[English] 日本語
Yorodumi
- PDB-6wyn: Transition metal inhibition and structural refinement of the M. t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wyn
TitleTransition metal inhibition and structural refinement of the M. tuberculosis esterase, Rv0045c
ComponentsPossible hydrolase
KeywordsHYDROLASE / serine esterase / allosteric regulation / conformational change
Function / homology: / carboxylesterase / carboxylesterase activity / Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / Esterase Rv0045c
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.81 Å
AuthorsMacbeth, M.R. / Johnson, R.J. / Hoops, G.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R15GM110641-01A1 United States
CitationJournal: Protein Sci. / Year: 2021
Title: Transition metal cation inhibition of Mycobacterium tuberculosis esterase RV0045C.
Authors: Bowles, I.E. / Pool, E.H. / Lancaster, B.S. / Lawson, E.K. / Savas, C.P. / Kartje, Z.J. / Severinac, L. / Cho, D.H. / Macbeth, M.R. / Johnson, R.J. / Hoops, G.C.
History
DepositionMay 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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: Possible hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6252
Polymers35,5901
Non-polymers351
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)130.810, 130.810, 48.870
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-607-

HOH

-
Components

#1: Protein Possible hydrolase


Mass: 35589.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv0045c / Plasmid: pET-28 / Details (production host): KanR / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Variant (production host): LOBSTR / References: UniProt: I6XU97
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.39 Å3/Da / Density % sol: 63.73 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.2 M MgCl2, 0.1 M Imidazole pH 7.4, 18% PEG 4000, 0.01 M spermidine, 1x10^-7 M ZnCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 1.279 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 18, 2018
RadiationMonochromator: Kohzu HLD-4 Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.279 Å / Relative weight: 1
ReflectionResolution: 1.72→113.28 Å / Num. obs: 42576 / % possible obs: 83.5 % / Redundancy: 17 % / CC1/2: 0.997 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.045 / Rrim(I) all: 0.195 / Net I/σ(I): 11.2 / Num. measured all: 723975 / Scaling rejects: 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.72-1.823.84.444806121240.0282.4925.1380.329
5.45-113.2821.50.0743671217090.9990.0170.07637.2100

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.35 Å113.28 Å
Translation6.35 Å113.28 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
STARANISOdata scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P2M

3p2m


Resolution: 1.81→113.28 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.924 / SU B: 2.969 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2329 1774 5 %RANDOM
Rwork0.207 ---
obs0.2083 34042 81.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 121.76 Å2 / Biso mean: 24.581 Å2 / Biso min: 7.04 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.81→113.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2202 0 1 212 2415
Biso mean--23.44 30.27 -
Num. residues----290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132255
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172074
X-RAY DIFFRACTIONr_angle_refined_deg1.891.633073
X-RAY DIFFRACTIONr_angle_other_deg1.4511.5714774
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6015291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.79320.781128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.94115340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.391522
X-RAY DIFFRACTIONr_chiral_restr0.0790.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022618
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02504
LS refinement shellResolution: 1.81→1.855 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.293 11 -
Rwork0.327 170 -
obs--5.61 %

+
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