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- PDB-3d40: Crystal structure of fosfomycin resistance kinase FomA from Strep... -

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Basic information

Entry
Database: PDB / ID: 3d40
TitleCrystal structure of fosfomycin resistance kinase FomA from Streptomyces wedmorensis complexed with diphosphate
ComponentsFomA protein
KeywordsTRANSFERASE / fosfomycin / antibiotic resistance / kinase / phosphoryl transfer
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
DIPHOSPHATE / Isopentenyl phosphate kinase
Similarity search - Component
Biological speciesStreptomyces wedmorensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsPakhomova, S. / Bartlett, S.G. / Augustus, A. / Kuzuyama, T. / Newcomer, M.E.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal Structure of Fosfomycin Resistance Kinase FomA from Streptomyces wedmorensis.
Authors: Pakhomova, S. / Bartlett, S.G. / Augustus, A. / Kuzuyama, T. / Newcomer, M.E.
History
DepositionMay 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)31,0512
Polymers30,8771
Non-polymers1741
Water4,161231
1
A: FomA protein
hetero molecules

A: FomA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1024
Polymers61,7542
Non-polymers3482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area3380 Å2
ΔGint-17.1 kcal/mol
Surface area21550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.361, 88.361, 79.046
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 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q56187
#2: Chemical ChemComp-DPO / DIPHOSPHATE


Mass: 173.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O7P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE RESEQUENCING OF THE PROTEIN CONFIRMED RESIDUE 31 IS ARG.

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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: 2.88 Å3/Da / Density % sol: 57.37 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 11% PEG 3350, 0.1 M tri-ammonium citrate, 0.1 M MES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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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: Mar 27, 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: 1.53→30 Å / Num. all: 52986 / Num. obs: 52986 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 27.7 Å2 / Rsym value: 0.04 / Net I/σ(I): 34.8
Reflection shellResolution: 1.53→1.58 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 4585 / Rsym value: 0.51 / % possible all: 85.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: model of SeMet FomA form based on MAD data

Resolution: 1.53→27.49 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.221 / SU ML: 0.04 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19801 834 1.6 %RANDOM
Rwork0.16864 ---
all0.16908 50201 --
obs0.16908 50201 94.29 %-
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: 26.933 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20.18 Å20 Å2
2--0.36 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.53→27.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1953 0 9 231 2193
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222001
X-RAY DIFFRACTIONr_angle_refined_deg1.7381.9712716
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4095250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.621.76585
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.52615325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6711522
X-RAY DIFFRACTIONr_chiral_restr0.1230.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021501
X-RAY DIFFRACTIONr_nbd_refined0.2110.2920
X-RAY DIFFRACTIONr_nbtor_refined0.3180.21397
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2194
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.221
X-RAY DIFFRACTIONr_mcbond_it1.251.51288
X-RAY DIFFRACTIONr_mcangle_it1.91722019
X-RAY DIFFRACTIONr_scbond_it2.8033793
X-RAY DIFFRACTIONr_scangle_it4.4184.5697
LS refinement shellHighest resolution: 1.53 Å / Num. reflection Rwork: 2784 / Total num. of bins used: 20

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