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- PDB-2xtk: ChiA1 from Aspergillus fumigatus in complex with acetazolamide -

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Basic information

Entry
Database: PDB / ID: 2xtk
TitleChiA1 from Aspergillus fumigatus in complex with acetazolamide
ComponentsCLASS III CHITINASE CHIA1
KeywordsHYDROLASE / GH18
Function / homology
Function and homology information


endochitinase activity / chitinase / 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 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...Chitinase Cts1-like / : / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Glycosyl hydrolases family 18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE / PHOSPHATE ION / Endochitinase A1
Similarity search - Component
Biological speciesASPERGILLUS FUMIGATUS (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSchuettelkopf, A.W. / van Aalten, D.M.F.
CitationJournal: Bioorg.Med.Chem. / Year: 2010
Title: Acetazolamide-Based Fungal Chitinase Inhibitors.
Authors: Schuttelkopf, A.W. / Gros, L. / Blair, D.E. / Frearson, J.A. / Van Aalten, D.M.F. / Gilbert, I.H.
History
DepositionOct 11, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
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 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-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 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)70,13820
Polymers68,1742
Non-polymers1,96418
Water6,684371
1
A: CLASS III CHITINASE CHIA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,06910
Polymers34,0871
Non-polymers9829
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CLASS III CHITINASE CHIA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,06910
Polymers34,0871
Non-polymers9829
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.638, 125.831, 211.688
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-1342-

PO4

21A-2008-

HOH

31A-2046-

HOH

41A-2102-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.956702, -0.25278, 0.144306), (-0.044254, 0.616335, 0.78624), (-0.287686, 0.745811, -0.600835)
Vector: 29.197, -15.935, 122.319)

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Components

#1: Protein CLASS III CHITINASE CHIA1 / CHIA1


Mass: 34086.906 Da / Num. of mol.: 2 / Fragment: RESIDUES 29-337
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ASPERGILLUS FUMIGATUS (mold) / Strain: A1163 / Production host: PICHIA PASTORIS (fungus) / Strain (production host): X-33 / References: UniProt: B0Y2Y2, chitinase
#2: Chemical ChemComp-AZM / 5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE


Mass: 222.245 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6N4O3S2 / Comment: medication*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsEXPRESSED CONSTRUCT INCLUDES RESIDUES 29 TO 337 ONLY. PHE28 IS GENERATED BY THE CLONING SITE ...EXPRESSED CONSTRUCT INCLUDES RESIDUES 29 TO 337 ONLY. PHE28 IS GENERATED BY THE CLONING SITE PRECEDING THE INSERT.

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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: 3.74 Å3/Da / Density % sol: 67 % / Description: NONE
Crystal growDetails: 0.42-0.58 M NAH2PO4, 0.83-0.74 M K2HPO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Apr 11, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 67879 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.5
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.5 / % possible all: 92.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AFCHIA1 APOSTRUCTURE TO BE DEPOSITED

Resolution: 2→19.8 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.49 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24886 3440 5.1 %RANDOM
Rwork0.21585 ---
obs0.21752 64435 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.157 Å2
Baniso -1Baniso -2Baniso -3
1-3.73 Å20 Å20 Å2
2---1.35 Å20 Å2
3----2.38 Å2
Refinement stepCycle: LAST / Resolution: 2→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4805 0 106 371 5282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0225073
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5491.9476943
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2575621
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.9825.062241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38915707
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1741510
X-RAY DIFFRACTIONr_chiral_restr0.2260.2716
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213987
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.821.53081
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.41324946
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.16431992
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3014.51995
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.001→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 232 -
Rwork0.334 4433 -
obs--100 %

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