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

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Basic information

Entry
Database: PDB / ID: 3chd
TitleCrystal structure of Aspergillus fumigatus chitinase B1 in complex with dipeptide
ComponentsChitinase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / (beta-alpha)8 barrel / chitinase / peptide inhibitors / hydrolase / 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
Synthetic intermediate of ARGIFIN / Chem-WRG / Endochitinase B1
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Known phases / Resolution: 2 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 1.1Aug 31, 2009Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Aug 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,53818
Polymers95,3242
Non-polymers2,21416
Water14,898827
1
A: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6738
Polymers47,6621
Non-polymers1,0117
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,86510
Polymers47,6621
Non-polymers1,2039
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.067, 117.067, 99.953
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, AFUA_8G01410 / Plasmid: pLysS / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q873X9, chitinase
#2: Chemical ChemComp-WRG / (2S)-2-[[(2S)-2-acetamido-5-[[N-(methylcarbamoyl)carbamimidoyl]amino]pentanoyl]-methyl-amino]-3-phenyl-propanoic acid


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 434.489 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H30N6O5 / References: Synthetic intermediate of ARGIFIN
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 827 / 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: 3.57 Å3/Da / Density % sol: 65.5 %
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 19, 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→20 Å / Num. all: 90990 / Num. obs: 89613 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 16.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 2.5 / % possible all: 96

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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→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
Rfree0.215 889 -Random
Rwork0.177 ---
all0.177 90871 --
obs0.177 89564 98.6 %-
Displacement parametersBiso mean: 27.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6140 0 132 827 7099
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.57
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d1
LS refinement shellResolution: 2→2.04 Å /
RfactorNum. reflection
Rfree0.27 47
Rwork0.245 -
obs-5006

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