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- PDB-5v3d: Crystal structure of fosfomycin resistance protein from Klebsiell... -

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Basic information

Entry
Database: PDB / ID: 5v3d
TitleCrystal structure of fosfomycin resistance protein from Klebsiella pneumoniae with bound fosfomycin
ComponentsFosfomycin resistance protein
KeywordsTRANSFERASE / FosA / FosAKP / fosfomycin / glutathione transferase
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
FOSFOMYCIN / : / : / DI(HYDROXYETHYL)ETHER / Fosfomycin resistance protein / Fosfomycin resistance protein
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.539 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 7, 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 / pdbx_struct_conn_angle / struct_conn
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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,25110
Polymers32,6192
Non-polymers6328
Water4,990277
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, FosAKP shares high sequence similarity with previously reported FosA proteins.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7320 Å2
ΔGint-37 kcal/mol
Surface area12160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.071, 47.155, 149.517
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Fosfomycin resistance protein


Mass: 16309.347 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: W8UNW6, UniProt: A0A0E1CQ35*PLUS

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Non-polymers , 6 types, 285 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-FCN / FOSFOMYCIN / 1,2-EPOXYPROPYLPHOSPHONIC ACID / Fosfomycin


Mass: 138.059 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7O4P / Comment: antibiotic*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2.17 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1uL of FosAKP solution: 9mg/mL FosAKP in storage solution (75mM NaCl, 10mM Tris, pH 7.5), 6mM MnCl2, 6mM Fosfomycin. 1uL of mother liquor: 0.22 M KBr, 20% PEG2000 MME Crystals appear in 2-3 days

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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 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: 1.53869→29.2925 Å / Num. obs: 41623 / % possible obs: 93.61 % / Redundancy: 4.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.026 / Rrim(I) all: 0.058 / Net I/σ(I): 14.7
Reflection shell

Diffraction-ID: 1 / Redundancy: 4.2 %

Resolution (Å)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
1.54-1.580.7210.9170.3780.81997.5
6.88-29.290.0280.9980.0150.03290.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1lqp

1lqp


Resolution: 1.539→29.292 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.11
RfactorNum. reflection% reflection
Rfree0.2059 2065 5 %
Rwork0.1682 --
obs0.1701 41577 93.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 75.03 Å2 / Biso mean: 30.7136 Å2 / Biso min: 15.56 Å2
Refinement stepCycle: final / Resolution: 1.539→29.292 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2149 0 31 277 2457
Biso mean--33.26 39.68 -
Num. residues----275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062261
X-RAY DIFFRACTIONf_angle_d0.8853073
X-RAY DIFFRACTIONf_chiral_restr0.051328
X-RAY DIFFRACTIONf_plane_restr0.005394
X-RAY DIFFRACTIONf_dihedral_angle_d13.5061318
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5387-1.55820.28331550.2862590274591
1.5582-1.57870.33811430.26452790293397
1.5787-1.60030.32691540.25912787294197
1.6003-1.62310.26311450.24842718286396
1.6231-1.64740.25911430.24842679282295
1.6474-1.67310.28851410.22372842298397
1.6731-1.70050.33131490.22242695284496
1.7005-1.72990.2731370.21282801293897
1.7299-1.76130.25471390.20592763290296
1.7613-1.79520.25361460.19172739288596
1.7952-1.83180.23851380.19452741287996
1.8318-1.87160.25381460.17382700284695
1.8716-1.91520.1851390.172671281094
1.9152-1.96310.22871470.16412649279692
1.9631-2.01610.18711410.16582726286795
2.0161-2.07540.22281470.17672671281894
2.0754-2.14240.21351470.16582649279693
2.1424-2.2190.19921350.16142708284394
2.219-2.30780.16451360.16492623275993
2.3078-2.41270.21041420.17162619276191
2.4127-2.53990.2231350.17172619275492
2.5399-2.69890.22651330.16632660279392
2.6989-2.90710.19991320.16562579271191
2.9071-3.19940.16991300.15232578270890
3.1994-3.66160.18751350.15022553268889
3.6616-4.61030.16221350.13222515265089
4.6103-29.29780.18311250.15452500262587

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