[English] 日本語
Yorodumi
- PDB-5yx6: Crystal structure of Rv3272 from M. tuberculosis orthorhombic form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yx6
TitleCrystal structure of Rv3272 from M. tuberculosis orthorhombic form
ComponentsUncharacterized protein Rv3272
KeywordsTRANSFERASE / Rv3272 / CoA transferase / fatty acid metabolism / tuberculosis
Function / homologyTransferases; Transferring sulfur-containing groups; CoA-transferases / : / CoA-transferase family III / CoA-transferase family III domain 1 superfamily / CoA-transferase family III domain 3 superfamily / CoA-transferase family III / transferase activity / BENZAMIDINE / Probable fatty acyl-CoA transferase Rv3272
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsAnsari, A. / Shrimant, K.S. / Venkatesh Pratap, J.
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2019
Title: Rv3272 encodes a novel Family III CoA transferase that alters the cell wall lipid profile and protects mycobacteria from acidic and oxidative stress.
Authors: Karade, S.S. / Pandey, S. / Ansari, A. / Das, S. / Tripathi, S. / Arora, A. / Chopra, S. / Pratap, J.V. / Dasgupta, A.
History
DepositionDec 1, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name
Revision 1.2Dec 4, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.pdbx_Rsym_value
Revision 2.0Aug 18, 2021Group: 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_entity_nonpoly / pdbx_nonpoly_scheme / 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_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein Rv3272
B: Uncharacterized protein Rv3272
C: Uncharacterized protein Rv3272
D: Uncharacterized protein Rv3272
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,41517
Polymers170,0224
Non-polymers1,39413
Water6,269348
1
A: Uncharacterized protein Rv3272
B: Uncharacterized protein Rv3272
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,88810
Polymers85,0112
Non-polymers8778
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12730 Å2
ΔGint-75 kcal/mol
Surface area27240 Å2
MethodPISA
2
C: Uncharacterized protein Rv3272
D: Uncharacterized protein Rv3272
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,5277
Polymers85,0112
Non-polymers5175
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12590 Å2
ΔGint-74 kcal/mol
Surface area26910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.261, 101.922, 241.324
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Uncharacterized protein Rv3272 / Family III CoA transferase


Mass: 42505.445 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv3272 / Production host: Escherichia coli Bl21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: P96877
#2: Chemical
ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C7H8N2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.48 Å3/Da / Density % sol: 50.34 % / Description: elongated plate-like
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 200mM Disodium hydrogen phosphate, 22% PEG 3350, 2% Benzamidine hydrochloride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.87→46.95 Å / Num. obs: 114403 / % possible obs: 79.8 % / Redundancy: 5.16 % / Biso Wilson estimate: 36.29 Å2 / CC1/2: 0.672 / Rsym value: 0.174 / Net I/σ(I): 7.28
Reflection shellResolution: 1.87→1.99 Å / CC1/2: 0.25 / Rsym value: 3.5 / % possible all: 21.4

-
Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YIT

5yit


Resolution: 2.2→46.95 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.68
RfactorNum. reflection% reflection
Rfree0.251 1522 1.84 %
Rwork0.211 --
obs0.212 82809 95.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→46.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10572 0 99 348 11019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610875
X-RAY DIFFRACTIONf_angle_d1.07314847
X-RAY DIFFRACTIONf_dihedral_angle_d15.9823892
X-RAY DIFFRACTIONf_chiral_restr0.0431748
X-RAY DIFFRACTIONf_plane_restr0.0061962
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2710.61441140.58815912X-RAY DIFFRACTION78
2.271-2.35220.44981160.4516203X-RAY DIFFRACTION82
2.3522-2.44630.32521410.29387542X-RAY DIFFRACTION99
2.4463-2.55770.29491410.25597586X-RAY DIFFRACTION99
2.5577-2.69250.32011420.24387577X-RAY DIFFRACTION99
2.6925-2.86120.30671430.23597629X-RAY DIFFRACTION99
2.8612-3.08210.24691430.21877660X-RAY DIFFRACTION100
3.0821-3.39210.27971440.20327674X-RAY DIFFRACTION100
3.3921-3.88280.21611420.18717660X-RAY DIFFRACTION99
3.8828-4.89110.1851460.14627801X-RAY DIFFRACTION99
4.8911-46.95640.18011500.16178043X-RAY DIFFRACTION99

+
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