[English] 日本語
Yorodumi
- PDB-3f2f: Crystal structure of the mercury-bound form of MerB, the Organome... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3f2f
TitleCrystal structure of the mercury-bound form of MerB, the Organomercurial Lyase involved in a bacterial mercury resistance system
ComponentsAlkylmercury lyase
KeywordsLYASE / merb / organomercurial lyase / alkylmercury lyase / mercury resistance / Mercuric resistance / Plasmid
Function / homology
Function and homology information


alkylmercury lyase / alkylmercury lyase activity / organomercury catabolic process / 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
BROMIDE ION / : / Alkylmercury lyase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsLafrance-Vanasse, J. / Lefebvre, M. / Di Lello, P. / Sygusch, J. / Omichinski, J.G.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Crystal Structures of the Organomercurial Lyase MerB in Its Free and Mercury-bound Forms: INSIGHTS INTO THE MECHANISM OF METHYLMERCURY DEGRADATION
Authors: Lafrance-Vanasse, J. / Lefebvre, M. / Di Lello, P. / Sygusch, J. / Omichinski, J.G.
History
DepositionOct 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

-
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)46,5985
Polymers46,1172
Non-polymers4813
Water4,071226
1
A: Alkylmercury lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2592
Polymers23,0581
Non-polymers2011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alkylmercury lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3393
Polymers23,0581
Non-polymers2802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.108, 88.836, 51.584
Angle α, β, γ (deg.)90.00, 100.56, 90.00
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 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3) / References: UniProt: P77072, alkylmercury lyase
#2: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-BR / BROMIDE ION / Bromide


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


Mass: 18.015 Da / Num. of mol.: 226 / 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: 1.86 Å3/Da / Density % sol: 33.92 %
Crystal growTemperature: 296 K / pH: 5.5
Details: 20% polyethylene glycol 2000 MME, 0.2 M sodium acetate pH 5.5, 0.2 M potassium bromide, VAPOR DIFFUSION, HANGING DROP, temperature 296K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1.0084
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 4, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0084 Å / Relative weight: 1
ReflectionResolution: 1.97→25 Å / Num. obs: 45866 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 15.04 Å2 / Rsym value: 0.105
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 4.7 / Rsym value: 0.41 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F0O
Resolution: 1.98→24.38 Å / SU ML: 0.25 / σ(F): 0.02 / Phase error: 20.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.217 3845 8.59 %
Rwork0.173 --
obs0.176 44750 96.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.01 Å2 / ksol: 0.38 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.3841 Å20 Å21.73 Å2
2---0.2542 Å2-0 Å2
3----0.1299 Å2
Refinement stepCycle: LAST / Resolution: 1.98→24.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3096 0 3 226 3325
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d03160
X-RAY DIFFRACTIONf_angle_d0.994309
X-RAY DIFFRACTIONf_dihedral_angle_d15.491115
X-RAY DIFFRACTIONf_chiral_restr0.06511
X-RAY DIFFRACTIONf_plane_restr0552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.00520.20541020.17521137X-RAY DIFFRACTION70
2.0052-2.03160.23341350.16041397X-RAY DIFFRACTION94
2.0316-2.05940.24371390.16521491X-RAY DIFFRACTION94
2.0594-2.08880.23841410.171491X-RAY DIFFRACTION95
2.0888-2.120.21071450.1691507X-RAY DIFFRACTION95
2.12-2.15310.26671390.16441480X-RAY DIFFRACTION95
2.1531-2.18830.2471370.17741461X-RAY DIFFRACTION96
2.1883-2.2260.2121520.16961547X-RAY DIFFRACTION96
2.226-2.26650.23181420.16131471X-RAY DIFFRACTION96
2.2665-2.31010.19481450.15921526X-RAY DIFFRACTION97
2.3101-2.35720.22851430.16691529X-RAY DIFFRACTION97
2.3572-2.40840.22551430.16931516X-RAY DIFFRACTION98
2.4084-2.46440.22551450.17731534X-RAY DIFFRACTION98
2.4644-2.52590.23621430.17951561X-RAY DIFFRACTION97
2.5259-2.59410.22471420.18341514X-RAY DIFFRACTION98
2.5941-2.67040.25771470.17541561X-RAY DIFFRACTION99
2.6704-2.75650.24531380.19261542X-RAY DIFFRACTION99
2.7565-2.85480.25531460.18531551X-RAY DIFFRACTION99
2.8548-2.9690.23251470.18281561X-RAY DIFFRACTION99
2.969-3.10380.21761440.17011556X-RAY DIFFRACTION100
3.1038-3.26710.20241470.16461569X-RAY DIFFRACTION100
3.2671-3.47130.1821490.16271572X-RAY DIFFRACTION100
3.4713-3.73840.19751450.16261554X-RAY DIFFRACTION100
3.7384-4.1130.18241500.15251571X-RAY DIFFRACTION100
4.113-4.70440.19261500.15821588X-RAY DIFFRACTION100
4.7044-5.91310.19371460.17971544X-RAY DIFFRACTION100
5.9131-24.38320.21430.19041574X-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