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- PDB-3wh1: Crystal Structure of a Family GH19 Chitinase from Bryum coronatum... -

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Basic information

Entry
Database: PDB / ID: 3wh1
TitleCrystal Structure of a Family GH19 Chitinase from Bryum coronatum in complex with (GlcNAc)4 at 1.0 A resolution
ComponentsChitinase A
KeywordsHYDROLASE / Chitinase / Carbohydrate
Function / homology
Function and homology information


chitinase activity / chitin catabolic process / defense response to fungus / cell wall macromolecule catabolic process / carbohydrate metabolic process
Similarity search - Function
Endochitinase; domain 2 / Endochitinase, domain 2 / Glycoside hydrolase, family 19 / Glycoside hydrolase, family 19, catalytic / Chitinase class I / Lysozyme - #10 / Lysozyme / Lysozyme-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle ...Endochitinase; domain 2 / Endochitinase, domain 2 / Glycoside hydrolase, family 19 / Glycoside hydrolase, family 19, catalytic / Chitinase class I / Lysozyme - #10 / Lysozyme / Lysozyme-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesBryum coronatum (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsNumata, T. / Umemoto, N. / Ohnuma, T. / Fukamizo, T.
CitationJournal: Biochim.Biophys.Acta / Year: 2014
Title: Crystal structure of a "loopless" GH19 chitinase in complex with chitin tetrasaccharide spanning the catalytic center.
Authors: Ohnuma, T. / Umemoto, N. / Nagata, T. / Shinya, S. / Numata, T. / Taira, T. / Fukamizo, T.
History
DepositionAug 21, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / pdbx_validate_close_contact / 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 / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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 2.1Aug 24, 2022Group: Database references / Structure summary / Category: chem_comp / citation / database_2
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)23,8186
Polymers22,7391
Non-polymers1,0795
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.384, 58.375, 48.136
Angle α, β, γ (deg.)90.00, 115.47, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Chitinase A


Mass: 22738.990 Da / Num. of mol.: 1 / Fragment: UNP residues 24-228 / Mutation: E61A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bryum coronatum (plant) / Gene: bcchiA / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A9ZSX9, chitinase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 830.786 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.07 Å3/Da / Density % sol: 40.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.09M Tris-HCl(pH 8.5), 1.35M di-Ammonium hydrogen phosphate, 0.001M CoCl2, 0.01M Sodium acetate(pH 4.6), 0.1M 1,6-Hexanediol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 23, 2010
RadiationMonochromator: Numerical link type Si(111) double crystal monochromater, liquid nitrogen cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1→50 Å / Num. obs: 98800 / % possible obs: 98.6 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 33.25
Reflection shellResolution: 1→1.04 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 4.13 / Num. unique all: 30901 / % possible all: 94.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4IJ4

4ij4


Resolution: 1→44.06 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.473 / SU ML: 0.012 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 0.024 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.15506 4942 5 %RANDOM
Rwork0.14751 ---
obs0.14789 93726 98.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.163 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20.03 Å2
2---0.06 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1→44.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1575 0 73 242 1890
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221693
X-RAY DIFFRACTIONr_angle_refined_deg1.1861.9742307
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1275201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.86124.63482
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.31415228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.406158
X-RAY DIFFRACTIONr_chiral_restr0.0850.2246
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211324
X-RAY DIFFRACTIONr_mcbond_it0.6551.51004
X-RAY DIFFRACTIONr_mcangle_it1.11821605
X-RAY DIFFRACTIONr_scbond_it1.5083689
X-RAY DIFFRACTIONr_scangle_it2.334.5702
X-RAY DIFFRACTIONr_rigid_bond_restr0.67931693
X-RAY DIFFRACTIONr_sphericity_free2.3453242
X-RAY DIFFRACTIONr_sphericity_bonded2.30331648
LS refinement shellResolution: 0.999→1.025 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.175 327 -
Rwork0.177 6398 -
obs--90.44 %

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