[English] 日本語
Yorodumi
- PDB-6iiy: Crystal structure of deacetylase triple mutant (Orf2*T) that invo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6iiy
TitleCrystal structure of deacetylase triple mutant (Orf2*T) that involving in teicoplanin biosynthetic pathway
Componentsdeacetylase
KeywordsOXIDOREDUCTASE / antibiotics
Function / homology
Function and homology information


glycoside metabolic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / acyltransferase activity / ligase activity / glycosyltransferase activity / metal ion binding
Similarity search - Function
LmbE-like / N-acetylglucosaminyl phosphatidylinositol deacetylase-related / Putative deacetylase LmbE-like domain superfamily / GlcNAc-PI de-N-acetylase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / IMIDAZOLE / LmbE family N-acetylglucosaminyl deacetylase
Similarity search - Component
Biological speciesActinoplanes teichomyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å
AuthorsLi, T.L. / Huang, C.M.
CitationJournal: Acs Infect Dis. / Year: 2019
Title: Teicoplanin Reprogrammed with the N-Acyl-Glucosamine Pharmacophore at the Penultimate Residue of Aglycone Acquires Broad-Spectrum Antimicrobial Activities Effectively Killing Gram-Positive and -Negative Pathogens.
Authors: Huang, C.M. / Lyu, S.Y. / Lin, K.H. / Chen, C.L. / Chen, M.H. / Shih, H.W. / Hsu, N.S. / Lo, I.W. / Wang, Y.L. / Li, Y.S. / Wu, C.J. / Li, T.L.
History
DepositionOct 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.2Oct 21, 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3793
Polymers32,2511
Non-polymers1282
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-9 kcal/mol
Surface area11190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.451, 66.671, 43.390
Angle α, β, γ (deg.)90.00, 92.59, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein deacetylase


Mass: 32250.766 Da / Num. of mol.: 1 / Mutation: S98A,V121A,F193Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinoplanes teichomyceticus (bacteria)
Gene: tcp14 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6ZZJ1
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M imidazole malate pH8.5, 27.5 % PEG 10000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.29→30 Å / Num. obs: 63373 / % possible obs: 94.7 % / Redundancy: 3.9 % / Net I/σ(I): 43.7
Reflection shellResolution: 1.29→1.34 Å / Num. unique obs: 6163 / CC1/2: 0.98

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2X9L

2x9l


Resolution: 1.29→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.579 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.047 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18191 3139 5.1 %RANDOM
Rwork0.16174 ---
obs0.16276 58755 92.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.941 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å2-0.05 Å2
2---0.12 Å2-0 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.29→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1847 0 6 294 2147
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191941
X-RAY DIFFRACTIONr_bond_other_d0.0020.021748
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.942647
X-RAY DIFFRACTIONr_angle_other_deg0.92834039
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4655247
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.99223.40297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.36715294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6431517
X-RAY DIFFRACTIONr_chiral_restr0.080.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212226
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02417
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1931.576973
X-RAY DIFFRACTIONr_mcbond_other1.1871.577971
X-RAY DIFFRACTIONr_mcangle_it1.9492.361219
X-RAY DIFFRACTIONr_mcangle_other1.9492.3591220
X-RAY DIFFRACTIONr_scbond_it1.7781.828968
X-RAY DIFFRACTIONr_scbond_other1.7771.828969
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7742.661427
X-RAY DIFFRACTIONr_long_range_B_refined4.78420.5442288
X-RAY DIFFRACTIONr_long_range_B_other4.4419.5322205
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.289→1.322 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.197 192 -
Rwork0.187 3368 -
obs--72.34 %

+
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