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- PDB-5jcd: Crystal structure of OsCEBiP -

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Basic information

Entry
Database: PDB / ID: 5jcd
TitleCrystal structure of OsCEBiP
ComponentsChitin elicitor-binding protein
KeywordsSUGAR BINDING PROTEIN / chitin receptor
Function / homologyLysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / chitin binding / defense response / plasma membrane / Chitin elicitor-binding protein
Function and homology information
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 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: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitin elicitor-binding protein
B: Chitin elicitor-binding protein
C: Chitin elicitor-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9237
Polymers62,0383
Non-polymers8854
Water1,51384
1
A: Chitin elicitor-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1223
Polymers20,6791
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chitin elicitor-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1223
Polymers20,6791
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Chitin elicitor-binding protein


Theoretical massNumber of molelcules
Total (without water)20,6791
Polymers20,6791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.772, 77.274, 111.391
Angle α, β, γ (deg.)90.00, 99.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Chitin elicitor-binding protein / CEBiP


Mass: 20679.328 Da / Num. of mol.: 3 / Fragment: UNP residues 29-223
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: 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.: 4 / Source method: isolated from a natural 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.28 Å3/Da / Density % sol: 62.48 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2 M ammonium acetate, 0.1 M sodium acetate trihydrate, 30%(w/v) PEG4000

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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: Sep 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.39→29.6 Å / Num. obs: 31051 / % possible obs: 98.3 % / Redundancy: 4 % / Net I/σ(I): 22
Reflection shellResolution: 2.4→2.48 Å

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→29.6 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 31.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.276 1572 5.07 %
Rwork0.22 --
obs0.223 31030 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4319 0 54 84 4457
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094494
X-RAY DIFFRACTIONf_angle_d1.4036138
X-RAY DIFFRACTIONf_dihedral_angle_d14.6631637
X-RAY DIFFRACTIONf_chiral_restr0.077748
X-RAY DIFFRACTIONf_plane_restr0.007797
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3969-2.47420.33871370.26452580X-RAY DIFFRACTION95
2.4742-2.56260.33911270.24872603X-RAY DIFFRACTION96
2.5626-2.66520.30761480.24762610X-RAY DIFFRACTION96
2.6652-2.78640.3251290.2552662X-RAY DIFFRACTION98
2.7864-2.93310.32171510.24052679X-RAY DIFFRACTION99
2.9331-3.11670.32981430.23952678X-RAY DIFFRACTION99
3.1167-3.35710.28811470.23242724X-RAY DIFFRACTION100
3.3571-3.69430.25851550.21492715X-RAY DIFFRACTION100
3.6943-4.22760.23461450.20122716X-RAY DIFFRACTION100
4.2276-5.32130.24961390.18642771X-RAY DIFFRACTION100
5.3213-29.60260.2711510.22562720X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 16.3691 Å / Origin y: 43.112 Å / Origin z: 86.2985 Å
111213212223313233
T0.2082 Å2-0.0445 Å20.0078 Å2-0.2764 Å2-0.0152 Å2--0.2705 Å2
L0.1304 °20.0001 °20.1062 °2-0.1979 °20.0763 °2--0.4488 °2
S-0.0188 Å °0.1231 Å °0.0464 Å °0.0345 Å °-0.0242 Å °0.0366 Å °0.088 Å °-0.0013 Å °0 Å °
Refinement TLS groupSelection details: ALL

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