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

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Basic information

Entry
Database: PDB / ID: 3qvh
TitleCrystal structure of fosfomycin resistance kinase FomA from Streptomyces wedmorensis complexed with ADP
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 / : / 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 / 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 / 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)31,3042
Polymers30,8771
Non-polymers4271
Water3,045169
1
A: FomA protein
hetero molecules

A: FomA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6084
Polymers61,7542
Non-polymers8542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area4110 Å2
ΔGint-23 kcal/mol
Surface area21190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.670, 87.670, 78.890
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-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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.83 Å3/Da / Density % sol: 56.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 17 % PEG3350, 25 % glycerol, 0.1 M MES, 10 mM ADP, 50 mM MgCl2 , 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: Oct 26, 2009 / 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: 30430 / Num. obs: 30430 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 29.7 Å2 / Rsym value: 0.106 / Net I/σ(I): 12.3
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 2851 / Rsym value: 0.539 / % possible all: 93.2

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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→34.21 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.199 / SU ML: 0.07 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21329 417 1.5 %RANDOM
Rwork0.16503 ---
all0.16568 27860 --
obs0.16568 27860 93.24 %-
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: 35.948 Å2
Baniso -1Baniso -2Baniso -3
1-1.43 Å20.71 Å20 Å2
2--1.43 Å20 Å2
3----2.14 Å2
Refinement stepCycle: LAST / Resolution: 1.85→34.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1940 0 27 169 2136
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222032
X-RAY DIFFRACTIONr_bond_other_d0.0040.021382
X-RAY DIFFRACTIONr_angle_refined_deg2.0441.9852763
X-RAY DIFFRACTIONr_angle_other_deg1.11333336
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0545259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.14321.72881
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.14415314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9741521
X-RAY DIFFRACTIONr_chiral_restr0.1280.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212273
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02443
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_it1.3711.51292
X-RAY DIFFRACTIONr_mcbond_other0.3651.5536
X-RAY DIFFRACTIONr_mcangle_it2.35822056
X-RAY DIFFRACTIONr_scbond_it3.1073740
X-RAY DIFFRACTIONr_scangle_it5.0364.5707
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
Rfree0.265 30 -
Rwork0.246 1688 -
obs-1688 77.21 %
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)
11.5526-0.0350.04851.0309-0.15971.5301-0.01580.0947-0.2022-0.00840.0095-0.02270.2777-0.01840.00630.0679-0.01410.01470.0236-0.01980.0927-25.368216.681214.6529
21.36910.38170.09110.69580.08131.2046-0.02660.0533-0.0536-0.02520.00560.03410.1651-0.15020.0210.0416-0.01790.0150.0235-0.00680.0625-31.040919.377619.7574
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-8 - 70
2X-RAY DIFFRACTION2A71 - 262

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