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- PDB-3n12: Crystal stricture of chitinase in complex with zinc atoms from Ba... -

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Basic information

Entry
Database: PDB / ID: 3n12
TitleCrystal stricture of chitinase in complex with zinc atoms from Bacillus cereus NCTU2
ComponentsChitinase A
KeywordsHYDROLASE / chitinase / ChiNCTU2 / zinc atoms / complex
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
ACETIC ACID / chitinase
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / 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 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5896
Polymers36,2681
Non-polymers3225
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.753, 48.616, 66.752
Angle α, β, γ (deg.)90.00, 99.31, 90.00
Int Tables number4
Space group name H-MP1211

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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: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 5

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50mM zinc acetate dihydrate, 22%(w/v) PEG 8000 in 100mM sodium cacodylate buffer pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL12B211.28228
SYNCHROTRONSPring-8 BL12B221.28284, 1.25233, 1.2902
Detector
TypeIDDetectorDate
ADSC QUANTUM 4r1CCDNov 3, 2004
ADSC QUANTUM 4r2CCDJul 14, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.282281
21.282841
31.252331
41.29021
ReflectionResolution: 1.11→30 Å / Num. all: 125749 / Num. obs: 118833 / % possible obs: 94.5 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.055 / Rsym value: 0.038 / Net I/σ(I): 16.5
Reflection shellResolution: 1.11→1.16 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 2.9 / Num. unique all: 14413 / Rsym value: 0.481 / % possible all: 91.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.4.0067refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.2→16.47 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.95 / SU B: 0.623 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21309 4790 5.1 %RANDOM
Rwork0.198 ---
obs0.19875 89815 94.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.205 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å2-0.37 Å2
2---0.18 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.2→16.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2558 0 8 302 2868
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0222627
X-RAY DIFFRACTIONr_angle_refined_deg0.8771.953565
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9475331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.59825.085118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.14915411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.127156
X-RAY DIFFRACTIONr_chiral_restr0.0610.2375
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212043
X-RAY DIFFRACTIONr_mcbond_it0.3091.51640
X-RAY DIFFRACTIONr_mcangle_it0.60622623
X-RAY DIFFRACTIONr_scbond_it0.9783987
X-RAY DIFFRACTIONr_scangle_it1.414.5942
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 358 -
Rwork0.244 6492 -
obs--92.41 %

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