[English] 日本語
Yorodumi
- PDB-5u83: Crystal structure of a MerB-trimethytin complex. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5u83
TitleCrystal structure of a MerB-trimethytin complex.
ComponentsAlkylmercury lyase
KeywordsLYASE / METAL BINDING PROTEIN / Bacterial Proteins / Cysteine / Escherichia coli / Lyases / Mercury / trimethyltin
Function / homology
Function and homology information


alkylmercury lyase / alkylmercury lyase activity / response to mercury ion
Similarity search - Function
Beta-Lactamase - #410 / Alkylmercury lyase, helix-turn-helix domain / Helix-turn-helix domain of alkylmercury lyase / Alkylmercury lyase / : / Alkylmercury lyase / Beta-Lactamase / Winged helix DNA-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / BROMIDE ION / Trimethyltin chloride / Alkylmercury lyase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.609 Å
AuthorsWahba, H.M. / Stevenson, M. / Mansour, A. / Sygusch, J. / Wilcox, D.E. / Omichinski, J.G.
Funding support Canada, United States, 2items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
National Science Foundation (NSF, United States) United States
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Structural and Biochemical Characterization of Organotin and Organolead Compounds Binding to the Organomercurial Lyase MerB Provide New Insights into Its Mechanism of Carbon-Metal Bond Cleavage.
Authors: Wahba, H.M. / Stevenson, M.J. / Mansour, A. / Sygusch, J. / Wilcox, D.E. / Omichinski, J.G.
History
DepositionDec 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2Mar 28, 2018Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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: Alkylmercury lyase
B: Alkylmercury lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7137
Polymers46,1172
Non-polymers5975
Water8,377465
1
A: Alkylmercury lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3173
Polymers23,0581
Non-polymers2582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alkylmercury lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3964
Polymers23,0581
Non-polymers3383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.540, 89.072, 54.526
Angle α, β, γ (deg.)90.000, 98.650, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Alkylmercury lyase / Organomercurial lyase


Mass: 23058.268 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: merB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P77072, alkylmercury lyase
#2: Chemical ChemComp-ZN8 / Trimethyltin chloride


Mass: 199.267 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H9ClSn
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / 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: 2.01 Å3/Da / Density % sol: 38.69 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 23 % polyethylene glycol 2000 MME, 0.2 M sodium acetate pH 5.5, 0.2 M potassium bromide. Before flash freezing, the same precipitant was used except 25% polyethylene glycol MME was used as a cryo-protectant.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9724 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jan 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 45723 / % possible obs: 97 % / Redundancy: 3.5 % / Net I/σ(I): 17.92

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F0P

3f0p


Resolution: 1.609→33.586 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 19.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2011 3869 4.37 %
Rwork0.159 84621 -
obs0.1608 88490 95.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.94 Å2 / Biso mean: 24.7003 Å2 / Biso min: 6.57 Å2
Refinement stepCycle: final / Resolution: 1.609→33.586 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3178 0 23 465 3666
Biso mean--22.49 34 -
Num. residues----416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113287
X-RAY DIFFRACTIONf_angle_d1.4014485
X-RAY DIFFRACTIONf_chiral_restr0.052528
X-RAY DIFFRACTIONf_plane_restr0.007577
X-RAY DIFFRACTIONf_dihedral_angle_d13.61173
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6095-1.62910.2727930.24192064215766
1.6291-1.64970.27751060.24682274238071
1.6497-1.67140.27071100.22652484259478
1.6714-1.69430.29421220.20562670279285
1.6943-1.71850.22311280.20362805293388
1.7185-1.74420.21831340.20242945307992
1.7442-1.77140.24241430.20223126326998
1.7714-1.80050.24541410.1953105324698
1.8005-1.83150.21011480.18543205335399
1.8315-1.86480.22461450.17233106325199
1.8648-1.90070.24551430.16873128327199
1.9007-1.93950.20341490.15643184333399
1.9395-1.98160.19671410.158831373278100
1.9816-2.02770.16081450.152131993344100
2.0277-2.07840.18091430.15731153258100
2.0784-2.13460.21421450.160732033348100
2.1346-2.19740.21881480.152231603308100
2.1974-2.26830.2171420.147832163358100
2.2683-2.34940.19461440.145431123256100
2.3494-2.44340.22791410.154531793320100
2.4434-2.55460.19131480.153831873335100
2.5546-2.68920.18141430.144831323275100
2.6892-2.85760.17541500.157531873337100
2.8576-3.07810.20111430.162931473290100
3.0781-3.38760.17591470.15543163331099
3.3876-3.87720.20551470.146131873334100
3.8772-4.88250.1951400.134531463286100
4.8825-33.59360.18271400.16693055319596
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4718-0.1809-0.00310.45430.17181.137-0.02050.0023-0.02180.0902-0.02070.02890.02470.0014-0.00590.0869-0.0028-0.00150.0637-0.00410.090111.2255-2.831635.5243
20.2803-0.00380.08130.6832-0.14190.83890.0380.0287-0.0234-0.0077-0.07880.00820.0072-0.0167-0.03980.06630.00750.00230.11070.00850.10481.0381-6.25210.6033
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA1 - 208
2X-RAY DIFFRACTION2chain BB1 - 208

+
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