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

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Basic information

Entry
Database: PDB / ID: 3quo
TitleCrystal structure of fosfomycin resistance kinase FomA from Streptomyces wedmorensis complexed with ATP and fosfomycin
ComponentsFomA protein
KeywordsTRANSFERASE/TRANSFERASE inhibitor / fosfomycin / antibiotic resistance / phosphoryl transfer / kinase / TRANSFERASE-TRANSFERASE inhibitor complex
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 / FOSFOMYCIN / Isopentenyl phosphate kinase
Similarity search - Component
Biological speciesStreptomyces wedmorensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 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

Downloads & links

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Assembly

Deposited unit
A: FomA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5223
Polymers30,8771
Non-polymers6452
Water3,657203
1
A: FomA protein
hetero molecules

A: FomA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0446
Polymers61,7542
Non-polymers1,2904
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5210 Å2
ΔGint-23 kcal/mol
Surface area22300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.330, 87.330, 78.540
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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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-FCN / FOSFOMYCIN / 1,2-EPOXYPROPYLPHOSPHONIC ACID / Fosfomycin


Mass: 138.059 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O4P / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.8 Å3/Da / Density % sol: 56.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 17 % PEG3350, 25 % glycerol, 0.1 M MES, 10 mM ATP, 10 mM fosfomycin , pH 7.1, 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: Jun 10, 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: 1.58→50 Å / Num. all: 42575 / Num. obs: 42575 / % possible obs: 89 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 27.4 Å2 / Rsym value: 0.039 / Net I/σ(I): 35.6
Reflection shellResolution: 1.58→1.64 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 4204 / Rsym value: 0.561 / % possible all: 88.9

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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: 1.58→26.86 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.778 / SU ML: 0.045 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20287 604 1.5 %RANDOM
Rwork0.16137 ---
obs0.16194 39740 84.47 %-
all-39740 --
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: 31.701 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20.47 Å20 Å2
2--0.94 Å20 Å2
3----1.41 Å2
Refinement stepCycle: LAST / Resolution: 1.58→26.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2018 0 39 203 2260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0212131
X-RAY DIFFRACTIONr_bond_other_d0.0040.021442
X-RAY DIFFRACTIONr_angle_refined_deg2.1131.982903
X-RAY DIFFRACTIONr_angle_other_deg1.14733483
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.85266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.69421.68589
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.76815334
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4441522
X-RAY DIFFRACTIONr_chiral_restr0.1260.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212354
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02463
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_it1.2791.51325
X-RAY DIFFRACTIONr_mcbond_other0.4241.5543
X-RAY DIFFRACTIONr_mcangle_it2.1422122
X-RAY DIFFRACTIONr_scbond_it3.0933806
X-RAY DIFFRACTIONr_scangle_it4.8764.5777
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.58→1.621 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.446 39 -
Rwork0.318 2488 -
obs-2488 72.55 %
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)
11.53920.51080.34891.7470.63011.3554-0.0381-0.193-0.16570.04030.03230.04730.22960.0850.00580.05370.02310.00210.04180.03660.064626.377417.107914.5011
21.2704-0.38750.13190.5983-0.05051.09310.0181-0.0513-0.0698-0.011-0.0099-0.02630.17020.1639-0.00820.03550.02220.00550.03230.00850.047929.827119.05915.4123
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-9 - 46
2X-RAY DIFFRACTION2A47 - 263

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