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- PDB-5vb0: Crystal structure of fosfomycin resistance protein FosA3 -

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Basic information

Entry
Database: PDB / ID: 5vb0
TitleCrystal structure of fosfomycin resistance protein FosA3
ComponentsFosfomycin resistance protein FosA3
KeywordsTRANSFERASE / FosA / FosA3 / fosfomycin / glutathione transferase
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
: / NICKEL (II) ION / Glutathione transferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.689 Å
AuthorsKlontz, E. / Guenther, S. / Silverstein, Z. / Sundberg, E.
CitationJournal: Antimicrob. Agents Chemother. / Year: 2017
Title: Structure and Dynamics of FosA-Mediated Fosfomycin Resistance in Klebsiella pneumoniae and Escherichia coli.
Authors: Klontz, E.H. / Tomich, A.D. / Gunther, S. / Lemkul, J.A. / Deredge, D. / Silverstein, Z. / Shaw, J.F. / McElheny, C. / Doi, Y. / Wintrode, P.L. / MacKerell, A.D. / Sluis-Cremer, N. / Sundberg, E.J.
History
DepositionMar 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: 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_author.name
Revision 1.2Nov 8, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name
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 / 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 / _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_asym_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_conn.ptnr2_label_seq_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: Fosfomycin resistance protein FosA3
B: Fosfomycin resistance protein FosA3
C: Fosfomycin resistance protein FosA3
D: Fosfomycin resistance protein FosA3
E: Fosfomycin resistance protein FosA3
F: Fosfomycin resistance protein FosA3
G: Fosfomycin resistance protein FosA3
H: Fosfomycin resistance protein FosA3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,76122
Polymers129,9708
Non-polymers79214
Water00
1
A: Fosfomycin resistance protein FosA3
B: Fosfomycin resistance protein FosA3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7206
Polymers32,4922
Non-polymers2274
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
ΔGint-50 kcal/mol
Surface area13090 Å2
MethodPISA
2
C: Fosfomycin resistance protein FosA3
D: Fosfomycin resistance protein FosA3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7206
Polymers32,4922
Non-polymers2274
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-53 kcal/mol
Surface area13200 Å2
MethodPISA
3
E: Fosfomycin resistance protein FosA3
F: Fosfomycin resistance protein FosA3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6615
Polymers32,4922
Non-polymers1693
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-48 kcal/mol
Surface area13040 Å2
MethodPISA
4
G: Fosfomycin resistance protein FosA3
H: Fosfomycin resistance protein FosA3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6615
Polymers32,4922
Non-polymers1693
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-50 kcal/mol
Surface area13020 Å2
MethodPISA
5
A: Fosfomycin resistance protein FosA3
B: Fosfomycin resistance protein FosA3
C: Fosfomycin resistance protein FosA3
D: Fosfomycin resistance protein FosA3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,43912
Polymers64,9854
Non-polymers4558
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14420 Å2
ΔGint-116 kcal/mol
Surface area23710 Å2
MethodPISA
6
E: Fosfomycin resistance protein FosA3
F: Fosfomycin resistance protein FosA3
G: Fosfomycin resistance protein FosA3
H: Fosfomycin resistance protein FosA3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,32210
Polymers64,9854
Non-polymers3376
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14070 Å2
ΔGint-109 kcal/mol
Surface area23810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.608, 87.608, 357.038
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 1:20 or (resid 21 and (name...
21(chain B and (resseq 1:20 or (resid 21 and (name...
31(chain C and (resseq 1:20 or (resid 21 and (name...
41(chain E and (resseq 1:20 or (resid 21 and (name...
51(chain F and (resseq 1:20 or (resid 21 and (name...
61(chain G and (resseq 1:20 or (resid 21 and (name...
71(chain H and (resseq 1:20 or (resid 21 and (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
11METMETALAALA(chain A and (resseq 1:20 or (resid 21 and (name...AA1 - 201 - 20
12PHEPHEPHEPHE(chain A and (resseq 1:20 or (resid 21 and (name...AA2121
