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- PDB-1wvu: Crystal structure of chitinase C from Streptomyces griseus HUT6037 -

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Basic information

Entry
Database: PDB / ID: 1wvu
TitleCrystal structure of chitinase C from Streptomyces griseus HUT6037
Componentschitinase C
KeywordsHYDROLASE / family 19 chitinase / whole structure
Function / homology
Function and homology information


endochitinase activity / chitin catabolic process / 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 superfamily 5/12 / Carbohydrate-binding module family 5/12 / Chitin-binding domain type 3 / Seminal Fluid Protein PDC-109 (Domain B) / Carbohydrate-binding module family 5/12 ...Endochitinase; domain 2 / Endochitinase, domain 2 / Glycoside hydrolase, family 19 / Glycoside hydrolase, family 19, catalytic / Chitinase class I / Carbohydrate-binding module superfamily 5/12 / Carbohydrate-binding module family 5/12 / Chitin-binding domain type 3 / Seminal Fluid Protein PDC-109 (Domain B) / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Lysozyme - #10 / Ribbon / Lysozyme / Lysozyme-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptomyces griseus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.45 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 27, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)57,45515
Polymers56,9942
Non-polymers46113
Water3,261181
1
A: chitinase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7819
Polymers28,4971
Non-polymers2848
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: chitinase C
B: chitinase C
hetero molecules

A: chitinase C
B: chitinase C
hetero molecules

A: chitinase C
B: chitinase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,36645
Polymers170,9836
Non-polymers1,38339
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_456z-1/2,-x+1/2,-y+11
crystal symmetry operation12_565-y+1/2,-z+1,x+1/21
MethodPQS
Unit cell
Length a, b, c (Å)127.850, 127.850, 127.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein chitinase C / glycosyl hydrolase


Mass: 28497.170 Da / Num. of mol.: 2 / 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: GenBank: 2662299, UniProt: O50152*PLUS, chitinase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 3.1 Å3/Da / Density % sol: 59.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Sodium chloride, Sodium acetate buffer, pH 4.6, 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: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 17, 2001
RadiationMonochromator: UNDULATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→42.64 Å / Num. all: 24823 / Num. obs: 24823 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 46.661 Å2 / Rmerge(I) obs: 0.041 / Rsym value: 0.041 / Net I/σ(I): 14
Reflection shellResolution: 2.45→2.51 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.125 / Mean I/σ(I) obs: 5.2 / Num. unique all: 318 / Rsym value: 0.125 / % possible all: 75.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MLPHAREphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.45→35.47 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.92 / SU B: 6.276 / SU ML: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.284 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22272 1262 5.1 %RANDOM
Rwork0.17238 ---
all0.17494 23560 --
obs0.17494 23560 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: 32.22 Å2
Refinement stepCycle: LAST / Resolution: 2.45→35.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3541 0 13 181 3735
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223659
X-RAY DIFFRACTIONr_bond_other_d0.0010.023032
X-RAY DIFFRACTIONr_angle_refined_deg1.6461.9134993
X-RAY DIFFRACTIONr_angle_other_deg0.90137076
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.085459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6324.807181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82815510
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8011513
X-RAY DIFFRACTIONr_chiral_restr0.0960.2513
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024241
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02780
X-RAY DIFFRACTIONr_nbd_refined0.2260.2883
X-RAY DIFFRACTIONr_nbd_other0.1810.23056
X-RAY DIFFRACTIONr_nbtor_refined0.1990.21919
X-RAY DIFFRACTIONr_nbtor_other0.0890.21910
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2171
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.160.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0790.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9881.52851
X-RAY DIFFRACTIONr_mcbond_other0.1811.5955
X-RAY DIFFRACTIONr_mcangle_it1.26523636
X-RAY DIFFRACTIONr_scbond_it1.94531693
X-RAY DIFFRACTIONr_scangle_it2.9174.51357
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 61 -
Rwork0.237 1334 -
obs--100 %

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