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- PDB-3n1a: Crystal stricture of E145G/Y227F chitinase in complex with cyclo-... -

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Basic information

Entry
Database: PDB / ID: 3n1a
TitleCrystal stricture of E145G/Y227F chitinase in complex with cyclo-(L-His-L-Pro) from Bacillus cereus NCTU2
ComponentsChitinase A
KeywordsHYDROLASE / Chitinase / ChiNCTU2 / complex / cyclo-(L-His-L-Pro) / 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 (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
CYCLO-(L-HISTIDINE-L-PROLINE) INHIBITOR / chitinase
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 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 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Chitinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4142
Polymers36,1801
Non-polymers2341
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.737, 75.045, 79.081
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: 36179.562 Da / Num. of mol.: 1 / Mutation: E145G/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: Chemical ChemComp-CHQ / CYCLO-(L-HISTIDINE-L-PROLINE) INHIBITOR / (3S,8AR)-3-(1H-IMIDAZOL-5-YLMETHYL)HEXAHYDROPYRROLO[1,2-A]PYRAZINE-1,4-DIONE


Mass: 234.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14N4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2 Å3/Da / Density % sol: 38.46 %
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: Nov 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 20188 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.058 / Rsym value: 0.075 / Net I/σ(I): 27.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 7 % / Rmerge(I) obs: 0.058 / Mean I/σ(I) obs: 6.1 / Num. unique all: 1969 / Rsym value: 0.424 / % possible all: 99.9

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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: 2→29.73 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.357 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23751 1031 5.1 %RANDOM
Rwork0.19934 ---
obs0.20135 19103 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.948 Å2
Baniso -1Baniso -2Baniso -3
1--1.43 Å20 Å20 Å2
2--0.85 Å20 Å2
3---0.58 Å2
Refinement stepCycle: LAST / Resolution: 2→29.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2511 0 17 96 2624
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0222596
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.7071.9553525
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2875326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.48824.957115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.62115399
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8156
X-RAY DIFFRACTIONr_chiral_restr0.0490.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0212019
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2581.51616
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.48222588
X-RAY DIFFRACTIONr_scbond_it0.5723980
X-RAY DIFFRACTIONr_scangle_it0.9264.5937
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 68 -
Rwork0.249 1337 -
obs--94.87 %

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