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- PDB-3w3e: Structure of Vigna unguiculata chitinase with regulation activity... -

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Basic information

Entry
Database: PDB / ID: 3w3e
TitleStructure of Vigna unguiculata chitinase with regulation activity of the plant cell wall
ComponentsCotyledoneous yieldin-like protein
KeywordsHYDROLASE / alpha helical protein / Family 19 glycosidase / Regulatory protein of the cell wall yield threshold / cotyledon
Function / homology
Function and homology information


chitinase activity / chitin catabolic process / chitin binding / defense response / cell wall macromolecule catabolic process / carbohydrate metabolic process
Similarity search - Function
Chitinases family 19 signature 1. / Chitinases family 19 signature 2. / Endochitinase; domain 2 / Endochitinase, domain 2 / Glycoside hydrolase, family 19 / Glycoside hydrolase, family 19, catalytic / Chitinase class I / Lysozyme - #10 / Lysozyme / Lysozyme-like domain superfamily ...Chitinases family 19 signature 1. / Chitinases family 19 signature 2. / Endochitinase; domain 2 / Endochitinase, domain 2 / Glycoside hydrolase, family 19 / Glycoside hydrolase, family 19, catalytic / Chitinase class I / Lysozyme - #10 / Lysozyme / Lysozyme-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesVigna unguiculata (cowpea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMorohashi, K. / Sasaki, K. / Sakabe, N. / Sakabe, K.
Citation
Journal: To be Published
Title: Three-dimensional structure analysis of Vigna unguiculata chitinase with regulation activity of the yield threshold of cell wall
Authors: Morohashi, M. / Sasaki, K. / Sakabe, N. / Sakabe, K.
#1: Journal: J.SYNCHROTRON RADIAT. / Year: 1999
Title: Rotated-inclined focusing monochromator with simultaneous tuning of asymmetry factor and radius of curvature over a wide wavelength range
Authors: Sakabe, N. / Watanabe, N. / Suzuki, M. / Higashi, Y.
#2: Journal: Plant Cell.Physiol. / Year: 2001
Title: Distribution of yieldin, a regulatory protein of the cell wall yield threshold, in etiolated cowpea seedlings.
Authors: Okamoto-Nakazato, A. / Takahashi, K. / Katoh-Semba, R. / Katou, K.
History
DepositionDec 20, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Cotyledoneous yieldin-like protein
B: Cotyledoneous yieldin-like protein


Theoretical massNumber of molelcules
Total (without water)52,2022
Polymers52,2022
Non-polymers00
Water10,665592
1
A: Cotyledoneous yieldin-like protein


Theoretical massNumber of molelcules
Total (without water)26,1011
Polymers26,1011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cotyledoneous yieldin-like protein


Theoretical massNumber of molelcules
Total (without water)26,1011
Polymers26,1011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.700, 48.600, 65.200
Angle α, β, γ (deg.)97.70, 100.40, 106.30
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Cotyledoneous yieldin-like protein


Mass: 26100.967 Da / Num. of mol.: 2 / Fragment: UNP residues 28-269 / Source method: isolated from a natural source / Source: (natural) Vigna unguiculata (cowpea) / Organ: cotyledon / References: UniProt: Q8H0C9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 592 / 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: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 30mg/ml protein, 0.1M Tris HCl, 0.1M Lithium sulfate, 30% PEG6000, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 5, 2002 / Details: Platinum-coated silicon bent mirrors
RadiationMonochromator: Rotated-inclined focusing S(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→55.9 Å / Num. obs: 76333 / % possible obs: 92.1 % / Biso Wilson estimate: 24.07 Å2 / Rmerge(I) obs: 0.062

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.7.0029refinement
PROCESSdata reduction
PROCESSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DXJ

1dxj


Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.676 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23493 3515 5 %RANDOM
Rwork0.20222 ---
obs0.20386 66166 94.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.812 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20.63 Å2-0.64 Å2
2--0.16 Å2-0.97 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3678 0 0 592 4270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193782
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.9285140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5375482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.39823180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.81915536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8281530
X-RAY DIFFRACTIONr_chiral_restr0.0930.2524
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213028
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 222 -
Rwork0.319 4054 -
obs-4054 78.97 %

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