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- PDB-2a3a: Crystal structure of Aspergillus fumigatus chitinase B1 in comple... -

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Basic information

Entry
Database: PDB / ID: 2a3a
TitleCrystal structure of Aspergillus fumigatus chitinase B1 in complex with theophylline
Componentschitinase
KeywordsHYDROLASE / (beta-alpha)8 barrel / chitinase-theophylline complex
Function / homology
Function and homology information


endochitinase activity / chitinase / 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 / Glycosyl hydrolases family 18 (GH18) domain profile. / 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 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Chitinase A; domain 3 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Roll / Alpha Beta
Similarity search - Domain/homology
THEOPHYLLINE / Endochitinase B1
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / known phases / Resolution: 2.1 Å
AuthorsRao, F.V. / Andersen, O.A. / Vora, K.A. / DeMartino, J.A. / van Aalten, D.M.F.
CitationJournal: Chem.Biol. / Year: 2005
Title: Methylxanthine drugs are chitinase inhibitors: investigation of inhibition and binding modes.
Authors: Rao, F.V. / Andersen, O.A. / Vora, K.A. / Demartino, J.A. / van Aalten, D.M.
History
DepositionJun 24, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 27, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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)97,43717
Polymers95,3242
Non-polymers2,11415
Water13,493749
1
A: chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6718
Polymers47,6621
Non-polymers1,0097
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7679
Polymers47,6621
Non-polymers1,1058
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.229, 117.229, 100.021
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 / chitinase B1


Mass: 47661.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Plasmid: pLysS / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q873X9, chitinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-TEP / THEOPHYLLINE


Mass: 180.164 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C7H8N4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 749 / 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: 66 %
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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 11, 2004
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 78620 / Num. obs: 78620 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 31.2 Å2 / Rmerge(I) obs: 0.136 / Net I/σ(I): 13.1
Reflection shellResolution: 2.1→2.17 Å / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.6 / Num. unique all: 7728 / % possible all: 98

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASESfrom PDB entry 1W9Pphasing
CNS1refinement
RefinementMethod to determine structure: known phases
Starting model: PDB entry 1W9P

1w9p


Resolution: 2.1→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.226 779 1 %RANDOM
Rwork0.187 ---
obs0.187 78422 100 %-
all-78422 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.6 Å2 / ksol: 0.346 e/Å3
Displacement parametersBiso mean: 29.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6146 0 139 749 7034
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.47
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_mcangle_it2.082
X-RAY DIFFRACTIONc_scbond_it2.082
X-RAY DIFFRACTIONc_scangle_it3.262.5
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 15
RfactorNum. reflection
Rfree0.285 47
Rwork0.261 5071
obs-5118

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