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- PDB-5wew: Crystal structure of Klebsiella pneumoniae fosfomycin resistance ... -

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Basic information

Entry
Database: PDB / ID: 5wew
TitleCrystal structure of Klebsiella pneumoniae fosfomycin resistance protein (FosAKP) with inhibitor (ANY1) bound
ComponentsFosfomycin resistance protein
Keywordstransferase/transferase inhibitor / fosfomycin / FosA / FosAKP / glutathione S-transferase / ANY1 / TRANSFERASE / transferase-transferase inhibitor complex
Function / homology
Function and homology information


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 / : / Fosfomycin resistance protein
Similarity search - Component
Biological speciesKlebsiella pneumoniae 30684/NJST258_2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.178 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_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
B: Fosfomycin resistance protein
C: Fosfomycin resistance protein
D: Fosfomycin resistance protein
E: Fosfomycin resistance protein
F: Fosfomycin resistance protein
G: Fosfomycin resistance protein
H: Fosfomycin resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,21124
Polymers130,4758
Non-polymers4,73616
Water0
1
A: Fosfomycin resistance protein
B: Fosfomycin resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8036
Polymers32,6192
Non-polymers1,1844
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-48 kcal/mol
Surface area13110 Å2
MethodPISA
2
C: Fosfomycin resistance protein
D: Fosfomycin resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8036
Polymers32,6192
Non-polymers1,1844
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-47 kcal/mol
Surface area12410 Å2
MethodPISA
3
E: Fosfomycin resistance protein
F: Fosfomycin resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3407
Polymers32,6192
Non-polymers1,7215
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-49 kcal/mol
Surface area12100 Å2
MethodPISA
4
G: Fosfomycin resistance protein
H: Fosfomycin resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2665
Polymers32,6192
Non-polymers6473
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5600 Å2
ΔGint-43 kcal/mol
Surface area13290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.399, 197.615, 117.027
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 1 and (name N or name...
21(chain B and ((resid 1 and (name N or name...
31(chain C and ((resid 1 and (name N or name...
41(chain D and ((resid 1 and (name N or name...
51(chain F and (resseq 1:20 or (resid 21 and (name...
61(chain G and ((resid 1 and (name N or name...
71(chain H 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
11METMETMETMET(chain A and ((resid 1 and (name N or name...AA11
12METMETHISHIS(chain A and ((resid 1 and (name N or name...AA1 - 1401 - 140
13METMETHISHIS(chain A and ((resid 1 and (name N or name...AA1 - 1401 - 140
14METMETHISHIS(chain A and ((resid 1 and (name N or name...AA1 - 1401 - 140
15METMETHISHIS(chain A and ((resid 1 and (name N or name...AA1 - 1401 - 140
21METMETMETMET(chain B and ((resid 1 and (name N or name...BB11
22METMETHISHIS(chain B and ((resid 1 and (name N or name...BB1 - 1411 - 141
23METMETHISHIS(chain B and ((resid 1 and (name N or name...BB1 - 1411 - 141
24METMETHISHIS(chain B and ((resid 1 and (name N or name...BB1 - 1411 - 141
25METMETHISHIS(chain B and ((resid 1 and (name N or name...BB1 - 1411 - 141
31METMETMETMET(chain C and ((resid 1 and (name N or name...CC11
32METMETGLUGLU(chain C and ((resid 1 and (name N or name...CC1 - 1381 - 138
33METMETGLUGLU(chain C and ((resid 1 and (name N or name...CC1 - 1381 - 138
34METMETGLUGLU(chain C and ((resid 1 and (name N or name...CC1 - 1381 - 138
35METMETGLUGLU(chain C and ((resid 1 and (name N or name...CC1 - 1381 - 138
41METMETMETMET(chain D and ((resid 1 and (name N or name...DD11
42METMETPHEPHE(chain D and ((resid 1 and (name N or name...DD1 - 1371 - 137
43METMETPHEPHE(chain D and ((resid 1 and (name N or name...DD1 - 1371 - 137
44METMETPHEPHE(chain D and ((resid 1 and (name N or name...DD1 - 1371 - 137
45METMETPHEPHE(chain D and ((resid 1 and (name N or name...DD1 - 1371 - 137
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
53METMETPHEPHE(chain F and (resseq 1:20 or (resid 21 and (name...FF1 - 1371 - 137
54METMETPHEPHE(chain F and (resseq 1:20 or (resid 21 and (name...FF1 - 1371 - 137
55METMETPHEPHE(chain F and (resseq 1:20 or (resid 21 and (name...FF1 - 1371 - 137
56METMETPHEPHE(chain F and (resseq 1:20 or (resid 21 and (name...FF1 - 1371 - 137
57METMETPHEPHE(chain F and (resseq 1:20 or (resid 21 and (name...FF1 - 1371 - 137
58METMETPHEPHE(chain F and (resseq 1:20 or (resid 21 and (name...FF1 - 1371 - 137
59METMETPHEPHE(chain F and (resseq 1:20 or (resid 21 and (name...FF1 - 1371 - 137
510METMETPHEPHE(chain F and (resseq 1:20 or (resid 21 and (name...FF1 - 1371 - 137
61METMETMETMET(chain G and ((resid 1 and (name N or name...GG11
62METMETHISHIS(chain G and ((resid 1 and (name N or name...GG1 - 1411 - 141
63METMETHISHIS(chain G and ((resid 1 and (name N or name...GG1 - 1411 - 141
64METMETHISHIS(chain G and ((resid 1 and (name N or name...GG1 - 1411 - 141
65METMETHISHIS(chain G and ((resid 1 and (name N or name...GG1 - 1411 - 141
71METMETMETMET(chain H and ((resid 1 and (name N or name...HH11
72METMETHISHIS(chain H and ((resid 1 and (name N or name...HH1 - 1411 - 141
73METMETHISHIS(chain H and ((resid 1 and (name N or name...HH1 - 1411 - 141
74METMETHISHIS(chain H and ((resid 1 and (name N or name...HH1 - 1411 - 141
75METMETHISHIS(chain H and ((resid 1 and (name N or name...HH1 - 1411 - 141