13METMETHISHIS(chain A and (resseq 1:20 or (resid 21 and (name...AA1 - 1431 - 143
14METMETHISHIS(chain A and (resseq 1:20 or (resid 21 and (name...AA1 - 1431 - 143
15METMETHISHIS(chain A and (resseq 1:20 or (resid 21 and (name...AA1 - 1431 - 143
16METMETHISHIS(chain A and (resseq 1:20 or (resid 21 and (name...AA1 - 1431 - 143
17METMETHISHIS(chain A and (resseq 1:20 or (resid 21 and (name...AA1 - 1431 - 143
18METMETHISHIS(chain A and (resseq 1:20 or (resid 21 and (name...AA1 - 1431 - 143
21METMETALAALA(chain B and (resseq 1:20 or (resid 21 and (name...BB1 - 201 - 20
22PHEPHEPHEPHE(chain B and (resseq 1:20 or (resid 21 and (name...BB2121
23METMETASPASP(chain B and (resseq 1:20 or (resid 21 and (name...BB1 - 1381 - 138
24METMETASPASP(chain B and (resseq 1:20 or (resid 21 and (name...BB1 - 1381 - 138
25METMETASPASP(chain B and (resseq 1:20 or (resid 21 and (name...BB1 - 1381 - 138
26METMETASPASP(chain B and (resseq 1:20 or (resid 21 and (name...BB1 - 1381 - 138
27METMETASPASP(chain B and (resseq 1:20 or (resid 21 and (name...BB1 - 1381 - 138
28METMETASPASP(chain B and (resseq 1:20 or (resid 21 and (name...BB1 - 1381 - 138
31METMETALAALA(chain C and (resseq 1:20 or (resid 21 and (name...CC1 - 201 - 20
32PHEPHEPHEPHE(chain C and (resseq 1:20 or (resid 21 and (name...CC2121
33METMETHISHIS(chain C and (resseq 1:20 or (resid 21 and (name...CC1 - 1431 - 143
34METMETHISHIS(chain C and (resseq 1:20 or (resid 21 and (name...CC1 - 1431 - 143
35METMETHISHIS(chain C and (resseq 1:20 or (resid 21 and (name...CC1 - 1431 - 143
36METMETHISHIS(chain C and (resseq 1:20 or (resid 21 and (name...CC1 - 1431 - 143
37METMETHISHIS(chain C and (resseq 1:20 or (resid 21 and (name...CC1 - 1431 - 143
38METMETHISHIS(chain C and (resseq 1:20 or (resid 21 and (name...CC1 - 1431 - 143
41METMETALAALA(chain E and (resseq 1:20 or (resid 21 and (name...EE1 - 201 - 20
42PHEPHEPHEPHE(chain E and (resseq 1:20 or (resid 21 and (name...EE2121
43METMETASPASP(chain E and (resseq 1:20 or (resid 21 and (name...EE1 - 1381 - 138
44METMETASPASP(chain E and (resseq 1:20 or (resid 21 and (name...EE1 - 1381 - 138
45METMETASPASP(chain E and (resseq 1:20 or (resid 21 and (name...EE1 - 1381 - 138
46METMETASPASP(chain E and (resseq 1:20 or (resid 21 and (name...EE1 - 1381 - 138
47METMETASPASP(chain E and (resseq 1:20 or (resid 21 and (name...EE1 - 1381 - 138
48METMETASPASP(chain E and (resseq 1:20 or (resid 21 and (name...EE1 - 1381 - 138
51METMETALAALA(chain F and (resseq 1:20 or (resid 21 and (name...FF1 - 201 - 20
52PHEPHEPHEPHE(chain F and (resseq 1:20 or (resid 21 and (name...FF2121
53METMETHISHIS(chain F and (resseq 1:20 or (resid 21 and (name...FF1 - 1431 - 143
54METMETHISHIS(chain F and (resseq 1:20 or (resid 21 and (name...FF1 - 1431 - 143
55METMETHISHIS(chain F and (resseq 1:20 or (resid 21 and (name...FF1 - 1431 - 143
56METMETHISHIS(chain F and (resseq 1:20 or (resid 21 and (name...FF1 - 1431 - 143
57METMETHISHIS(chain F and (resseq 1:20 or (resid 21 and (name...FF1 - 1431 - 143
58METMETHISHIS(chain F and (resseq 1:20 or (resid 21 and (name...FF1 - 1431 - 143
61METMETALAALA(chain G and (resseq 1:20 or (resid 21 and (name...GG1 - 201 - 20
62PHEPHEPHEPHE(chain G and (resseq 1:20 or (resid 21 and (name...GG2121
63METMETPHEPHE(chain G and (resseq 1:20 or (resid 21 and (name...GG1 - 1371 - 137
64METMETPHEPHE(chain G and (resseq 1:20 or (resid 21 and (name...GG1 - 1371 - 137
65METMETPHEPHE(chain G and (resseq 1:20 or (resid 21 and (name...GG1 - 1371 - 137
66METMETPHEPHE(chain G and (resseq 1:20 or (resid 21 and (name...GG1 - 1371 - 137
67METMETPHEPHE(chain G and (resseq 1:20 or (resid 21 and (name...GG1 - 1371 - 137
68METMETPHEPHE(chain G and (resseq 1:20 or (resid 21 and (name...GG1 - 1371 - 137
71METMETALAALA(chain H and (resseq 1:20 or (resid 21 and (name...HH1 - 201 - 20
72PHEPHEPHEPHE(chain H and (resseq 1:20 or (resid 21 and (name...HH2121
73METMETHISHIS(chain H and (resseq 1:20 or (resid 21 and (name...HH1 - 1431 - 143
74METMETHISHIS(chain H and (resseq 1:20 or (resid 21 and (name...HH1 - 1431 - 143
75METMETHISHIS(chain H and (resseq 1:20 or (resid 21 and (name...HH1 - 1431 - 143
76METMETHISHIS(chain H and (resseq 1:20 or (resid 21 and (name...HH1 - 1431 - 143
77METMETHISHIS(chain H and (resseq 1:20 or (resid 21 and (name...HH1 - 1431 - 143
78METMETHISHIS(chain H and (resseq 1:20 or (resid 21 and (name...HH1 - 1431 - 143

