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- PDB-6c3u: Crystal structure of Klebsiella pneumoniae fosfomycin resistance ... -

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Basic information

Entry
Database: PDB / ID: 6c3u
TitleCrystal structure of Klebsiella pneumoniae fosfomycin resistance protein (FosAKP) with inhibitor (ANY2) bound
ComponentsFosA family fosfomycin resistance glutathione transferase
KeywordsTRANSFERASE/INHIBITOR / fosfomycin / FosA / FosAKP / glutathione S-transferase / ANY2 / TRANSFERASE / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


dioxygenase activity / glutathione transferase / glutathione 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-NY2 / FosA family fosfomycin resistance glutathione transferase / Putative glyoxalase/bleomycin resistance protein/dioxygenase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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
DepositionJan 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 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: FosA family fosfomycin resistance glutathione transferase
B: FosA family fosfomycin resistance glutathione transferase
C: FosA family fosfomycin resistance glutathione transferase
D: FosA family fosfomycin resistance glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,85013
Polymers65,2374
Non-polymers1,6129
Water12,863714
1
A: FosA family fosfomycin resistance glutathione transferase
B: FosA family fosfomycin resistance glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4717
Polymers32,6192
Non-polymers8525
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-47 kcal/mol
Surface area12380 Å2
MethodPISA
2
C: FosA family fosfomycin resistance glutathione transferase
D: FosA family fosfomycin resistance glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3796
Polymers32,6192
Non-polymers7604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-46 kcal/mol
Surface area12320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.765, 68.837, 90.312
Angle α, β, γ (deg.)90.000, 90.460, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 2:23 or resseq 25:43 or (resid...
21(chain B and (resseq 2:23 or resseq 25:43 or (resid...
31(chain C and (resseq 2:23 or resseq 25:43 or (resid...
41(chain D and (resseq 2:23 or resseq 25:43 or (resid...

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
11LEULEUGLNGLN(chain A and (resseq 2:23 or resseq 25:43 or (resid...AA2 - 232 - 23
12LEULEUGLYGLY(chain A and (resseq 2:23 or resseq 25:43 or (resid...AA25 - 4325 - 43
13ASPASPASPASP(chain A and (resseq 2:23 or resseq 25:43 or (resid...AA4444
14METMETGLUGLU(chain A and (resseq 2:23 or resseq 25:43 or (resid...AA1 - 1381 - 138
15METMETGLUGLU(chain A and (resseq 2:23 or resseq 25:43 or (resid...AA1 - 1381 - 138
16METMETGLUGLU(chain A and (resseq 2:23 or resseq 25:43 or (resid...AA1 - 1381 - 138
17METMETGLUGLU(chain A and (resseq 2:23 or resseq 25:43 or (resid...AA1 - 1381 - 138
18METMETGLUGLU(chain A and (resseq 2:23 or resseq 25:43 or (resid...AA1 - 1381 - 138
19METMETGLUGLU(chain A and (resseq 2:23 or resseq 25:43 or (resid...AA1 - 1381 - 138
21LEULEUGLNGLN(chain B and (resseq 2:23 or resseq 25:43 or (resid...BB2 - 232 - 23
22LEULEUGLYGLY(chain B and (resseq 2:23 or resseq 25:43 or (resid...BB25 - 4325 - 43
23ASPASPASPASP(chain B and (resseq 2:23 or resseq 25:43 or (resid...BB4444
24METMETGLUGLU(chain B and (resseq 2:23 or resseq 25:43 or (resid...BB1 - 1381 - 138
25METMETGLUGLU(chain B and (resseq 2:23 or resseq 25:43 or (resid...BB1 - 1381 - 138
26METMETGLUGLU(chain B and (resseq 2:23 or resseq 25:43 or (resid...BB1 - 1381 - 138
27METMETGLUGLU(chain B and (resseq 2:23 or resseq 25:43 or (resid...BB1 - 1381 - 138
28METMETGLUGLU(chain B and (resseq 2:23 or resseq 25:43 or (resid...BB1 - 1381 - 138
29METMETGLUGLU(chain B and (resseq 2:23 or resseq 25:43 or (resid...BB1 - 1381 - 138
31LEULEUGLNGLN(chain C and (resseq 2:23 or resseq 25:43 or (resid...CC2 - 232 - 23
32LEULEUGLYGLY(chain C and (resseq 2:23 or resseq 25:43 or (resid...CC25 - 4325 - 43
33ASPASPASPASP(chain C and (resseq 2:23 or resseq 25:43 or (resid...CC4444
34METMETGLUGLU(chain C and (resseq 2:23 or resseq 25:43 or (resid...CC1 - 1381 - 138
35METMETGLUGLU(chain C and (resseq 2:23 or resseq 25:43 or (resid...CC1 - 1381 - 138
36METMETGLUGLU(chain C and (resseq 2:23 or resseq 25:43 or (resid...CC1 - 1381 - 138
37METMETGLUGLU(chain C and (resseq 2:23 or resseq 25:43 or (resid...CC1 - 1381 - 138
38METMETGLUGLU(chain C and (resseq 2:23 or resseq 25:43 or (resid...CC1 - 1381 - 138
39METMETGLUGLU(chain C and (resseq 2:23 or resseq 25:43 or (resid...CC1 - 1381 - 138
41LEULEUGLNGLN(chain D and (resseq 2:23 or resseq 25:43 or (resid...DD2 - 232 - 23
42LEULEUGLYGLY(chain D and (resseq 2:23 or resseq 25:43 or (resid...DD25 - 4325 - 43
43ASPASPASPASP(chain D and (resseq 2:23 or resseq 25:43 or (resid...DD4444
44METMETPHEPHE(chain D and (resseq 2:23 or resseq 25:43 or (resid...DD1 - 1371 - 137
45METMETPHEPHE(chain D and (resseq 2:23 or resseq 25:43 or (resid...DD1 - 1371 - 137
46METMETPHEPHE(chain D and (resseq 2:23 or resseq 25:43 or (resid...DD1 - 1371 - 137
47METMETPHEPHE(chain D and (resseq 2:23 or resseq 25:43 or (resid...DD1 - 1371 - 137
48METMETPHEPHE(chain D and (resseq 2:23 or resseq 25:43 or (resid...DD1 - 1371 - 137
49METMETPHEPHE(chain D and (resseq 2:23 or resseq 25:43 or (resid...DD1 - 1371 - 137

