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

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Basic information

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


isopentenyl phosphate kinase / isopentenyl phosphate kinase activity / glutamate 5-kinase activity / proline biosynthetic process / isoprenoid biosynthetic process / ATP binding / cytosol
Similarity search - Function
Fosfomycin resistance kinase, FomA-type / Carbamate kinase / Acetylglutamate kinase-like / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily / Amino acid kinase family / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-FV1 / Isopentenyl phosphate kinase
Similarity search - Component
Biological speciesStreptomyces wedmorensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 25, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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_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)31,5664
Polymers30,8771
Non-polymers6903
Water2,450136
1
A: FomA protein
hetero molecules

A: FomA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1338
Polymers61,7542
Non-polymers1,3796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area4550 Å2
ΔGint-48 kcal/mol
Surface area21800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.380, 87.380, 79.000
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+1

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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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-FV1 / dihydroxy{[(2R,3S)-3-methyloxiran-2-yl]phosphonato-kappaO}oxovanadium


Mass: 238.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O7PV
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.82 Å3/Da / Density % sol: 56.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 17% PEG3350, 25% glycerol, 0.1M MES, 10mM AD, 50mM MgCl2, 10mM fosfomycin, 10mM NaVO3, pH 7.0, 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 14, 2008 / 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: 1.85→40 Å / Num. all: 29919 / Num. obs: 29919 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 34.9 Å2 / Rsym value: 0.046 / Net I/σ(I): 31.4
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 2931 / Rsym value: 0.705 / % possible all: 99.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3D40

3d40


Resolution: 1.85→27.32 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.66 / SU ML: 0.081 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21938 411 1.5 %RANDOM
Rwork0.16407 ---
all0.16485 27413 --
obs0.16485 27413 92.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.142 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20.33 Å20 Å2
2--0.66 Å20 Å2
3----0.99 Å2
Refinement stepCycle: LAST / Resolution: 1.85→27.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2064 0 40 136 2240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0212183
X-RAY DIFFRACTIONr_bond_other_d0.0040.021473
X-RAY DIFFRACTIONr_angle_refined_deg2.0021.9792972
X-RAY DIFFRACTIONr_angle_other_deg1.13133560
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1315277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.07221.86891
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.67915338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2911522
X-RAY DIFFRACTIONr_chiral_restr0.1190.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212439
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02474
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1681.51368
X-RAY DIFFRACTIONr_mcbond_other0.3261.5565
X-RAY DIFFRACTIONr_mcangle_it2.00222185
X-RAY DIFFRACTIONr_scbond_it3.4213815
X-RAY DIFFRACTIONr_scangle_it4.7924.5783
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 22 -
Rwork0.242 1592 -
obs-1592 72.57 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.06140.7086-0.43322.312-1.17721.72120.11060.1998-0.2063-0.1767-0.08420.160.0473-0.2876-0.02640.07290.0219-0.03380.1284-0.04660.11392.08431.997525.3976
21.5436-0.69920.55830.9862-0.1531.520.003-0.1059-0.0801-0.01410.01150.07890.0194-0.1914-0.01440.0163-0.01330.00230.0347-0.00430.06517.083931.585237.8443
32.62090.0468-0.39491.42910.47873.20980.08550.154-0.0248-0.1333-0.11390.2604-0.1119-0.5730.02840.03460.0428-0.04060.1424-0.01220.0841-8.255640.817429.2888
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 50
2X-RAY DIFFRACTION2A51 - 176
3X-RAY DIFFRACTION3A177 - 262

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