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Components

#1: Protein
Fosfomycin resistance 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.: 8
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, BK259_26930, BK292_28610, BK334_27385, BK337_26185, BK373_27910, BK375_28485, BK383_28445, BK400_25020, pCTXM123_C0996_13, pEC012_ ...Gene: fosA3, BJJ90_27535, BJJ90_28665, BK248_24890, BK251_28530, BK259_26930, 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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: Mn
#3: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: Ni

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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: 2.64 Å3/Da / Density % sol: 53.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.95
Details: FosA3, protein was concentrated to 9mg/ml and combined with 6mM fosfomycin and 6mM MnCl2. The solution was centrifuged (13500 rpm for 5 minutes) and 250nL of the supernatant was combined ...Details: FosA3, protein was concentrated to 9mg/ml and combined with 6mM fosfomycin and 6mM MnCl2. The solution was centrifuged (13500 rpm for 5 minutes) and 250nL of the supernatant was combined with 250nL of mother liquor (7% ethylene glycol, 7% PEG6000, 0.1M HEPES pH 6.95) in sitting drops

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.68856→29.7532 Å / Num. obs: 39913 / % possible obs: 99.9 % / Redundancy: 9.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.028 / Rrim(I) all: 0.085 / Net I/σ(I): 20.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2.69-2.89.70.6470.9580.2180.68399.7
9.69-29.757.80.030.9990.0110.03296.8

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V3D

5v3d


Resolution: 2.689→29.753 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.5
RfactorNum. reflection% reflection
Rfree0.2491 -4.79 %
Rwork0.205 --
obs0.2071 39869 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 147.23 Å2 / Biso mean: 65.6076 Å2 / Biso min: 32.68 Å2
Refinement stepCycle: final / Resolution: 2.689→29.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8586 0 14 0 8600
Biso mean--70.37 --
Num. residues----1091
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068823
X-RAY DIFFRACTIONf_angle_d0.97311972
X-RAY DIFFRACTIONf_chiral_restr0.0541257
X-RAY DIFFRACTIONf_plane_restr0.0061551
X-RAY DIFFRACTIONf_dihedral_angle_d13.3845104
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3693X-RAY DIFFRACTION7.918TORSIONAL
12B3693X-RAY DIFFRACTION7.918TORSIONAL
13C3693X-RAY DIFFRACTION7.918TORSIONAL
14E3693X-RAY DIFFRACTION7.918TORSIONAL
15F3693X-RAY DIFFRACTION7.918TORSIONAL
16G3693X-RAY DIFFRACTION7.918TORSIONAL
17H3693X-RAY DIFFRACTION7.918TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6886-2.72540.35931340.31282783291798
2.7254-2.76430.361510.286927762927100
2.7643-2.80550.33011480.289228603008100
2.8055-2.84930.36211220.288727742896100
2.8493-2.8960.30651400.279928102950100
2.896-2.94590.36591480.271528112959100
2.9459-2.99940.29941580.245827542912100
2.9994-3.0570.31671610.24828012962100
3.057-3.11940.3641410.251928252966100
3.1194-3.18710.30911550.239927462901100
3.1871-3.26120.29471410.246428803021100
3.2612-3.34260.35891260.252428162942100
3.3426-3.43290.26371460.242827722918100
3.4329-3.53370.26851040.229128632967100
3.5337-3.64760.27461480.229228312979100
3.6476-3.77770.28381300.20427802910100
3.7777-3.92860.23281180.206828172935100
3.9286-4.1070.23021360.183928332969100
4.107-4.32290.20811100.172928272937100
4.3229-4.59290.21551500.159228232973100
4.5929-4.9460.16011320.161128082940100
4.946-5.4410.2151630.172128022965100
5.441-6.2220.22451740.193827712945100
6.222-7.81550.25731340.198628202954100
7.8155-29.7550.17931620.161627792941100

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