[English] 日本語
Yorodumi
- PDB-5wep: Crystal structure of fosfomycin resistance protein FosA3 with inh... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wep
TitleCrystal structure of fosfomycin resistance protein FosA3 with inhibitor (ANY1) bound
ComponentsFosA3
Keywordstransferase/transferase inhibitor / fosfomycin / FosA / FosA3 / glutathione S-transferase / ANY1 / TRANSFERASE / transferase-transferase inhibitor complex
Function / homology
Function and homology information


transferase activity
Similarity search - Function
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
Chem-A81 / FosA family fosfomycin resistance glutathione transferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.502 Å
AuthorsKlontz, E.H. / Sundberg, E.J.
CitationJournal: Antimicrob. Agents Chemother. / Year: 2019
Title: Small-Molecule Inhibitor of FosA Expands Fosfomycin Activity to Multidrug-Resistant Gram-Negative Pathogens.
Authors: Tomich, A.D. / Klontz, E.H. / Deredge, D. / Barnard, J.P. / McElheny, C.L. / Eshbach, M.L. / Weisz, O.A. / Wintrode, P. / Doi, Y. / Sundberg, E.J. / Sluis-Cremer, N.
History
DepositionJul 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 13, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc / Item: _citation.journal_volume / _citation.title
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FosA3
B: FosA3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6976
Polymers32,4922
Non-polymers1,2054
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, FosA3 shares high sequence identity with other FosA enzymes known to be homodimers.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-117 kcal/mol
Surface area12470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.181, 73.181, 123.818
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 1:2 or (resid 3 and (name...
21(chain B and ((resid 1 and (name N or name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETLEULEU(chain A and (resseq 1:2 or (resid 3 and (name...AA1 - 21 - 2
12GLNGLNGLNGLN(chain A and (resseq 1:2 or (resid 3 and (name...AA33
13METMETASPASP(chain A and (resseq 1:2 or (resid 3 and (name...AA1 - 1381 - 138
14METMETASPASP(chain A and (resseq 1:2 or (resid 3 and (name...AA1 - 1381 - 138
15METMETASPASP(chain A and (resseq 1:2 or (resid 3 and (name...AA1 - 1381 - 138
21METMETMETMET(chain B and ((resid 1 and (name N or name...BB11
22METMETPHEPHE(chain B and ((resid 1 and (name N or name...BB1 - 1371 - 137
23METMETPHEPHE(chain B and ((resid 1 and (name N or name...BB1 - 1371 - 137
24METMETPHEPHE(chain B and ((resid 1 and (name N or name...BB1 - 1371 - 137
25METMETPHEPHE(chain B and ((resid 1 and (name N or name...BB1 - 1371 - 137

-
Components

#1: Protein FosA3 / Fosfomycin resistance protein / Fosfomycin resistance protein FosA / Fosfomycin resistance protein ...Fosfomycin resistance protein / Fosfomycin resistance protein FosA / Fosfomycin resistance protein FosA3 / FosA3 / Glutathione transferase / Glutathione transferase FosA


Mass: 16246.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: fosA3, BJJ90_27535, BJJ90_28665, BK248_24890, BK251_28530, BK292_28610, BK334_27385, BK337_26185, BK373_27910, BK375_28485, BK383_28445, BK400_25020, pCTXM123_C0996_13, pEC012_00045, pHN7A8_014, pHNFP460_053
Production host: Escherichia coli (E. coli) / References: UniProt: D7UQM0
#2: Chemical ChemComp-A81 / 6,6'-(4-nitro-1H-pyrazole-3,5-diyl)bis(3-bromopyrazolo[1,5-a]pyrimidin-2(1H)-one)


Mass: 537.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H7Br2N9O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: Protein solution: 12 mg/ml FosA3 6mM MnCl2 2.5mM ANY1 100mM KCl Centrifuge 19,150 for 10 min. Combine 250nL supernatant with 250nL mother liquor (20% PEG3350, 200mM Magnesium formate) in ...Details: Protein solution: 12 mg/ml FosA3 6mM MnCl2 2.5mM ANY1 100mM KCl Centrifuge 19,150 for 10 min. Combine 250nL supernatant with 250nL mother liquor (20% PEG3350, 200mM Magnesium formate) in sitting drops. Crystals appeared after 1 week.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332, 0.9201
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.03321
20.92011
ReflectionResolution: 3.5→28.933 Å / Num. obs: 4378 / % possible obs: 96.4 % / Redundancy: 5.7 % / Biso Wilson estimate: 125.75 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.037 / Rrim(I) all: 0.091 / Net I/σ(I): 14.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
3.5-3.845.40.7170.7920.3280.79194.3
8.58-28.934.90.0360.9980.0170.0491.4

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHASER1.10.1_2155phasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VB0

5vb0


Resolution: 3.502→28.933 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.2
RfactorNum. reflection% reflection
Rfree0.2586 222 5.08 %
Rwork0.2139 --
obs0.2162 4368 95.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 186.99 Å2 / Biso mean: 123.1448 Å2 / Biso min: 83.34 Å2
Refinement stepCycle: final / Resolution: 3.502→28.933 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1996 0 62 0 2058
Biso mean--118.56 --
Num. residues----271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032119
X-RAY DIFFRACTIONf_angle_d0.6782907
X-RAY DIFFRACTIONf_chiral_restr0.038311
X-RAY DIFFRACTIONf_plane_restr0.005368
X-RAY DIFFRACTIONf_dihedral_angle_d11.2571173
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1064X-RAY DIFFRACTION9.757TORSIONAL
12B1064X-RAY DIFFRACTION9.757TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2 / % reflection obs: 95 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.5019-4.40950.33541100.270619912101
4.4095-28.93440.23171120.193321552267

+
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://pdbjlvh1.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