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- PDB-3qun: Crystal structure of fosfomycin resistance kinase FomA from Strep... -

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Basic information

Entry
Database: PDB / ID: 3qun
TitleCrystal structure of fosfomycin resistance kinase FomA from Streptomyces wedmorensis complexed with MgATP
ComponentsFomA protein
KeywordsTRANSFERASE / fosfomycin / antibiotic resistance / phosphoryl transfer / kinase
Function / homology
Function and homology information


isopentenyl phosphate kinase / isopentenyl phosphate kinase activity / isoprenoid biosynthetic process / kinase activity / phosphorylation / ATP binding
Similarity search - Function
Fosfomycin resistance kinase, FomA-type / Carbamate kinase / Acetylglutamate kinase-like / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Isopentenyl phosphate kinase
Similarity search - Component
Biological speciesStreptomyces wedmorensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsPakhomova, S. / Bartlett, S.G. / Doerner, P.A. / Newcomer, M.E.
CitationJournal: Biochemistry / Year: 2011
Title: Structural and biochemical insights into the mechanism of fosfomycin phosphorylation by fosfomycin resistance kinase FomA.
Authors: Pakhomova, S. / Bartlett, S.G. / Doerner, P.A. / Newcomer, M.E.
History
DepositionFeb 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Database references
Revision 1.2Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FomA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5004
Polymers30,8771
Non-polymers6243
Water1,946108
1
A: FomA protein
hetero molecules

A: FomA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0018
Polymers61,7542
Non-polymers1,2476
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5040 Å2
ΔGint-41 kcal/mol
Surface area20080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.876, 85.876, 80.152
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe second part of the biological assembly is generated by the two-fold axis: y,x,-z

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Components

#1: Protein FomA protein


Mass: 30876.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces wedmorensis (bacteria) / Gene: fomA, fosfomycin resistance kinase / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q56187
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#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.: 108 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AUTHORS STATE THAT THE DEPOSITED SEQUENCE UNPROT ENTRY Q56187 IS WRONG AT POSITION 31

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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: 2.76 Å3/Da / Density % sol: 55.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 17% PEG3350, 15% glycerol, 0.1M MES, 10mM ATP, 10 mM MgCl2, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 1.38079 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 16, 2007 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.38079 Å / Relative weight: 1
ReflectionResolution: 1.87→40 Å / Num. all: 26774 / Num. obs: 26774 / % possible obs: 93.4 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 33.2 Å2 / Rsym value: 0.036 / Net I/σ(I): 32
Reflection shellResolution: 1.87→1.94 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 2724 / Rsym value: 0.454 / % possible all: 96.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3D40

3d40


Resolution: 1.87→23.01 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.959 / SU B: 5.518 / SU ML: 0.082 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20541 403 1.6 %RANDOM
Rwork0.18494 ---
obs0.18527 24958 88.56 %-
all-24958 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.874 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20.2 Å20 Å2
2--0.4 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.87→23.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1865 0 38 108 2011
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221983
X-RAY DIFFRACTIONr_bond_other_d0.0030.021346
X-RAY DIFFRACTIONr_angle_refined_deg1.7631.9962694
X-RAY DIFFRACTIONr_angle_other_deg1.00533253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8445248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.98421.77279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.42415312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8641521
X-RAY DIFFRACTIONr_chiral_restr0.10.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022189
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02423
X-RAY DIFFRACTIONr_nbd_refined0.2290.2407
X-RAY DIFFRACTIONr_nbd_other0.2090.21471
X-RAY DIFFRACTIONr_nbtor_refined0.1830.2951
X-RAY DIFFRACTIONr_nbtor_other0.0910.21071
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2121
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1450.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4010.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3270.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2440.26
X-RAY DIFFRACTIONr_mcbond_it1.641.51577
X-RAY DIFFRACTIONr_mcbond_other0.2851.5509
X-RAY DIFFRACTIONr_mcangle_it1.91521991
X-RAY DIFFRACTIONr_scbond_it2.4693838
X-RAY DIFFRACTIONr_scangle_it3.6034.5703
LS refinement shellResolution: 1.87→1.918 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 28 -
Rwork0.257 1628 -
obs-1628 79.69 %

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