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- PDB-4mck: Crystal structure of Family GH19, Class IV chitinase from Zea mays -

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Basic information

Entry
Database: PDB / ID: 4mck
TitleCrystal structure of Family GH19, Class IV chitinase from Zea mays
ComponentsChitinase
KeywordsHYDROLASE
Function / homology
Function and homology information


amino sugar metabolic process / chitinase activity / endochitinase activity / chitinase / chitin catabolic process / chitin binding / polysaccharide catabolic process / defense response to fungus / cell wall macromolecule catabolic process / extracellular region
Similarity search - Function
Chitinases family 19 signature 1. / Endochitinase; domain 2 / Endochitinase, domain 2 / Chitinases family 19 signature 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. / Endochitinase; domain 2 / Endochitinase, domain 2 / Chitinases family 19 signature 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
Endochitinase A / chitinase
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsChaudet, M.M. / Rose, D.R.
CitationJournal: Protein Sci. / Year: 2014
Title: Crystallographic structure of ChitA, a glycoside hydrolase family 19, plant class IV chitinase from Zea mays.
Authors: Chaudet, M.M. / Naumann, T.A. / Price, N.P. / Rose, D.R.
History
DepositionAug 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2May 7, 2014Group: Database references
Revision 1.3Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitinase


Theoretical massNumber of molelcules
Total (without water)22,0301
Polymers22,0301
Non-polymers00
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.152, 65.167, 72.334
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Chitinase


Mass: 22029.662 Da / Num. of mol.: 1 / Fragment: catalytic module (UNP residues 81-278) / Mutation: E62Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Strain: LH82 / Gene: chiA / Plasmid: pPICZ'alpha'A / Production host: Komagataella pastoris (fungus) / Strain (production host): X-33
References: UniProt: Q6JBL3, UniProt: P29022*PLUS, chitinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE AUTHORS HAVE VERIFIED THE PROTEIN SEQUENCE BIOCHEMICALLY.

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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: 1.99 Å3/Da / Density % sol: 38.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.5 M ammonium sulfate, 0.1 M Tris, 0.16 M potassium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 12, 2012
RadiationMonochromator: VariMax HF optic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.5→48.416 Å / Num. obs: 28893 / % possible obs: 96.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 54.6 / Redundancy: 10.5 % / Biso Wilson estimate: 16.34 Å2 / Rmerge(I) obs: 0.044
Reflection shellHighest resolution: 1.5 Å / Mean I/σ(I) obs: 3.3 / % possible all: 63.2

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HBD

3hbd


Resolution: 1.5→25.915 Å / SU ML: 0.1 / σ(F): 1.5 / Phase error: 20.25 / Stereochemistry target values: ML
Details: FREE R WAS USED FOR CROSS-VALIDATION, BUT THE FREE R TEST SET WAS UNAVAILABLE AT THE TIME OF DEPOSITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2031 3775 7.2 %RANDOM
Rwork0.1784 ---
obs0.1802 27880 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.8 Å2
Refinement stepCycle: LAST / Resolution: 1.5→25.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1563 0 0 303 1866
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071612
X-RAY DIFFRACTIONf_angle_d1.2482182
X-RAY DIFFRACTIONf_dihedral_angle_d13.49560
X-RAY DIFFRACTIONf_chiral_restr0.084213
X-RAY DIFFRACTIONf_plane_restr0.005295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.51890.278850.26751077X-RAY DIFFRACTION59
1.5189-1.53890.29121110.25531412X-RAY DIFFRACTION75
1.5389-1.55990.24571200.23051601X-RAY DIFFRACTION85
1.5599-1.58220.25381300.21151690X-RAY DIFFRACTION93
1.5822-1.60580.24891420.20991832X-RAY DIFFRACTION97
1.6058-1.63090.2341430.19781895X-RAY DIFFRACTION100
1.6309-1.65770.17121430.18451812X-RAY DIFFRACTION100
1.6577-1.68620.25351480.17781906X-RAY DIFFRACTION100
1.6862-1.71690.23151430.18491838X-RAY DIFFRACTION100
1.7169-1.74990.20121450.18261874X-RAY DIFFRACTION100
1.7499-1.78560.21891470.20231857X-RAY DIFFRACTION100
1.7856-1.82440.2221470.1851876X-RAY DIFFRACTION100
1.8244-1.86690.19541490.19191875X-RAY DIFFRACTION100
1.8669-1.91350.19611410.1851867X-RAY DIFFRACTION100
1.9135-1.96530.23981460.19221878X-RAY DIFFRACTION100
1.9653-2.02310.19361450.1951856X-RAY DIFFRACTION100
2.0231-2.08830.24621460.18441884X-RAY DIFFRACTION100
2.0883-2.1630.22881420.17421872X-RAY DIFFRACTION100
2.163-2.24950.19311440.18261843X-RAY DIFFRACTION100
2.2495-2.35180.23671460.18811862X-RAY DIFFRACTION100
2.3518-2.47570.20621480.17981888X-RAY DIFFRACTION100
2.4757-2.63070.22811450.1881840X-RAY DIFFRACTION100
2.6307-2.83360.2081440.17611878X-RAY DIFFRACTION100
2.8336-3.11830.19511410.17391880X-RAY DIFFRACTION100
3.1183-3.56850.16081450.15981863X-RAY DIFFRACTION100
3.5685-4.49220.1571490.14871866X-RAY DIFFRACTION100
4.4922-25.9190.19081400.16911864X-RAY DIFFRACTION100

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