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- PDB-3wl1: Crystal structure of Ostrinia furnacalis Group I chitinase cataly... -

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Basic information

Entry
Database: PDB / ID: 3wl1
TitleCrystal structure of Ostrinia furnacalis Group I chitinase catalytic domain in complex with reaction products (GlcNAc)2,3
ComponentsChitinase
KeywordsHYDROLASE / glycosyl hydrolase / insect / Ostrinia furnacalis
Function / homology
Function and homology information


endochitinase activity / chitinase / 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 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Chitinase A; domain 3 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Roll / Alpha Beta
Similarity search - Domain/homology
triacetyl-beta-chitotriose / chitinase
Similarity search - Component
Biological speciesOstrinia furnacalis (Asian corn borer)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.772 Å
AuthorsChen, L. / Liu, T. / Zhou, Y. / Chen, Q. / 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
DepositionNov 5, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
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 / entity_name_com / 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_molecule_features / 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.label_entity_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 / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_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 2.1Nov 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 2.2Oct 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4905
Polymers44,9961
Non-polymers1,4944
Water7,855436
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.835, 93.835, 122.227
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) / Production host: Komagataella pastoris (fungus) / References: UniProt: Q2V6H4, 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 / triacetyl-beta-chitotriose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: triacetyl-beta-chitotriose
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 436 / 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: 3.45 Å3/Da / Density % sol: 64.37 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
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: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 3, 2013
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. all: 59102 / Num. obs: 58900 / % possible obs: 99.66 % / Redundancy: 16.2 % / Biso Wilson estimate: 16.78 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 36.93
Reflection shellResolution: 1.77→1.8 Å / Redundancy: 15 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 8.55 / Num. unique all: 2916 / Rsym value: 0.424 / % possible all: 99.05

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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: 1.772→30.762 Å / SU ML: 0.13 / σ(F): 1.34 / Phase error: 18.12 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflectionSelection details
Rfree0.1686 2920 3.39 %random
Rwork0.1428 ---
obs0.1437 56387 73.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.772→30.762 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3075 0 100 436 3611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0193282
X-RAY DIFFRACTIONf_angle_d1.7814464
X-RAY DIFFRACTIONf_dihedral_angle_d18.5231211
X-RAY DIFFRACTIONf_chiral_restr0.132470
X-RAY DIFFRACTIONf_plane_restr0.009562
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7722-1.80130.2391940.1894265250
1.8013-1.83230.2323940.17271450
1.8323-1.86570.183960.1719266950
1.8657-1.90150.2003920.1637271150
1.9015-1.94030.1954980.1597273151
1.9403-1.98250.1603980.1593274451
1.9825-2.02860.15331010.1535286153
2.0286-2.07940.19871040.1501297455
2.0794-2.13560.15991060.142312858
2.1356-2.19840.15531190.1391341063
2.1984-2.26930.16971310.1367394373
2.2693-2.35040.16981540.1364439282
2.3504-2.44450.18461640.1435476589
2.4445-2.55570.17441720.1419499393
2.5557-2.69030.16471820.1476513995
2.6903-2.85880.16991790.149522097
2.8588-3.07930.1871980.1532530699
3.0793-3.38890.18551930.1416528399
3.3889-3.87840.16281810.1295519097
3.8784-4.88320.12721820.1195525398
4.8832-30.7670.17481820.1595516996
Refinement TLS params.Method: refined / Origin x: -41.2354 Å / Origin y: 19.4273 Å / Origin z: 26.4255 Å
111213212223313233
T0.1128 Å2-0.0272 Å20.0086 Å2-0.0952 Å20.0127 Å2--0.1174 Å2
L0.9134 °2-0.2766 °2-0.0164 °2-0.9001 °20.0847 °2--1.2533 °2
S0.0117 Å °0.0184 Å °0.0184 Å °0.0341 Å °0.039 Å °-0.0165 Å °-0.0257 Å °-0.0365 Å °0.0022 Å °
Refinement TLS groupSelection details: ALL

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