama, T.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Novel carbohydrate-recognition mode of the invertebrate C-type lectin SPL-1 from Saxidomus purpuratus revealed by the GlcNAc-complex crystal in the presence of Ca2.
Authors: Unno, H. / Higuchi, S. / Goda, S. / Hatakeyama, T.
History
DepositionMar 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 29, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acetylglucosamine-specific lectin
B: N-acetylglucosamine-specific lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4838
Polymers35,8802
Non-polymers6036
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-48 kcal/mol
Surface area13020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.460, 44.460, 303.613
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein N-acetylglucosamine-specific lectin / SPL-A


Mass: 17981.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saxidomus purpuratus (invertebrata) / References: UniProt: A0A2Z6G7U6
#2: Protein N-acetylglucosamine-specific lectin / SPL-B


Mass: 17898.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saxidomus purpuratus (invertebrata) / References: UniProt: A0A2Z6G7U3
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.41 Å3/Da / Density % sol: 49.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10mM CaCl2, 10mM GlcNAc, 28% PEG 8000, 0.1M Tris-HCl (pH8.5), 0.2M sodium acetate, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→43.4 Å / Num. obs: 37198 / % possible obs: 100 % / Redundancy: 20.8 % / CC1/2: 1 / Rmerge(I) obs: 0.05 / Net I/σ(I): 30
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1950 / CC1/2: 0.942

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Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A7T

6a7t


Resolution: 1.7→38.23 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.965 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.097
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2161 1782 4.8 %RANDOM
Rwork0.203 ---
obs0.2037 35272 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 92.62 Å2 / Biso mean: 37.882 Å2 / Biso min: 23.98 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.7→38.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2193 0 34 139 2366
Biso mean--36.49 42.86 -
Num. residues----273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132304
X-RAY DIFFRACTIONr_bond_other_d0.0380.0181823
X-RAY DIFFRACTIONr_angle_refined_deg1.9281.6473136
X-RAY DIFFRACTIONr_angle_other_deg2.5851.6064271
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4135271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.1124.074135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.44515335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.672158
X-RAY DIFFRACTIONr_chiral_restr0.1340.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022644
X-RAY DIFFRACTIONr_gen_planes_other0.0170.02534
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 115 -
Rwork0.269 2601 -
all-2716 -
obs--99.85 %

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