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- PDB-5wep: Crystal structure of fosfomycin resistance protein FosA3 with inh... -

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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


glutathione transferase / transferase activity / metal ion binding
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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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.

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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

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Phasing

PhasingMethod: molecular replacement

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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

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