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- PDB-4tx7: Crystal structure of chitinase (GH19) from Vigna unguiculata -

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Basic information

Entry
Database: PDB / ID: 4tx7
TitleCrystal structure of chitinase (GH19) from Vigna unguiculata
ComponentsClass I chitinase
KeywordsHYDROLASE / Chitinase Family 19 Glycoside Hydrolase
Function / homology
Function and homology information


chitinase / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / defense response / cell wall macromolecule catabolic 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 / Chitin-binding, type 1, conserved site / Chitin recognition protein / Chitin recognition or binding domain signature. ...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 / 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 / Lysozyme - #10 / Lysozyme / Lysozyme-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesVigna unguiculata subsp. sesquipedalis (yard-long-bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsPereira, H.M. / Castro-Landin, P.G. / Brandao-Neto, J. / Grangeiro, T.B.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq) Brazil
Sao Paulo Research Foundation (FAPESP) Brazil
CitationJournal: Biochimie / Year: 2017
Title: Production in Pichia pastoris, antifungal activity and crystal structure of a class I chitinase from cowpea (Vigna unguiculata): Insights into sugar binding mode and hydrolytic action.
Authors: Landim, P.G. / Correia, T.O. / Silva, F.D. / Nepomuceno, D.R. / Costa, H.P. / Pereira, H.M. / Lobo, M.D. / Moreno, F.B. / Brandao-Neto, J. / Medeiros, S.C. / Vasconcelos, I.M. / Oliveira, J. ...Authors: Landim, P.G. / Correia, T.O. / Silva, F.D. / Nepomuceno, D.R. / Costa, H.P. / Pereira, H.M. / Lobo, M.D. / Moreno, F.B. / Brandao-Neto, J. / Medeiros, S.C. / Vasconcelos, I.M. / Oliveira, J.T. / Sousa, B.L. / Barroso-Neto, I.L. / Freire, V.N. / Carvalho, C.P. / Monteiro-Moreira, A.C. / Grangeiro, T.B.
History
DepositionJul 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2017Group: Database references
Revision 1.2Nov 22, 2017Group: Data collection / Refinement description / Category: diffrn_source / software
Item: _diffrn_source.pdbx_synchrotron_site / _software.classification / _software.name
Revision 1.3Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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

Downloads & links

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Assembly

Deposited unit
A: Class I chitinase


Theoretical massNumber of molelcules
Total (without water)26,5541
Polymers26,5541
Non-polymers00
Water6,864381
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.320, 69.320, 114.870
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-408-

HOH

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Components

#1: Protein Class I chitinase


Mass: 26554.355 Da / Num. of mol.: 1 / Fragment: UNP residues 43-287
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vigna unguiculata subsp. sesquipedalis (yard-long-bean)
Plasmid: pPICZalphaA / Production host: Komagataella pastoris (fungus) / Strain (production host): KM71H / References: UniProt: Q9FUH3, chitinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 3 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 2.0M Sodium formate, 100mM Sodium acetate trihydrate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 25/09/2011
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.55→53.21 Å / Num. obs: 46943 / % possible obs: 99.7 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 11.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-IDRejects% possible all
1.55-1.595.40.6572.41099.3
6.93-53.214.60.0591098

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
DNAdata collection
XDSdata reduction
PDB_EXTRACT3.14data extraction
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
xia2data scaling
GDAdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CQL

3cql


Resolution: 1.55→53.205 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1732 2369 5.05 %
Rwork0.1491 44534 -
obs0.1503 46903 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.69 Å2 / Biso mean: 21.9522 Å2 / Biso min: 10.8 Å2
Refinement stepCycle: final / Resolution: 1.55→53.205 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1874 0 0 381 2255
Biso mean---35.9 -
Num. residues----245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151967
X-RAY DIFFRACTIONf_angle_d1.462688
X-RAY DIFFRACTIONf_chiral_restr0.076269
X-RAY DIFFRACTIONf_plane_restr0.011365
X-RAY DIFFRACTIONf_dihedral_angle_d12.727699
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.58170.28071290.23422608X-RAY DIFFRACTION99
1.5817-1.61610.23341360.21352571X-RAY DIFFRACTION99
1.6161-1.65360.19011480.192544X-RAY DIFFRACTION99
1.6536-1.6950.23131310.1752587X-RAY DIFFRACTION100
1.695-1.74080.18791440.1642584X-RAY DIFFRACTION99
1.7408-1.79210.19181440.15822565X-RAY DIFFRACTION100
1.7921-1.84990.18731500.15482588X-RAY DIFFRACTION100
1.8499-1.9160.16551340.15562624X-RAY DIFFRACTION100
1.916-1.99270.16071350.1512568X-RAY DIFFRACTION100
1.9927-2.08340.17451220.14322654X-RAY DIFFRACTION100
2.0834-2.19330.18611450.13942590X-RAY DIFFRACTION100
2.1933-2.33070.16731440.1432632X-RAY DIFFRACTION100
2.3307-2.51070.16131370.14372619X-RAY DIFFRACTION100
2.5107-2.76330.4751500.13942649X-RAY DIFFRACTION100
2.7633-3.16310.15711310.14972676X-RAY DIFFRACTION100
3.1631-3.9850.16881450.14132669X-RAY DIFFRACTION100
3.985-53.230.18021440.13772806X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.5755-0.3047-0.16691.80280.21211.9820.13770.0406-0.36290.0122-0.0487-0.01870.34790.0612-0.03080.24740.0131-0.01320.1057-0.02050.1843-35.72465.7868-11.7221
21.5595-0.4714-0.09251.21220.22361.32570.0189-0.0348-0.13620.00260.01340.02070.18620.0049-0.04330.1646-0.0239-0.00150.0943-0.00350.1229-39.608513.6023-7.9203
32.5182-0.4753-0.13891.13840.11521.53190.12880.09940.2978-0.1611-0.0579-0.0329-0.1002-0.0912-0.05810.1526-0.00370.0260.11520.01670.1442-44.332927.9176-13.9705
40.39670.4186-0.33760.94631.3786.2721-0.02390.0287-0.0269-0.23670.177-0.1545-0.59850.3853-0.16190.2135-0.06470.01620.1721-0.02180.1949-30.178627.46634.6165
51.4037-0.4062-0.40991.15260.41631.5091-0.0222-0.0968-0.0759-0.0010.0430.02720.1020.0488-0.00760.1645-0.0042-0.00870.13660.01480.1356-39.044416.38056.1662
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 43 through 69 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 70 through 141 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 142 through 203 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 204 through 234 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 235 through 287 )A0

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