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- PDB-4txe: ScCTS1 in complex with compound 5 -

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Basic information

Entry
Database: PDB / ID: 4txe
TitleScCTS1 in complex with compound 5
ComponentsEndochitinase
KeywordsHYDROLASE / chitinase / plant-type / inhibitor
Function / homology
Function and homology information


endochitinase activity / septum digestion after cytokinesis / fungal-type cell wall / fungal-type vacuole / cellular bud neck / chitinase / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process ...endochitinase activity / septum digestion after cytokinesis / fungal-type cell wall / fungal-type vacuole / cellular bud neck / chitinase / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / cell wall organization / nuclear envelope / endoplasmic reticulum / extracellular region
Similarity search - Function
Carbohydrate-binding module family 19 / Carbohydrate binding domain (family 19) / Chitinase Cts1-like / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Glycosidases / Glycoside hydrolase superfamily ...Carbohydrate-binding module family 19 / Carbohydrate binding domain (family 19) / Chitinase Cts1-like / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-38F / Endochitinase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSchuettelkopf, A.W. / van Aalten, D.M.F.
CitationJournal: FEBS Lett / Year: 2014
Title: Screening-based discovery of Aspergillus fumigatus plant-type chitinase inhibitors
Authors: Lockhart, D.E. / Schuettelkopf, A.W. / Blair, D.E. / van Aalten, D.M.F.
History
DepositionJul 3, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 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
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: Endochitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8422
Polymers31,5301
Non-polymers3111
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.773, 112.159, 37.164
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-557-

HOH

21A-559-

HOH

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Components

#1: Protein Endochitinase / Soluble cell wall protein 2


Mass: 31530.234 Da / Num. of mol.: 1 / Fragment: UNP residues 22-315
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CTS1, SCW2, YLR286C, L8003.13 / Production host: Komagataella pastoris (fungus) / References: UniProt: P29029, chitinase
#2: Chemical ChemComp-38F / (2S)-1-(2,3-dihydro-1H-inden-2-ylamino)-3-(3,4-dimethylphenoxy)propan-2-ol


Mass: 311.418 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H25NO2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 293.14 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES, 0.8 M NaH2PO4, 0.8 M KH2PO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 27572 / % possible obs: 94.9 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 23.7
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 5.6 / % possible all: 61.5

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Processing

SoftwareName: REFMAC / Version: 5.8.0069 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2UY2

2uy2


Resolution: 1.8→19.99 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.755 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19108 1386 5 %RANDOM
Rwork0.16055 ---
obs0.16211 26152 94.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.629 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å20 Å2
2---0.55 Å20 Å2
3----0.07 Å2
Refinement stepCycle: 1 / Resolution: 1.8→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2174 0 23 210 2407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022268
X-RAY DIFFRACTIONr_bond_other_d00.021987
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.9523098
X-RAY DIFFRACTIONr_angle_other_deg3.8873.0064588
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0940.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022681
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02535
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7951.8661160
X-RAY DIFFRACTIONr_mcbond_other0.7951.8641159
X-RAY DIFFRACTIONr_mcangle_it1.3952.7921451
X-RAY DIFFRACTIONr_mcangle_other1.3952.7941452
X-RAY DIFFRACTIONr_scbond_it0.8261.8851108
X-RAY DIFFRACTIONr_scbond_other0.8251.8851109
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3772.8031646
X-RAY DIFFRACTIONr_long_range_B_refined3.83818.9912128
X-RAY DIFFRACTIONr_long_range_B_other3.40818.6982022
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 68 -
Rwork0.25 1264 -
obs--63.61 %
Refinement TLS params.Method: refined / Origin x: 42.6658 Å / Origin y: 21.7709 Å / Origin z: 32.3922 Å
111213212223313233
T0.0303 Å2-0.0104 Å2-0.0075 Å2-0.0326 Å2-0.0016 Å2--0.0056 Å2
L1.219 °2-0.4902 °2-0.0525 °2-1.2793 °2-0.0012 °2--0.706 °2
S-0.019 Å °0.0269 Å °0.0629 Å °-0.0426 Å °0.0074 Å °-0.0208 Å °-0.0592 Å °0.0174 Å °0.0116 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 312
2X-RAY DIFFRACTION1L1
3X-RAY DIFFRACTION1W1 - 248
4X-RAY DIFFRACTION1X1 - 9999

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