[English] 日本語
Yorodumi
- PDB-8g7f: Crystal Structure of FosB from Bacillus cereus with Zinc and 1-hy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8g7f
TitleCrystal Structure of FosB from Bacillus cereus with Zinc and 1-hydroxypropylphosphonic acid
ComponentsMetallothiol transferase FosB
KeywordsTRANSFERASE / FosB / inhibitor / homodimer / bacillithiol-S-transferase
Function / homology
Function and homology information


transferase activity, transferring alkyl or aryl (other than methyl) groups / Transferases; Transferring alkyl or aryl groups, other than methyl groups / response to antibiotic / magnesium ion binding / cytoplasm
Similarity search - Function
Metallothiol transferase FosB / : / 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
Similarity search - Domain/homology
[(1S)-1-hydroxypropyl]phosphonic acid / FORMIC ACID / Metallothiol transferase FosB
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsTravis, S. / Pang, A.H. / Tsodikov, O.V. / Garneau-Tsodikova, S. / Thompson, M.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R15GM148956 United States
CitationJournal: Rsc Med Chem / Year: 2023
Title: Identification and analysis of small molecule inhibitors of FosB from Staphylococcus aureus.
Authors: Travis, S. / Green, K.D. / Thamban Chandrika, N. / Pang, A.H. / Frantom, P.A. / Tsodikov, O.V. / Garneau-Tsodikova, S. / Thompson, M.K.
History
DepositionFeb 16, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Metallothiol transferase FosB
B: Metallothiol transferase FosB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,75914
Polymers32,9772
Non-polymers78212
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7520 Å2
ΔGint-133 kcal/mol
Surface area13040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.200, 68.273, 69.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Metallothiol transferase FosB / Fosfomycin resistance protein


Mass: 16488.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: fosB, BCE_2111 / Production host: Escherichia coli (E. coli)
References: UniProt: Q739M9, Transferases; Transferring alkyl or aryl groups, other than methyl groups

-
Non-polymers , 6 types, 224 molecules

#2: Chemical ChemComp-1JJ / [(1S)-1-hydroxypropyl]phosphonic acid


Mass: 140.075 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H9O4P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


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

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Protein solution (10 mg/mL FosB in 20 mM HEPES buffer, pH 7.5 and 5 mM inhibitor) and reservoir solution (125 mM Mg formate and 20% (w/v) poly(ethylene glycol) (PEG) 3350) were mixed in a ...Details: Protein solution (10 mg/mL FosB in 20 mM HEPES buffer, pH 7.5 and 5 mM inhibitor) and reservoir solution (125 mM Mg formate and 20% (w/v) poly(ethylene glycol) (PEG) 3350) were mixed in a Hampton Research VDX plate with a 1:1 ratio of the solutions. Cryoprotected in its reservoir solution with 20% glycerol added prior to rapid freezing in liquid nitrogen

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. obs: 20106 / % possible obs: 99.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.969 / Χ2: 0.089 / Net I/σ(I): 3.3 / Num. measured all: 147605
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.04-2.083.90.719270.4571100
2.08-2.1140.64818390.4761100
2.11-2.1540.56919010.471100
2.15-2.240.48618960.4611100
2.2-2.2540.46818800.4521100
2.25-2.340.4118830.4811100
2.3-2.353.90.36518850.4721100
2.35-2.423.90.34418830.483199.9
2.42-2.493.90.33418910.4731100
2.49-2.573.80.27818880.496199.9
2.57-2.663.70.24418820.509199.9
2.66-2.773.50.20818790.562199.5
2.77-2.893.50.16318880.539199.8
2.89-3.054.10.15319060.5761100
3.05-3.244.20.12318780.636199.9
3.24-3.494.10.10218830.6561100
3.49-3.844.10.07818720.7211100
3.84-4.3940.05918940.637199.9
4.39-5.543.50.04818890.554199.6
5.54-504.20.04618960.484199.8

-
Processing

Software
NameVersionClassification
REFMAC8.0.008refinement
SCALEPACKdata scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JH6

4jh6


Resolution: 2.04→47.27 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.928 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21492 1028 5.1 %RANDOM
Rwork0.16136 ---
obs0.16395 19077 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.595 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å2-0 Å2
2---0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.04→47.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2324 0 41 212 2577
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132437
X-RAY DIFFRACTIONr_bond_other_d0.0340.0152201
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.6453282
X-RAY DIFFRACTIONr_angle_other_deg2.2611.5845063
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4915280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.91922.317164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35415422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6441519
X-RAY DIFFRACTIONr_chiral_restr0.0730.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022781
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02617
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3711.9491114
X-RAY DIFFRACTIONr_mcbond_other1.371.9511115
X-RAY DIFFRACTIONr_mcangle_it2.0462.9151393
X-RAY DIFFRACTIONr_mcangle_other2.0452.9161394
X-RAY DIFFRACTIONr_scbond_it2.122.2891323
X-RAY DIFFRACTIONr_scbond_other2.1042.281318
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4123.3021889
X-RAY DIFFRACTIONr_long_range_B_refined4.89423.512766
X-RAY DIFFRACTIONr_long_range_B_other4.79223.1852715
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.041→2.094 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.213 69 -
Rwork0.225 1381 -
obs--99.66 %

+
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