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- PDB-1itx: Catalytic Domain of Chitinase A1 from Bacillus circulans WL-12 -

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Basic information

Entry
Database: PDB / ID: 1itx
TitleCatalytic Domain of Chitinase A1 from Bacillus circulans WL-12
ComponentsGlycosyl Hydrolase
KeywordsHYDROLASE / Alpha-Beta (TIM) Barrel
Function / homology
Function and homology information


endochitinase activity / chitinase / chitin catabolic process / chitin binding / polysaccharide catabolic process / carbohydrate binding / extracellular region
Similarity search - Function
Carbohydrate-binding module family 5/12 / Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / 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 ...Carbohydrate-binding module family 5/12 / Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / 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 / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Roll / Immunoglobulin-like fold / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus circulans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsIwahori, F. / Matsumoto, T. / Watanabe, T. / Nonaka, T.
Citation
Journal: PROC.JPN.ACAD.,SER.B / Year: 1999
Title: Three-dimensional structure of the catalytic domain of chitinase A1 from Bacillus circulans WL-12 at a very high resolution
Authors: Matsumoto, T. / Nonaka, T. / Hashimoto, M. / Watanabe, T. / Mitsui, Y.
#1: Journal: FEBS LETT. / Year: 2001
Title: Trp122 and Trp134 on the surface of the catalytic domain are essential for crystalline chitin hydrolysis by Bacillus circulans chitinase A1
Authors: Watanabe, T. / Ishibashi, A. / Ariga, Y. / Hashimoto, M. / Nikaidou, N. / Sugiyama, J. / Matsumoto, T. / Nonaka, T.
#2: Journal: PROTEIN PEPT.LETT. / Year: 1999
Title: Crystallization and A Preliminary Crystallographic Analysis of the Catalytic Domain of Chitinase Al from Bacillus Circulans WL-12
Authors: Matsumoto, T. / Nonaka, T. / Katouda, H. / Hashimoto, M. / Watanabe, T. / Mitsui, Y.
#3: Journal: J.BIOL.CHEM. / Year: 1993
Title: Identification of glutamic acid 204 and aspartic acid 200 in chitinase A1 of Bacillus circulans WL-12 as essential residues for chitinase activity
Authors: Watanabe, T. / Kobori, K. / Miyashita, K. / Fujii, T. / Sakai, H. / Uchida, M. / Tanaka, H.
#4: Journal: J.BIOL.CHEM. / Year: 1990
Title: Gene cloning of chitinase A1 from Bacillus circulans WL-12 revealed its evolutionary relationship to Serratia chitinase and to the type III homology units of fibronectin
Authors: Watanabe, T. / Suzuki, K. / Oyanagi, W. / Ohnishi, K. / Tanaka, H.
#5: Journal: J.BIOL.CHEM. / Year: 2001
Title: Roles of the exposed aromatic residues in crystalline chitin hydrolysis by chitinase A from Serratia marcescens 2170
Authors: Uchiyama, T. / Katouno, f. / Nikaidou, N. / Nonaka, T. / Sugiyama, J. / Watanabe, T.
History
DepositionFeb 13, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycosyl Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,54212
Polymers45,5291
Non-polymers1,01311
Water13,872770
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.0073, 46.8388, 55.7001
Angle α, β, γ (deg.)109.2931, 95.4547, 116.6796
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Glycosyl Hydrolase / Chitinase A1


Mass: 45529.199 Da / Num. of mol.: 1 / Fragment: Catalytic Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus circulans (bacteria) / Gene: CHIA1 / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: P20533, chitinase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 770 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.97 Å3/Da / Density % sol: 37.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: PEG 4000, potassium dihydrophosphate, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.5 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 18, 2001
RadiationMonochromator: undulator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.5 Å / Relative weight: 1
ReflectionResolution: 1.1→36.793 Å / Num. all: 139823 / Num. obs: 139823 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 5.943 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Net I/σ(I): 10.1
Reflection shellResolution: 1.1→1.13 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 2.4 / Num. unique all: 10242 / Rsym value: 0.248 / % possible all: 97.2

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
ARP/wARPmodel building
REFMAC5refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CTN

1ctn


Resolution: 1.1→36.793 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.979 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Some waters are listed as disorders coupled with some parts of the protein molecules.
RfactorNum. reflection% reflectionSelection details
Rfree0.13719 7125 5.1 %RANDOM
Rwork0.11628 ---
all0.11735 139823 --
obs0.11735 139823 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 8.354 Å2
Refinement stepCycle: LAST / Resolution: 1.1→36.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3221 0 66 770 4057
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_angle_other_deg0.86437345
X-RAY DIFFRACTIONr_angle_refined_deg1.6751.935088
X-RAY DIFFRACTIONr_bond_other_d0.0020.023115
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213685
X-RAY DIFFRACTIONr_chiral_restr0.1030.2545
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1813497
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.215581
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02739
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024175
X-RAY DIFFRACTIONr_mcangle_it1.57323683
X-RAY DIFFRACTIONr_nbd_other0.4660.33568
X-RAY DIFFRACTIONr_nbd_refined0.8310.31141
X-RAY DIFFRACTIONr_nbtor_other1.1370.530
X-RAY DIFFRACTIONr_scangle_it2.7644.51399
X-RAY DIFFRACTIONr_mcbond_it1.0771.52260
X-RAY DIFFRACTIONr_scbond_it1.96631425
X-RAY DIFFRACTIONr_rigid_bond_restr1.1723685
X-RAY DIFFRACTIONr_sphericity_bonded2.23723584
X-RAY DIFFRACTIONr_sphericity_free2.9122770
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.568
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3040.3132
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2930.327
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.5560
X-RAY DIFFRACTIONr_xyhbond_nbd_other
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.212 545 -
Rwork0.178 9684 -
obs-9684 95.8 %

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