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Components

#1: Protein
FosA family fosfomycin resistance glutathione transferase / Glutathione transferase


Mass: 16309.347 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: AGG09_10885, B8011_01255, BL102_0004085, CEO55_05040 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A086IRG1, UniProt: A0A0H3GM04*PLUS
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-NY2 / 3-bromo-6-(4-nitro-1H-pyrazol-3-yl)pyrazolo[1,5-a]pyrimidin-2(1H)-one


Mass: 325.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H5BrN6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 714 / Source method: isolated from a natural source / Formula: H2O

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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: 2.13 Å3/Da / Density % sol: 42.33 % / Description: Single rectangular prisms
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Mother liquor: 20% PEG 3350 0.1M Bis Tris pH 5.5 0.2M NH4SO4 Protein at 11.5 mg/mL was combined with ANY2 at a final concentration of 2.5mM, and MnCl2 at 0.6mM. Sample was centrifuged and ...Details: Mother liquor: 20% PEG 3350 0.1M Bis Tris pH 5.5 0.2M NH4SO4 Protein at 11.5 mg/mL was combined with ANY2 at a final concentration of 2.5mM, and MnCl2 at 0.6mM. Sample was centrifuged and supernatant 1uL of supernatant was combined with 1uL of mother liquor. Crystals were improved by streak seeding

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.85→37.53 Å / Num. obs: 45290 / % possible obs: 95 % / Redundancy: 3.4 % / Net I/σ(I): 9.01
Reflection shellResolution: 1.85→1.916 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.76 / Num. unique obs: 4448 / % possible all: 97

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5v3d

5v3d


Resolution: 1.85→37.527 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.82
RfactorNum. reflection% reflection
Rfree0.2118 2280 5.13 %
Rwork0.1845 --
obs0.1859 44417 94.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 54.32 Å2 / Biso mean: 21.6612 Å2 / Biso min: 8.1 Å2
Refinement stepCycle: final / Resolution: 1.85→37.527 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4273 0 86 714 5073
Biso mean--28.1 30.19 -
Num. residues----551
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034482
X-RAY DIFFRACTIONf_angle_d0.6386103
X-RAY DIFFRACTIONf_chiral_restr0.044642
X-RAY DIFFRACTIONf_plane_restr0.004783
X-RAY DIFFRACTIONf_dihedral_angle_d10.8992562
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2291X-RAY DIFFRACTION7.083TORSIONAL
12B2291X-RAY DIFFRACTION7.083TORSIONAL
13C2291X-RAY DIFFRACTION7.083TORSIONAL
14D2291X-RAY DIFFRACTION7.083TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8501-1.89030.30071440.27752632277695
1.8903-1.93430.3251200.26592634275494
1.9343-1.98270.26081310.23582633276495
1.9827-2.03630.26081470.21582660280795
2.0363-2.09620.28051450.22412553269893
2.0962-2.16380.27231240.20412573269792
2.1638-2.24120.27171610.20632531269293
2.2412-2.33090.2283980.19562687278595
2.3309-2.4370.21631290.19142676280596
2.437-2.56540.2421660.1962661282797
2.5654-2.72610.231570.19562654281196
2.7261-2.93650.20661640.18342572273693
2.9365-3.23190.1791870.16682691287897
3.2319-3.69920.18081530.14912671282496
3.6992-4.65920.15841400.1412570271092
4.6592-37.53450.1561140.17272739285394

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