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- PDB-3n17: Crystal stricture of E145Q/Y227F chitinase in complex with NAG fr... -

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Basic information

Entry
Database: PDB / ID: 3n17
TitleCrystal stricture of E145Q/Y227F chitinase in complex with NAG from Bacillus cereus NCTU2
ComponentsChitinase A
KeywordsHYDROLASE / Chitinase / ChiNCTU2 / complex / NAG / mutation
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 / Glycosyl hydrolases family 18 (GH18) domain profile. / 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 / Glycosyl hydrolases family 18 (GH18) domain profile. / 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: 1.2 Å
AuthorsHsieh, Y.-C. / Wu, Y.-J. / Wu, W.-G. / Li, Y.-K. / Chen, C.-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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6752
Polymers36,2511
Non-polymers4241
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.644, 76.362, 76.911
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: 36250.641 Da / Num. of mol.: 1 / Mutation: E145Q/Y227F
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: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 1

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Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.57 %
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: Apr 9, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→30 Å / Num. obs: 87759 / % possible obs: 97.2 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.047 / Rsym value: 0.056 / Net I/σ(I): 43.3
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.056 / Mean I/σ(I) obs: 8.5 / Num. unique all: 7859 / Rsym value: 0.199 / % possible all: 88.1

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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: 1.2→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.955 / SU B: 0.477 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1872 4387 5 %RANDOM
Rwork0.17562 ---
obs0.1762 83269 97.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.287 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2508 0 29 291 2828
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0222635
X-RAY DIFFRACTIONr_angle_refined_deg0.9891.963586
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5745333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.51225.042119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.45115406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.797156
X-RAY DIFFRACTIONr_chiral_restr0.0690.2382
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212042
X-RAY DIFFRACTIONr_mcbond_it0.3431.51618
X-RAY DIFFRACTIONr_mcangle_it0.67922595
X-RAY DIFFRACTIONr_scbond_it1.13331017
X-RAY DIFFRACTIONr_scangle_it1.6944.5987
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 289 -
Rwork0.183 5463 -
obs--87.55 %

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