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- PDB-3n11: Crystal stricture of wild-type chitinase from Bacillus cereus NCTU2 -

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Basic information

Entry
Database: PDB / ID: 3n11
TitleCrystal stricture of wild-type chitinase from Bacillus cereus NCTU2
ComponentsChitinase A
KeywordsHYDROLASE / chitinase / ChiNCTU2 / wild-type
Function / homology
Function and homology information


chitinase / chitin binding / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding
Similarity search - Function
: / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Glycosidases / Glycoside hydrolase superfamily ...: / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsHsieh, Y.-C. / Chen, C.-J. / Li, Y.-K. / Wu, Y.-J.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Crystal structures of bacillus cereus NCTU2 chitinase complexes with chitooligomers reveal novel substrate binding for catalysis: a chitinase without chitin-binding and insertion domains
Authors: Hsieh, Y.-C. / Wu, Y.-J. / Chiang, T.-Y. / Kuo, C.-Y. / Shrestha, K.L. / Chao, C.-F. / Huang, Y.-C. / Chuankhayan, P. / Wu, W.-G. / Li, Y.-K. / Chen, C.-J.
History
DepositionMay 15, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitinase A


Theoretical massNumber of molelcules
Total (without water)36,2681
Polymers36,2681
Non-polymers00
Water6,161342
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.515, 76.051, 76.615
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Chitinase A / ChiNCTU2


Mass: 36267.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: NCTU2 / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / References: UniProt: D0VV09, chitinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE IS CONFLICT BETWEEN THE REPORTED SEQUENCE AND DATABASE REFERENCE SEQUENCE. ACCORDING TO THE ...THERE IS CONFLICT BETWEEN THE REPORTED SEQUENCE AND DATABASE REFERENCE SEQUENCE. ACCORDING TO THE ELECTRON DENSITY THE POSITION 277 IS OBVIOUSLY VAL THAN ALA.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 36.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50mM potassium phosphate monobasic, 20%(w/v) PEG 8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 12, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→30 Å / Num. all: 62982 / Num. obs: 62227 / % possible obs: 98.9 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 34.7
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 6.2 / Num. unique all: 5979 / Rsym value: 0.239 / % possible all: 96.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.4.0067refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3N12

3n12


Resolution: 1.35→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.95 / SU B: 0.995 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21527 3158 5.1 %RANDOM
Rwork0.20236 ---
obs0.20302 58994 98.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.532 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20 Å2
2--1.24 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2501 0 0 342 2843
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0222567
X-RAY DIFFRACTIONr_angle_refined_deg0.8981.9483485
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8195324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.49924.957115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.85915398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.917156
X-RAY DIFFRACTIONr_chiral_restr0.060.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211995
X-RAY DIFFRACTIONr_mcbond_it0.1731.51601
X-RAY DIFFRACTIONr_mcangle_it0.33222563
X-RAY DIFFRACTIONr_scbond_it0.4663966
X-RAY DIFFRACTIONr_scangle_it0.7494.5922
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 224 -
Rwork0.249 4145 -
obs--95.29 %

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