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Components

#1: Protein
Fosfomycin resistance protein


Mass: 16309.347 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae 30684/NJST258_2 (bacteria)
Gene: KPNJ2_04803 / Production host: Escherichia coli (E. coli) / References: UniProt: W8UNW6
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#3: 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.: 8 / Source method: obtained synthetically / Formula: C15H7Br2N9O4

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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: 2.67 Å3/Da / Density % sol: 53.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Protein stock: 12mg/ml FosAKP 6mM MnCl2 2.5mM ANY1 100mM KCl Centrifuge 19,150 x g for 10 min then take 1uL supernatant and combine with 1uL mother liquor (0.02M CaCl2, 0.1M sodium acetate ...Details: Protein stock: 12mg/ml FosAKP 6mM MnCl2 2.5mM ANY1 100mM KCl Centrifuge 19,150 x g for 10 min then take 1uL supernatant and combine with 1uL mother liquor (0.02M CaCl2, 0.1M sodium acetate pH 4.6, 30% MPD) in hanging drops.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.178→39.01 Å / Num. obs: 21310 / % possible obs: 90 % / Redundancy: 3.8 % / Biso Wilson estimate: 47.54 Å2 / CC1/2: 0.955 / Rmerge(I) obs: 0.326 / Rpim(I) all: 0.171 / Rrim(I) all: 0.371 / Net I/σ(I): 4.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
3.18-3.43.80.9680.5770.5061.10291.6
8.99-39.0140.0670.9970.0350.07687.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
PHASER1.10.1_2155phasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V3D

5v3d


Resolution: 3.178→37.748 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.82
RfactorNum. reflection% reflection
Rfree0.2621 1105 5.2 %
Rwork0.2209 --
obs0.2229 21263 89.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 119.02 Å2 / Biso mean: 41.8813 Å2 / Biso min: 16.32 Å2
Refinement stepCycle: final / Resolution: 3.178→37.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8406 0 248 0 8654
Biso mean--41.91 --
Num. residues----1094
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028922
X-RAY DIFFRACTIONf_angle_d0.49212195
X-RAY DIFFRACTIONf_chiral_restr0.041276
X-RAY DIFFRACTIONf_plane_restr0.0031545
X-RAY DIFFRACTIONf_dihedral_angle_d8.7265017
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4327X-RAY DIFFRACTION1.568TORSIONAL
12B4327X-RAY DIFFRACTION1.568TORSIONAL
13C4327X-RAY DIFFRACTION1.568TORSIONAL
14D4327X-RAY DIFFRACTION1.568TORSIONAL
15F4327X-RAY DIFFRACTION1.568TORSIONAL
16G4327X-RAY DIFFRACTION1.568TORSIONAL
17H4327X-RAY DIFFRACTION1.568TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1778-3.32230.31621280.28932524265290
3.3223-3.49740.31141310.2672567269892
3.4974-3.71630.29621610.23212526268791
3.7163-4.00290.26581610.22842523268490
4.0029-4.40520.24611370.19782479261689
4.4052-5.04140.21211310.17822536266789
5.0414-6.34670.29111340.2152483261787
6.3467-37.7510.21311220.21262520264285

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