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- PDB-4tx6: AfChiA1 in complex with compound 1 -

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Basic information

Entry
Database: PDB / ID: 4tx6
TitleAfChiA1 in complex with compound 1
ComponentsClass III chitinase ChiA1
KeywordsHYDROLASE / plant-type / inhibition
Function / homology
Function and homology information


chitinase / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / side of membrane / extracellular region / plasma membrane
Similarity search - Function
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-38B / PHOSPHATE ION / chitinase
Similarity search - Component
Biological speciesAspergillus fumigatus A1163 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
Authorsvan 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 2, 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: Class III chitinase ChiA1
B: Class III chitinase ChiA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,03818
Polymers68,1942
Non-polymers1,84416
Water14,034779
1
A: Class III chitinase ChiA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,11410
Polymers34,0971
Non-polymers1,0179
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Class III chitinase ChiA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9248
Polymers34,0971
Non-polymers8277
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.398, 128.514, 212.102
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-405-

PO4

21A-553-

HOH

31A-579-

HOH

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Components

#1: Protein Class III chitinase ChiA1


Mass: 34096.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus A1163 (mold) / Strain: CEA10 / CBS 144.89 / FGSC A1163 / Gene: AFUB_052270 / Production host: Komagataella pastoris (fungus) / References: UniProt: B0Y2Y2
#2: Chemical ChemComp-38B / 3-(2-methoxyphenyl)-6-methyl[1,2]oxazolo[5,4-d]pyrimidin-4(5H)-one


Mass: 257.245 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H11N3O3
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 779 / 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: 3.82 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 293.14 K / Method: vapor diffusion, hanging drop / Details: 0.42-0.58 M NaH2PO4, 0.74-0.83 M K2HPO4

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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: May 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.9→24.98 Å / Num. obs: 81562 / % possible obs: 99.3 % / Redundancy: 3.8 % / Biso Wilson estimate: 22.4 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 16.1
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 3.3 / % possible all: 98.5

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Processing

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

2xvp


Resolution: 1.9→24.98 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.876 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18385 4089 5 %RANDOM
Rwork0.15444 ---
obs0.15589 77470 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.448 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2--0.52 Å20 Å2
3----0.63 Å2
Refinement stepCycle: 1 / Resolution: 1.9→24.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4805 0 108 779 5692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.025079
X-RAY DIFFRACTIONr_bond_other_d00.024440
X-RAY DIFFRACTIONr_angle_refined_deg1.5781.9526952
X-RAY DIFFRACTIONr_angle_other_deg3.7413.00110206
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_restr0.0930.2716
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215887
X-RAY DIFFRACTIONr_gen_planes_other0.0160.021218
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_it1.4221.6612485
X-RAY DIFFRACTIONr_mcbond_other1.4151.6582484
X-RAY DIFFRACTIONr_mcangle_it2.2562.4783106
X-RAY DIFFRACTIONr_mcangle_other2.2572.4813107
X-RAY DIFFRACTIONr_scbond_it2.2951.972594
X-RAY DIFFRACTIONr_scbond_other2.2071.9352539
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.512.8133760
X-RAY DIFFRACTIONr_long_range_B_refined6.44619.2545285
X-RAY DIFFRACTIONr_long_range_B_other5.74418.2354803
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 287 -
Rwork0.21 5519 -
obs--97.29 %
Refinement TLS params.Method: refined / Origin x: 19.2411 Å / Origin y: 26.5557 Å / Origin z: 75.5907 Å
111213212223313233
T0.0031 Å2-0.0065 Å20.0028 Å2-0.0438 Å2-0.0001 Å2--0.0059 Å2
L0.2817 °2-0.0016 °2-0.0026 °2-0.748 °20.1367 °2--0.2288 °2
S-0.0069 Å °0.0095 Å °-0.0207 Å °0.0101 Å °-0.0064 Å °0.0414 Å °0.0163 Å °-0.0212 Å °0.0133 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 9999
2X-RAY DIFFRACTION1B1 - 9999
3X-RAY DIFFRACTION1L1 - 9999
4X-RAY DIFFRACTION1W1 - 9999
5X-RAY DIFFRACTION1X1 - 9999

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