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- PDB-5xfh: Crystal structure of Orysata lectin in complex with biantennary N... -

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Basic information

Entry
Database: PDB / ID: 5xfh
TitleCrystal structure of Orysata lectin in complex with biantennary N-glycan
ComponentsSalt stress-induced protein
KeywordsSUGAR BINDING PROTEIN / Lectin / Jacalin-related lectin / N-glycan / Glycobiology
Function / homology
Function and homology information


carbohydrate binding
Similarity search - Function
Jacalin-like lectin domain, plant / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Jacalin-like lectin domain superfamily / Mainly Beta
Similarity search - Domain/homology
Salt stress-induced protein
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.903 Å
AuthorsNagae, M. / Yamaguchi, Y.
Funding support Japan, 2items
OrganizationGrant numberCountry
MEXT15K18496 Japan
MEXT17K07303 Japan
CitationJournal: Glycobiology / Year: 2017
Title: Distinct roles for each N-glycan branch interacting with mannose-binding type Jacalin-related lectins Orysata and Calsepa.
Authors: Nagae, M. / Mishra, S.K. / Hanashima, S. / Tateno, H. / Yamaguchi, Y.
History
DepositionApr 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Salt stress-induced protein
B: Salt stress-induced protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5013
Polymers30,4282
Non-polymers1,0731
Water2,810156
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint22 kcal/mol
Surface area13020 Å2
Unit cell
Length a, b, c (Å)45.783, 71.620, 97.201
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 Salt stress-induced protein / Salt protein / Protein lectin-like / Protein mannose-binding lectin


Mass: 15214.007 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: SALT, ML, Os01g0348900, LOC_Os01g24710, B1051E10.18, P0440D10.39
Production host: Escherichia coli (E. coli) / References: UniProt: Q0JMY8
#2: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a1122h-1b_1-5][a1122h-1a_1-5][a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2-3-4-2-3/a3-b1_a6-e1_b2-c1_c4-d1_e2-f1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe experimental info of UNIPROT (Q0JMY8, SALT_ORYSJ) shows conflict at this position in AAB53810 (Ref. 2).

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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: 2.62 Å3/Da / Density % sol: 53.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M bis-tris (pH 5.5), 0.1 M ammonium acetate, 17% (w/v) polyethylene glycol 10000

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 21, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→100 Å / Num. obs: 25693 / % possible obs: 99.7 % / Redundancy: 7.9 % / Rsym value: 0.046 / Net I/σ(I): 47.3
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 6 / Num. unique obs: 1235 / Rsym value: 0.368 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XXQ

1xxq


Resolution: 1.903→33.325 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.22 1305 5.09 %
Rwork0.1894 --
obs0.1911 25640 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.903→33.325 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2117 0 73 156 2346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122257
X-RAY DIFFRACTIONf_angle_d1.3983082
X-RAY DIFFRACTIONf_dihedral_angle_d10.9181306
X-RAY DIFFRACTIONf_chiral_restr0.093362
X-RAY DIFFRACTIONf_plane_restr0.01385
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9027-1.97890.29411340.2362598X-RAY DIFFRACTION98
1.9789-2.06890.26361310.21162664X-RAY DIFFRACTION99
2.0689-2.1780.27181580.19222657X-RAY DIFFRACTION99
2.178-2.31440.25121260.18972683X-RAY DIFFRACTION100
2.3144-2.49310.23941440.20162689X-RAY DIFFRACTION100
2.4931-2.74380.25321360.20142715X-RAY DIFFRACTION100
2.7438-3.14060.23951500.1982722X-RAY DIFFRACTION100
3.1406-3.95580.20181510.18412742X-RAY DIFFRACTION100
3.9558-33.33010.18541750.17392865X-RAY DIFFRACTION100

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