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- PDB-3wqv: Crystal structure of Ostrinia furnacalis Group I chitinase cataly... -

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Basic information

Entry
Database: PDB / ID: 3wqv
TitleCrystal structure of Ostrinia furnacalis Group I chitinase catalytic domain in complex with a(GlcN)5
ComponentsChitinase
KeywordsHYDROLASE / family-18 chitinases / inhibition / deacetylated chitooligosaccharides
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 / Chitinase II ...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. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / 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: 2.043 Å
AuthorsChen, L. / Zhou, Y. / Yang, Q.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Fully deacetylated chitooligosaccharides act as efficient glycoside hydrolase family 18 chitinase inhibitors.
Authors: Chen, L. / Zhou, Y. / Qu, M. / Zhao, Y. / Yang, Q.
History
DepositionFeb 3, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_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

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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)46,5005
Polymers44,9961
Non-polymers1,5054
Water7,746430
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.222, 94.222, 122.430
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: 44995.613 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 19-407
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ostrinia furnacalis (Asian corn borer) / Gene: OfChtI(OfCht5) / Plasmid: pPIC9 / Production host: Komagataella pastoris (fungus) / Strain (production host): GS115 / References: UniProt: Q2V6H4, chitinase
#2: Polysaccharide 2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2- ...2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 823.794 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNb1-4DGlcpNb1-4DGlcpNb1-4DGlcpNb1-4DGlcpNb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1b_1-5_2*N]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpN]{[(4+1)][b-D-GlcpN]{[(4+1)][b-D-GlcpN]{[(4+1)][b-D-GlcpN]{[(4+1)][b-D-GlcpN]{}}}}}LINUCSPDB-CARE
#3: 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
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 430 / 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: 3.49 Å3/Da / Density % sol: 64.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM HEPES pH 7.5, 25% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97869 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 2013
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97869 Å / Relative weight: 1
ReflectionResolution: 2.043→50 Å / Num. all: 39003 / Num. obs: 38955 / % possible obs: 99.9 % / Redundancy: 17.1 % / Biso Wilson estimate: 21.74 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 24.08
Reflection shellResolution: 2.04→2.08 Å / Redundancy: 17.1 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 11.76 / Num. unique all: 1916 / Rsym value: 0.37 / % 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: 3W4R

3w4r


Resolution: 2.043→38.707 Å / SU ML: 0.12 / σ(F): 1.35 / Phase error: 16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1676 2002 5.15 %random
Rwork0.1495 ---
obs0.1505 38902 99.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.043→38.707 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3075 0 99 430 3604
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043288
X-RAY DIFFRACTIONf_angle_d0.8814475
X-RAY DIFFRACTIONf_dihedral_angle_d19.9571224
X-RAY DIFFRACTIONf_chiral_restr0.06471
X-RAY DIFFRACTIONf_plane_restr0.003559
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0427-2.09380.17331410.1576257898
2.0938-2.15040.16961470.14962627100
2.1504-2.21360.17771430.14752614100
2.2136-2.28510.19541430.15212631100
2.2851-2.36670.22981380.15882645100
2.3667-2.46150.19261420.16782642100
2.4615-2.57350.20061390.16052644100
2.5735-2.70910.20021420.16012632100
2.7091-2.87880.16961430.15392644100
2.8788-3.1010.18091430.15562620100
3.101-3.41290.17541450.14772659100
3.4129-3.90640.1351470.13262658100
3.9064-4.920.13581480.12652647100
4.92-38.71360.15381410.1677265999
Refinement TLS params.Method: refined / Origin x: -41.3539 Å / Origin y: 19.6952 Å / Origin z: 5.9246 Å
111213212223313233
T0.0751 Å2-0.0241 Å20.0076 Å2-0.0551 Å20.0047 Å2--0.0813 Å2
L0.3677 °2-0.1879 °20.0111 °2-0.4743 °2-0.0442 °2--0.7284 °2
S-0.0026 Å °0.0102 Å °-0.0089 Å °0.0384 Å °0.0467 Å °-0.0162 Å °0.0151 Å °-0.0469 Å °0.1023 Å °
Refinement TLS groupSelection details: ALL

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