[English] 日本語
Yorodumi
- PDB-8r37: Klebsiella pneumoniae fosfomycin-resistance protein (FosAKP) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8r37
TitleKlebsiella pneumoniae fosfomycin-resistance protein (FosAKP)
ComponentsFosA family fosfomycin resistance glutathione transferase
KeywordsTRANSFERASE / Antibiotic resistance / Klebsiella pneumoniae / Glutathione / Fosfomycin / metalloenzyme / biosensor
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity
Similarity search - Function
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
FOSFOMYCIN / : / : / L(+)-TARTARIC ACID / FosA family fosfomycin resistance glutathione transferase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsPapageorgiou, A.C. / Varotsou, C. / Labrou, N.E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int J Mol Sci / Year: 2023
Title: Structural Studies of Klebsiella pneumoniae Fosfomycin-Resistance Protein and Its Application for the Development of an Optical Biosensor for Fosfomycin Determination.
Authors: Varotsou, C. / Ataya, F. / Papageorgiou, A.C. / Labrou, N.E.
History
DepositionNov 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: FosA family fosfomycin resistance glutathione transferase
A: FosA family fosfomycin resistance glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,69718
Polymers32,9912
Non-polymers70616
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.620, 47.030, 149.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Protein , 1 types, 2 molecules BA

#1: Protein FosA family fosfomycin resistance glutathione transferase


Mass: 16495.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The last eight C-terminal residues are flexible and not modelled.
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: fosA / Production host: Escherichia coli (E. coli) / References: UniProt: A0A086IRG1

-
Non-polymers , 6 types, 398 molecules

#2: Chemical ChemComp-FCN / FOSFOMYCIN / 1,2-EPOXYPROPYLPHOSPHONIC ACID / Fosfomycin


Mass: 138.059 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O4P / Comment: antibiotic*YM
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.16 Å3/Da / Density % sol: 43.05 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: PEG3350 18% w/v, potassium sodium tartrate 0.2 M, MnCl2 6 mM

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9919 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9919 Å / Relative weight: 1
ReflectionResolution: 1.48→149.2 Å / Num. obs: 48410 / % possible obs: 99.4 % / Redundancy: 9.8 % / Biso Wilson estimate: 21.01 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.089 / Net I/σ(I): 11.8
Reflection shellResolution: 1.48→1.51 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2174 / CC1/2: 0.666 / Rrim(I) all: 1.452 / % possible all: 92.2

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→44.85 Å / SU ML: 0.1838 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.4427
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2057 2304 4.78 %
Rwork0.1731 45939 -
obs0.1746 48243 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.59 Å2
Refinement stepCycle: LAST / Resolution: 1.48→44.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2180 0 32 382 2594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00552285
X-RAY DIFFRACTIONf_angle_d0.91163113
X-RAY DIFFRACTIONf_chiral_restr0.0845333
X-RAY DIFFRACTIONf_plane_restr0.0073404
X-RAY DIFFRACTIONf_dihedral_angle_d9.4323315
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.510.35331330.34282615X-RAY DIFFRACTION91.75
1.51-1.550.33321370.30892755X-RAY DIFFRACTION97.64
1.55-1.590.28661400.25662799X-RAY DIFFRACTION98.46
1.59-1.630.25071370.23252889X-RAY DIFFRACTION99.7
1.63-1.680.24291430.2172850X-RAY DIFFRACTION99.77
1.68-1.730.24991420.21132830X-RAY DIFFRACTION99.8
1.73-1.790.23151450.19762862X-RAY DIFFRACTION99.77
1.79-1.860.24871130.19392899X-RAY DIFFRACTION99.87
1.86-1.950.21621450.17282872X-RAY DIFFRACTION99.8
1.95-2.050.21811760.17592855X-RAY DIFFRACTION99.9
2.05-2.180.21211460.16792876X-RAY DIFFRACTION99.9
2.18-2.350.21271460.17522898X-RAY DIFFRACTION99.93
2.35-2.590.21821440.17992912X-RAY DIFFRACTION99.93
2.59-2.960.20521620.18252929X-RAY DIFFRACTION99.97
2.96-3.730.18611490.14972962X-RAY DIFFRACTION99.97
3.73-44.850.16941460.14813136X-RAY DIFFRACTION99.88

+
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