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- PDB-2cwr: Crystal structure of chitin biding domain of chitinase from Pyroc... -

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Basic information

Entry
Database: PDB / ID: 2cwr
TitleCrystal structure of chitin biding domain of chitinase from Pyrococcus furiosus
Componentschitinase
KeywordsHYDROLASE / chitinase / chitin-binding domain / Pyrococcus furiosus / endoglucanase / chitin / hyperthermophilic
Function / homology
Function and homology information


polysaccharide binding / chitin binding / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Immunoglobulin-like - #290 / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 ...Immunoglobulin-like - #290 / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Glycoside hydrolase superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsUegaki, K. / Nakamura, T. / Ishikawa, K. / Matsumura, H.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Tertiary structure and carbohydrate recognition by the chitin-binding domain of a hyperthermophilic chitinase from Pyrococcus furiosus.
Authors: Nakamura, T. / Mine, S. / Hagihara, Y. / Ishikawa, K. / Ikegami, T. / Uegaki, K.
History
DepositionJun 24, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 11, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: chitinase


Theoretical massNumber of molelcules
Total (without water)10,9641
Polymers10,9641
Non-polymers00
Water2,540141
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.827, 48.827, 84.993
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein chitinase /


Mass: 10964.104 Da / Num. of mol.: 1 / Fragment: chitin-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: PF1233 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U1H5, chitinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.3 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, magnesium acetate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER / Detector: CCD / Date: Oct 14, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 11986 / % possible obs: 96.8 % / Observed criterion σ(I): 14.2 / Redundancy: 12.7 % / Biso Wilson estimate: 14.3 Å2 / Rmerge(I) obs: 0.076
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.233 / Mean I/σ(I) obs: 3 / % possible all: 80.5

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Processing

Software
NameVersionClassification
CNS1refinement
BBSdata reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→32.06 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1258850.71 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1186 10.3 %RANDOM
Rwork0.194 ---
obs0.194 11545 97 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.9514 Å2 / ksol: 0.400825 e/Å3
Displacement parametersBiso mean: 21.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.57 Å20 Å20 Å2
2--3.57 Å20 Å2
3----7.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→32.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms738 0 0 141 879
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d26.5
X-RAY DIFFRACTIONc_improper_angle_d0.56
X-RAY DIFFRACTIONc_mcbond_it2.591.5
X-RAY DIFFRACTIONc_mcangle_it3.682
X-RAY DIFFRACTIONc_scbond_it3.932
X-RAY DIFFRACTIONc_scangle_it5.72.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.267 165 10 %
Rwork0.227 1483 -
obs--85.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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