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- PDB-5jce: Crystal structure of OsCEBiP complex -

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Basic information

Entry
Database: PDB / ID: 5jce
TitleCrystal structure of OsCEBiP complex
ComponentsChitin elicitor-binding protein
KeywordsSUGAR BINDING PROTEIN / rice chitin receptor
Function / homology
Function and homology information


chitin binding / defense response / : / plasma membrane
Similarity search - Function
Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain
Similarity search - Domain/homology
triacetyl-beta-chitotriose / Chitin elicitor-binding protein
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsChai, J.J. / Liu, S.M. / Wang, J.Z.
CitationJournal: Structure / Year: 2016
Title: Molecular Mechanism for Fungal Cell Wall Recognition by Rice Chitin Receptor OsCEBiP
Authors: Liu, S.M. / Wang, J.Z. / Han, Z. / Gong, X. / Zhang, H. / Chai, J.J.
History
DepositionApr 15, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / 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 / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / 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.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 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: Chitin elicitor-binding protein
B: Chitin elicitor-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8347
Polymers62,3222
Non-polymers1,5125
Water0
1
A: Chitin elicitor-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0103
Polymers31,1611
Non-polymers8492
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint6 kcal/mol
Surface area14820 Å2
MethodPISA
2
B: Chitin elicitor-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8254
Polymers31,1611
Non-polymers6643
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint3 kcal/mol
Surface area14580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.448, 99.771, 87.647
Angle α, β, γ (deg.)90.00, 103.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Chitin elicitor-binding protein / CEBiP


Mass: 31160.926 Da / Num. of mol.: 2 / Fragment: UNP residues 29-325
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: CEBIP, Os03g0133400, LOC_Os03g04110, OJ1006F06.19, OsJ_30068
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q8H8C7
#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.: 1
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: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
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

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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: 4.03 Å3/Da / Density % sol: 69.45 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris, 2.0 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: AGILENT EOS CCD / Detector: CCD / Date: Mar 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.51→39.2 Å / Num. obs: 33694 / % possible obs: 97.6 % / Redundancy: 3.6 % / Net I/σ(I): 17.2
Reflection shellResolution: 2.51→2.6 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JCD

5jcd


Resolution: 2.51→39.16 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.63
RfactorNum. reflection% reflection
Rfree0.256 1999 5.94 %
Rwork0.22 --
obs0.222 33668 97.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.51→39.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4308 0 99 0 4407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014507
X-RAY DIFFRACTIONf_angle_d1.2786141
X-RAY DIFFRACTIONf_dihedral_angle_d14.3191590
X-RAY DIFFRACTIONf_chiral_restr0.048763
X-RAY DIFFRACTIONf_plane_restr0.006788
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5124-2.57520.34281170.31631848X-RAY DIFFRACTION80
2.5752-2.64480.35241420.29572269X-RAY DIFFRACTION98
2.6448-2.72260.35521450.28552286X-RAY DIFFRACTION99
2.7226-2.81040.35311430.28022272X-RAY DIFFRACTION99
2.8104-2.91090.32141450.26452300X-RAY DIFFRACTION99
2.9109-3.02740.31891470.25892324X-RAY DIFFRACTION99
3.0274-3.16510.22861440.24732279X-RAY DIFFRACTION100
3.1651-3.33190.31041460.23352312X-RAY DIFFRACTION100
3.3319-3.54050.27671470.22612311X-RAY DIFFRACTION100
3.5405-3.81370.25441450.19822304X-RAY DIFFRACTION99
3.8137-4.1970.19561440.18812288X-RAY DIFFRACTION99
4.197-4.80340.21051440.17992271X-RAY DIFFRACTION98
4.8034-6.04820.23831460.19692325X-RAY DIFFRACTION99
6.0482-39.16110.22681440.21512280X-RAY DIFFRACTION96

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