[English] 日本語
Yorodumi
- PDB-4nay: Crystal Structure of FosB from Staphylococcus aureus with Zn and ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nay
TitleCrystal Structure of FosB from Staphylococcus aureus with Zn and Sulfate at 1.42 Angstrom Resolution - SAD Phasing
ComponentsMetallothiol transferase FosB
KeywordsTRANSFERASE / Bacillithiol-S-transferase
Function / homology
Function and homology information


Transferases; Transferring alkyl or aryl groups, other than methyl groups / transferase activity, transferring alkyl or aryl (other than methyl) groups / response to antibiotic / magnesium ion binding / cytoplasm
Similarity search - Function
Metallothiol transferase FosB / : / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta
Similarity search - Domain/homology
Metallothiol transferase FosB
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.42 Å
AuthorsThompson, M.K. / Goodman, M.C. / Jagessar, K. / Harp, J. / Keithly, M.E. / Cook, P.D. / Armstrong, R.N.
CitationJournal: Biochemistry / Year: 2014
Title: Structure and Function of the Genomically Encoded Fosfomycin Resistance Enzyme, FosB, from Staphylococcus aureus.
Authors: Thompson, M.K. / Keithly, M.E. / Goodman, M.C. / Hammer, N.D. / Cook, P.D. / Jagessar, K.L. / Harp, J. / Skaar, E.P. / Armstrong, R.N.
History
DepositionOct 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Structure summary
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Metallothiol transferase FosB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8585
Polymers17,5051
Non-polymers3544
Water1,802100
1
A: Metallothiol transferase FosB
hetero molecules

A: Metallothiol transferase FosB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,71710
Polymers35,0102
Non-polymers7078
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area6580 Å2
ΔGint-185 kcal/mol
Surface area12670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.495, 62.905, 44.912
Angle α, β, γ (deg.)90.000, 121.910, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

21A-306-

HOH

31A-363-

HOH

-
Components

#1: Protein Metallothiol transferase FosB / Fosfomycin resistance protein


Mass: 17504.869 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: N315 / Gene: fosB, SA2124 / Plasmid: pET20 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P60864, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.14 Å3/Da / Density % sol: 42.54 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 3350, Ammonium Sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.2823 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2823 Å / Relative weight: 1
ReflectionResolution: 1.42→50 Å / Num. obs: 27859 / % possible obs: 99.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.052 / Χ2: 1.73 / Net I/σ(I): 50.83
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.42-1.4460.40213670.7391100
1.44-1.476.30.37814070.7971100
1.47-1.56.80.32713770.8251100
1.5-1.5370.28813920.8711100
1.53-1.567.10.25313880.9551100
1.56-1.67.20.20213850.9841100
1.6-1.647.30.17213891.0781100
1.64-1.687.20.15213861.1631100
1.68-1.737.20.13213911.3041100
1.73-1.797.30.1213971.531100
1.79-1.857.30.09713981.5511100
1.85-1.937.40.07913931.7241100
1.93-2.017.40.0713891.9591100
2.01-2.127.40.06413742.1811100
2.12-2.257.30.06214082.6681100
2.25-2.437.40.05813902.7781100
2.43-2.677.40.05113962.7861100
2.67-3.067.40.04414022.811100
3.06-3.857.30.03614082.6361100
3.85-506.90.03314222.679198.7

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.42→40.56 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.966 / WRfactor Rfree: 0.1756 / WRfactor Rwork: 0.1355 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.9231 / SU B: 1.513 / SU ML: 0.027 / SU R Cruickshank DPI: 0.0534 / SU Rfree: 0.0521 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1664 1397 5 %RANDOM
Rwork0.1295 ---
obs0.1314 27859 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.34 Å2 / Biso mean: 19.2652 Å2 / Biso min: 8.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20.14 Å2
2--0.14 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.42→40.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1081 0 16 100 1197
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.021176
X-RAY DIFFRACTIONr_angle_refined_deg2.2811.9331603
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1035140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.83423.65163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.88715199
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.063156
X-RAY DIFFRACTIONr_chiral_restr0.1690.2173
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02902
X-RAY DIFFRACTIONr_rigid_bond_restr9.30431176
X-RAY DIFFRACTIONr_sphericity_free33.496533
X-RAY DIFFRACTIONr_sphericity_bonded15.12151211
LS refinement shellResolution: 1.42→1.454 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 100 -
Rwork0.212 1756 -
all-1856 -
obs--90.85 %

+
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