[English] 日本語
Yorodumi
- PDB-6jmb: Crystal structure of Ostrinia furnacalis Group IV chitinase in co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6jmb
TitleCrystal structure of Ostrinia furnacalis Group IV chitinase in complex with allosamidin
Componentsofchtiv-allosamidin
KeywordsHYDROLASE / chitinase / group IV / allosamidin
Function / homology
Function and homology information


chitinase activity / chitin catabolic process / chitin binding / carbohydrate metabolic process / extracellular region
Similarity search - Function
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 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Allosamidin / ALLOSAMIZOLINE / Group IV chitinase
Similarity search - Component
Biological speciesOstrinia furnacalis (Asian corn borer)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.389 Å
AuthorsLiu, T. / Yang, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31425021 China
CitationJournal: Insect Biochem.Mol.Biol. / Year: 2020
Title: Structure and property of group IV insect chitinase, a potential drug target and biopesticide
Authors: Liu, T. / Guo, X. / Bu, Y. / Zhou, Y. / Duan, Y. / Yang, Q.
History
DepositionMar 7, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.year
Revision 2.0Apr 13, 2022Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list
Revision 2.1Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ofchtiv-allosamidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5843
Polymers43,9431
Non-polymers6412
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-4 kcal/mol
Surface area14040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.625, 71.707, 72.155
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein ofchtiv-allosamidin


Mass: 43943.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ostrinia furnacalis (Asian corn borer) / Plasmid: pPIC9k / Production host: Pichia (fungus) / Strain (production host): GS115 / References: UniProt: A0A482LWB1*PLUS
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-allopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-allopyranose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
References: Allosamidin
DescriptorTypeProgram
DAllpNAcb1-4DAllpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2222h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-AllpNAc]{[(4+1)][b-D-AllpNAc]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-AMI / ALLOSAMIZOLINE


Type: Oligosaccharide / Class: Inhibitor / Mass: 216.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N2O4 / References: Allosamidin
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20%(v/v) 1,4-butanediol, 100mM sodium acetate, 100mM acetic acid, pH 4.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.97778 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97778 Å / Relative weight: 1
ReflectionResolution: 1.389→50 Å / Num. obs: 124774 / % possible obs: 100 % / Redundancy: 8.5 % / Rsym value: 0.058 / Net I/σ(I): 9.7
Reflection shellResolution: 1.39→1.41 Å / Redundancy: 8.2 % / Num. unique obs: 5609 / Rsym value: 0.372 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5wup

5wup


Resolution: 1.389→25.431 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 15.2
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I_MINUS AND I_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.1595 3493 2.8 %
Rwork0.1494 --
obs0.1497 124774 92.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.389→25.431 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2937 0 43 285 3265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053081
X-RAY DIFFRACTIONf_angle_d0.8544215
X-RAY DIFFRACTIONf_dihedral_angle_d15.7611070
X-RAY DIFFRACTIONf_chiral_restr0.081463
X-RAY DIFFRACTIONf_plane_restr0.005547
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3889-1.40790.1787960.17892658X-RAY DIFFRACTION51
1.4079-1.4280.2019860.17383162X-RAY DIFFRACTION60
1.428-1.44940.19331010.16663564X-RAY DIFFRACTION68
1.4494-1.4720.1839850.16013962X-RAY DIFFRACTION75
1.472-1.49610.20951060.15854382X-RAY DIFFRACTION83
1.4961-1.52190.17341510.15694635X-RAY DIFFRACTION89
1.5219-1.54960.19361310.15734967X-RAY DIFFRACTION94
1.5496-1.57940.18791740.15415025X-RAY DIFFRACTION96
1.5794-1.61160.15991350.15125189X-RAY DIFFRACTION99
1.6116-1.64670.18591550.15315225X-RAY DIFFRACTION100
1.6467-1.6850.15681570.1515198X-RAY DIFFRACTION100
1.685-1.72710.14421340.1485263X-RAY DIFFRACTION100
1.7271-1.77380.16851380.14455217X-RAY DIFFRACTION100
1.7738-1.8260.15451820.14135215X-RAY DIFFRACTION100
1.826-1.88490.14581440.14445279X-RAY DIFFRACTION100
1.8849-1.95220.13971780.14615208X-RAY DIFFRACTION100
1.9522-2.03030.14961320.14355244X-RAY DIFFRACTION100
2.0303-2.12270.13551540.14375259X-RAY DIFFRACTION100
2.1227-2.23460.1451420.14665227X-RAY DIFFRACTION100
2.2346-2.37450.15881460.15255237X-RAY DIFFRACTION100
2.3745-2.55760.17191640.14865226X-RAY DIFFRACTION100
2.5576-2.81470.16151660.15985217X-RAY DIFFRACTION100
2.8147-3.22130.17871320.15395250X-RAY DIFFRACTION100
3.2213-4.05590.15161470.14765243X-RAY DIFFRACTION100
4.0559-25.43530.15311570.1425229X-RAY DIFFRACTION100

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more