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- PDB-5gpr: Crystal structure of chitinase-h from Ostrinia furnacalis -

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Basic information

Entry
Database: PDB / ID: 5gpr
TitleCrystal structure of chitinase-h from Ostrinia furnacalis
ComponentsChitinase
KeywordsHYDROLASE / Chitinase / Ostrinia furnacalis / three dimensional structure
Function / homology
Function and homology information


chitinase activity / chitin catabolic process / chitin binding / carbohydrate metabolic process / extracellular region
Similarity search - Function
Chitinase A N-terminal / Chitinase A, N-terminal domain / 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. / Glycoside hydrolase family 18, catalytic domain ...Chitinase A N-terminal / Chitinase A, N-terminal domain / 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. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Chitinase A; domain 3 / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Roll / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesOstrinia furnacalis (Asian corn borer)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.23 Å
AuthorsLiu, T. / Zhou, Y. / Chen, L. / Yang, Q.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31425021 China
MOELJQ2014006 China
MOEDUT16QY48 China
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structure, Catalysis, and Inhibition of OfChi-h, the Lepidoptera-exclusive Insect Chitinase.
Authors: Liu, T. / Chen, L. / Zhou, Y. / Jiang, X. / Duan, Y. / Yang, Q.
History
DepositionAug 4, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jul 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_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 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

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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)61,5123
Polymers61,0701
Non-polymers4422
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.908, 114.419, 122.639
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Chitinase


Mass: 61069.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ostrinia furnacalis (Asian corn borer) / Gene: OfChi-h / Plasmid: pPIC9 / Production host: Komagataella pastoris (fungus) / Strain (production host): CBS 7435 / References: UniProt: Q4AE59
#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.: 1 / Source method: isolated from a natural source / Formula: H2O

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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: 2.81 Å3/Da / Density % sol: 56.18 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES pH 7.0, 30% v/v Jeffamine ED-2001, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97861 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 3.23→50 Å / Num. obs: 12123 / % possible obs: 100 % / Redundancy: 11.7 % / Net I/σ(I): 8.94

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W4R

3w4r


Resolution: 3.23→44.972 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2565 1159 10 %
Rwork0.2115 --
obs0.2161 11586 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.23→44.972 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4197 0 28 1 4226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054344
X-RAY DIFFRACTIONf_angle_d0.85898
X-RAY DIFFRACTIONf_dihedral_angle_d14.5181559
X-RAY DIFFRACTIONf_chiral_restr0.033612
X-RAY DIFFRACTIONf_plane_restr0.004767
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2301-3.37710.30711460.27071257X-RAY DIFFRACTION100
3.3771-3.55510.31551300.24571288X-RAY DIFFRACTION100
3.5551-3.77770.27581510.22451285X-RAY DIFFRACTION100
3.7777-4.06920.27981440.21141277X-RAY DIFFRACTION100
4.0692-4.47840.22371400.18731294X-RAY DIFFRACTION100
4.4784-5.12560.22121480.18571295X-RAY DIFFRACTION100
5.1256-6.45470.26811440.22131329X-RAY DIFFRACTION100
6.4547-44.97620.23681560.19941402X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 14.1864 Å / Origin y: 14.396 Å / Origin z: 161.3651 Å
111213212223313233
T0.3668 Å20.0091 Å20.0017 Å2-0.3534 Å20.0068 Å2--0.4237 Å2
L0.3234 °20.0606 °2-0.1785 °2-0.2313 °2-0.3423 °2--1.1349 °2
S0.0448 Å °0.0151 Å °0.078 Å °0.0197 Å °0.032 Å °0.053 Å °-0.1062 Å °-0.0765 Å °-0.0572 Å °
Refinement TLS groupSelection details: all

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