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- PDB-3che: Crystal structure of Aspergillus fumigatus chitinase B1 in comple... -

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Basic information

Entry
Database: PDB / ID: 3che
TitleCrystal structure of Aspergillus fumigatus chitinase B1 in complex with tripeptide
Components
  • Chitinase
  • Peptide inhibitor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / (beta-alpha)8 barrel / chitinase / peptide inhibitors / Glycosidase / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


chitinase / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / extracellular region
Similarity search - Function
Chitinase A; domain 3 - #10 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase insertion domain superfamily / : / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain ...Chitinase A; domain 3 - #10 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase insertion domain superfamily / : / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Chitinase A; domain 3 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Roll / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Known phases / Resolution: 2.05 Å
AuthorsAndersen, O.A. / van Aalten, D.M.F.
CitationJournal: Chem.Biol. / Year: 2008
Title: Structure-based dissection of the natural product cyclopentapeptide chitinase inhibitor argifin.
Authors: Andersen, O.A. / Nathubhai, A. / Dixon, M.J. / Eggleston, I.M. / van Aalten, D.M.
History
DepositionMar 9, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitinase
B: Chitinase
C: Peptide inhibitor
D: Peptide inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,54416
Polymers96,3914
Non-polymers1,15312
Water16,394910
1
A: Chitinase
C: Peptide inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6767
Polymers48,1952
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chitinase
D: Peptide inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8689
Polymers48,1952
Non-polymers6727
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.419, 117.419, 99.538
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Chitinase / Class V chitinase ChiB1


Mass: 47661.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Gene: chiB1 / Plasmid: pLysS / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q873X9, chitinase
#2: Protein/peptide Peptide inhibitor


Mass: 533.578 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 910 / 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: 3.6 Å3/Da / Density % sol: 65.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: Tris/HCl, Li2SO4, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 18, 2006
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.05→20 Å / Num. all: 84764 / Num. obs: 84294 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 20.6 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 14.3
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 2.7 / Num. unique all: 8096 / % possible all: 95.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESfrom pdb entry 1W9Pphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: Known phases
Starting model: PDB entry 1W9V

1w9v


Resolution: 2.05→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.195 834 -Random
Rwork0.172 ---
all0.172 84600 --
obs0.172 84246 99.6 %-
Displacement parametersBiso mean: 21.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6218 0 60 910 7188
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.53
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.94
LS refinement shellResolution: 2.05→2.09 Å
RfactorNum. reflection
Rfree0.209 834
Rwork0.225 -
obs-4873

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