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- PDB-3w4r: Crystal structure of an insect chitinase from the Asian corn bore... -

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Basic information

Entry
Database: PDB / ID: 3w4r
TitleCrystal structure of an insect chitinase from the Asian corn borer, Ostrinia furnacalis
ComponentsChitinase
KeywordsHYDROLASE / insect / glycosyl hydrolase / chitin
Function / homology
Function and homology information


chitinase / chitinase activity / chitin catabolic process / chitin binding / carbohydrate metabolic process / extracellular region
Similarity search - Function
Chitin-binding domain type 2 / Chitin binding domain / Chitin binding Peritrophin-A domain / Chitin-binding type-2 domain profile. / Chitin binding domain superfamily / Chitinase A; domain 3 - #10 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase insertion domain superfamily / : ...Chitin-binding domain type 2 / Chitin binding domain / Chitin binding Peritrophin-A domain / Chitin-binding type-2 domain profile. / Chitin binding domain superfamily / Chitinase A; domain 3 - #10 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase insertion domain superfamily / : / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Chitinase A; domain 3 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Roll / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesOstrinia furnacalis (Asian corn borer)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsChen, L. / Liu, T. / Zhou, Y. / Shen, X. / Yang, Q.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural characteristics of an insect group I chitinase, an enzyme indispensable to moulting
Authors: Chen, L. / Liu, T. / Zhou, Y. / Chen, Q. / Shen, X. / Yang, Q.
History
DepositionJan 10, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1May 7, 2014Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 8, 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4473
Polymers62,0041
Non-polymers4422
Water10,034557
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.761, 93.761, 121.964
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Chitinase


Mass: 62004.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ostrinia furnacalis (Asian corn borer) / References: UniProt: Q2V6H4, chitinase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 557 / 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: 2.5 Å3/Da / Density % sol: 50.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50mM HEPES, 100mM NaCl, 200mM ammonium sulfate, 20% PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 66546 / Num. obs: 66546 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 22.3 % / Rmerge(I) obs: 0.093 / Rsym value: 0.093
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 22.1 % / Rmerge(I) obs: 0.364 / Rsym value: 0.364 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FXY

3fxy


Resolution: 1.7→43.759 Å / SU ML: 0.11 / σ(F): 0 / Phase error: 14.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1594 1967 2.98 %
Rwork0.1467 --
obs0.1471 65911 98.92 %
all-66546 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→43.759 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3075 0 28 557 3660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0213213
X-RAY DIFFRACTIONf_angle_d1.7884355
X-RAY DIFFRACTIONf_dihedral_angle_d13.1961164
X-RAY DIFFRACTIONf_chiral_restr0.141446
X-RAY DIFFRACTIONf_plane_restr0.01558
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7003-1.74280.16251380.15154447X-RAY DIFFRACTION96
1.7428-1.790.17461390.15294469X-RAY DIFFRACTION98
1.79-1.84260.17321410.15274549X-RAY DIFFRACTION98
1.8426-1.90210.15911370.15224522X-RAY DIFFRACTION98
1.9021-1.97010.18181410.14534550X-RAY DIFFRACTION99
1.9701-2.0490.16191400.14994594X-RAY DIFFRACTION99
2.049-2.14220.15111400.1414570X-RAY DIFFRACTION99
2.1422-2.25510.14851380.14064619X-RAY DIFFRACTION100
2.2551-2.39640.15641430.1494568X-RAY DIFFRACTION100
2.3964-2.58140.17591400.15494609X-RAY DIFFRACTION100
2.5814-2.84120.16931440.15464627X-RAY DIFFRACTION100
2.8412-3.25220.15981420.15064625X-RAY DIFFRACTION100
3.2522-4.09690.15321420.13344600X-RAY DIFFRACTION99
4.0969-43.77360.14551420.14644595X-RAY DIFFRACTION98

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