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- PDB-1ehh: CRYSTAL STRUCTURE OF URTICA DIOICA AGGLUTININ ISOLECTIN VI COMPLE... -

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Basic information

Entry
Database: PDB / ID: 1ehh
TitleCRYSTAL STRUCTURE OF URTICA DIOICA AGGLUTININ ISOLECTIN VI COMPLEX WITH TRI-N-ACETYLCHITOTRIOSE
ComponentsAGGLUTININ ISOLECTIN VI
KeywordsPLANT PROTEIN / Two homologous hevein-like domains
Function / homology
Function and homology information


Chitin-binding, type 1, conserved site / Chitin recognition protein / Chitin recognition or binding domain signature. / Chitin-binding type-1 domain profile. / Chitin binding domain / Chitin-binding, type 1 / Endochitinase-like superfamily
Similarity search - Domain/homology
triacetyl-beta-chitotriose / : / Agglutinin isolectin V
Similarity search - Component
Biological speciesUrtica dioica (great nettle)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsHarata, K. / Muraki, M.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Crystal structures of Urtica dioica agglutinin and its complex with tri-N-acetylchitotriose.
Authors: Harata, K. / Muraki, M.
History
DepositionFeb 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AGGLUTININ ISOLECTIN VI
B: AGGLUTININ ISOLECTIN VI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9544
Polymers18,6992
Non-polymers1,2552
Water1,49583
1
A: AGGLUTININ ISOLECTIN VI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9772
Polymers9,3491
Non-polymers6281
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AGGLUTININ ISOLECTIN VI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9772
Polymers9,3491
Non-polymers6281
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.550, 56.790, 55.300
Angle α, β, γ (deg.)90.00, 92.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein AGGLUTININ ISOLECTIN VI


Mass: 9349.346 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Urtica dioica (great nettle) / References: GenBank: 4164468, UniProt: Q9S7B3*PLUS
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: triacetyl-beta-chitotriose
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.14 Å3/Da / Density % sol: 42.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG1000, sodium citrate, tri-N-acetylchitotriose, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 %(w/v)PEG10001reservoir
20.1 Mcitrate1reservoir
3protein1drop

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Data collection

DiffractionMean temperature: 286 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Jun 14, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→18.91 Å / Num. all: 13723 / Num. obs: 13723 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 14.7
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.362 / Num. unique all: 597 / % possible all: 33.5
Reflection
*PLUS
Num. measured all: 44173

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Processing

Software
NameVersionClassification
MADNESSdata collection
MERGEFdata reduction
X-PLORmodel building
X-PLOR3.1refinement
MADNESSdata reduction
MERGEFdata scaling
X-PLORphasing
RefinementResolution: 1.9→8 Å / σ(F): 2 / Stereochemistry target values: CHARMM
RfactorNum. reflection% reflectionSelection details
Rfree0.253 992 -Random
Rwork0.183 ---
obs-9258 63 %-
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1282 0 86 83 1451
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg3.18
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_deg

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