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

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Basic information

Entry
Database: PDB / ID: 2iuz
TitleCrystal structure of Aspergillus fumigatus chitinase B1 in complex with C2-dicaffeine
ComponentsCHITINASE
KeywordsHYDROLASE / GLYCOSIDASE / (BETA-ALPHA)8 BARREL / CHITINASE-C2DICAFFEINE 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
Chem-D1H / Endochitinase B1
Similarity search - Component
Biological speciesASPERGILLUS FUMIGATUS (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.95 Å
AuthorsSchuttelkopf, A.W. / Andersen, O.A. / Rao, F.V. / Allwood, M. / Lloyd, C.M. / Eggleston, I.M. / Van Aalten, D.M.F.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Screening-Based Discovery and Structural Dissection of a Novel Family 18 Chitinase Inhibitor
Authors: Schuttelkopf, A.W. / Andersen, O.A. / Rao, F.V. / Allwood, M. / Lloyd, C.M. / Eggleston, I.M. / Van Aalten, D.M.F.
History
DepositionJun 8, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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)97,15315
Polymers95,3242
Non-polymers1,82913
Water15,871881
1
A: CHITINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6258
Polymers47,6621
Non-polymers9637
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CHITINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5297
Polymers47,6621
Non-polymers8676
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)116.782, 116.782, 99.420
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 / ASPERGILLUS FUMIGATUS CHITINASE B1 / CLASS V CHITINASE CHIB1


Mass: 47661.836 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-433
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ASPERGILLUS FUMIGATUS (mold) / Plasmid: PLYSS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q873X9, chitinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-D1H / 1,1'-ETHANE-1,2-DIYLBIS(3,7-DIMETHYL-3,7-DIHYDRO-1H-PURINE-2,6-DIONE) / 1-(2-(THEOBROMINE-1-YL)ETHYL)-BROMINE


Mass: 386.365 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H18N8O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 881 / 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 % / Description: REFINEMENT STARTED FROM STRUCTURE 1W9P
Crystal growpH: 9.5 / Details: 0.1 M TRIS/HCL PH 9.5, 1.4 M LI2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9686
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 3, 2004 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. obs: 96150 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 21
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.4 / % possible all: 99.2

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.95→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2233 966 1 %RANDOM
Rwork0.1867 ---
obs0.1867 96114 99 %-
Solvent computationSolvent model: ANISOTROPIC / Bsol: 51.6564 Å2 / ksol: 0.367202 e/Å3
Displacement parametersBiso mean: 24.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.719 Å20 Å20 Å2
2---0.719 Å20 Å2
3---1.439 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.268 Å0.222 Å
Luzzati d res low-5 Å
Luzzati sigma a0.266 Å0.225 Å
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6141 0 111 881 7133
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.010389
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_deg1.49698
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.551.5
X-RAY DIFFRACTIONc_mcangle_it2.332
X-RAY DIFFRACTIONc_scbond_it2.122
X-RAY DIFFRACTIONc_scangle_it3.152.5
LS refinement shellResolution: 1.95→1.99 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.361 57 1 %
Rwork0.285 4853 -
obs--99 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5DRGCNS.PARDRGCNS.TOP

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