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- PDB-2dbt: Crystal structure of chitinase C from Streptomyces griseus HUT6037 -

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Basic information

Entry
Database: PDB / ID: 2dbt
TitleCrystal structure of chitinase C from Streptomyces griseus HUT6037
Componentschitinase C
KeywordsHYDROLASE / family 19 chitinase
Function / homology
Function and homology information


endochitinase activity / chitin catabolic process / defense response to fungus / cell wall macromolecule catabolic process / carbohydrate binding / carbohydrate metabolic process / extracellular region
Similarity search - Function
Endochitinase; domain 2 / Endochitinase, domain 2 / Glycoside hydrolase, family 19 / Glycoside hydrolase, family 19, catalytic / Chitinase class I / Carbohydrate-binding module family 5/12 / Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Lysozyme - #10 ...Endochitinase; domain 2 / Endochitinase, domain 2 / Glycoside hydrolase, family 19 / Glycoside hydrolase, family 19, catalytic / Chitinase class I / Carbohydrate-binding module family 5/12 / Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Lysozyme - #10 / Lysozyme / Lysozyme-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptomyces griseus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.14 Å
AuthorsKezuka, Y. / Watanabe, T. / Nonaka, T.
Citation
Journal: J.Mol.Biol. / Year: 2006
Title: Structural Studies of a Two-domain Chitinase from Streptomyces griseus HUT6037
Authors: Kezuka, Y. / Ohishi, M. / Itoh, Y. / Watanabe, J. / Mitsutomi, M. / Watanabe, T. / Nonaka, T.
#1: Journal: Biosci.Biotechnol.Biochem. / Year: 2002
Title: Functional analysis of the chitin-binding domain of a family 19 chitinase from Streptomyces griseus HUT6037: substrate-binding affinity and cis-dominant increase of antifungal function
Authors: Itoh, Y. / Kawase, T. / Nikaidou, N. / Fukada, H. / Mitsutomi, M. / Watanabe, T. / Itoh, Y.
#2: Journal: Microbiology / Year: 1999
Title: Family 19 chitinases of Streptomyces species: characterization and distribution
Authors: Watanabe, T. / Kanai, R. / Kawase, T. / Tanabe, T. / Mitsutomi, M. / Sakuda, S. / Miyashita, K.
#3: Journal: J.Bacteriol. / Year: 1996
Title: A modular family 19 chitinase found in the prokaryotic organism Streptomyces griseus HUT 6037
Authors: Ohno, T. / Armand, S. / Hata, T. / Nikaidou, N. / Henrissat, B. / Mitsutomi, M. / Watanabe, T.
History
DepositionDec 16, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 28, 2006Provider: 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: chitinase C
B: chitinase C
C: chitinase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,2066
Polymers85,4923
Non-polymers7153
Water37821
1
A: chitinase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7352
Polymers28,4971
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: chitinase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7352
Polymers28,4971
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: chitinase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7352
Polymers28,4971
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)153.116, 153.116, 90.031
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein chitinase C / glycosyl hydrolase


Mass: 28497.170 Da / Num. of mol.: 3 / Fragment: residues 30-294
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseus (bacteria) / Plasmid: pET12a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O50152, chitinase
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 3.56 Å3/Da / Density % sol: 65.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.3M Ammonium formate, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 27, 2002
RadiationMonochromator: Triangular Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3.14→58.32 Å / Num. all: 20454 / Num. obs: 20454 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 9.8
Reflection shellResolution: 3.14→3.221 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 3.1 / Num. unique all: 1497 / Rsym value: 0.247 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WVV

1wvv


Resolution: 3.14→58.32 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.884 / SU B: 13.353 / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.075 / ESU R Free: 0.348 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22524 1106 5.1 %RANDOM
Rwork0.17372 ---
obs0.17625 20454 100 %-
all-20454 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.688 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20.42 Å20 Å2
2--0.84 Å20 Å2
3----1.25 Å2
Refinement stepCycle: LAST / Resolution: 3.14→58.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4728 0 45 21 4794
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0214911
X-RAY DIFFRACTIONr_angle_refined_deg1.3161.9096699
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.715612
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.41325240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.90215684
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3181515
X-RAY DIFFRACTIONr_chiral_restr0.0980.2687
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023900
X-RAY DIFFRACTIONr_nbd_refined0.2260.22757
X-RAY DIFFRACTIONr_nbtor_refined0.3180.23461
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2201
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0880.23
X-RAY DIFFRACTIONr_mcbond_it0.451.53085
X-RAY DIFFRACTIONr_mcangle_it0.84824851
X-RAY DIFFRACTIONr_scbond_it1.08732098
X-RAY DIFFRACTIONr_scangle_it1.7774.51848
LS refinement shellResolution: 3.14→3.221 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 82 -
Rwork0.235 1497 -
obs--100 %

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