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- PDB-4e4b: Structure of the fusidic acid resistance protein FusB -

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Basic information

Entry
Database: PDB / ID: 4e4b
TitleStructure of the fusidic acid resistance protein FusB
ComponentsFar1
KeywordsMETAL BINDING PROTEIN / Zinc binding fold / Antibiotic resistance protein / Ribosome clearance / EF-G
Function / homology
Function and homology information


Monooxygenase - #250 / Elongation factor G-binding protein, N-terminal / Elongation factor G-binding protein, C-terminal treble-clef zinc-finger / EF-G binding protein, N-terminal domain superfamily / Elongation factor G-binding protein, N-terminal / FBP C-terminal treble-clef zinc-finger / Monooxygenase / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsCox, G. / Edwards, T.A. / O'Neill, A.J.
CitationJournal: To be Published
Title: Investigating the FusB:EF-G interface
Authors: Cox, G. / Edwards, T.A. / O'Neill, A.J.
History
DepositionMar 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_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

Downloads & links

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Assembly

Deposited unit
A: Far1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5732
Polymers25,5071
Non-polymers651
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.370, 89.100, 107.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-408-

HOH

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Components

#1: Protein Far1 / FusB / FusB protein / Fusidic acid resistance


Mass: 25507.404 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: far1, fusB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Gold / References: UniProt: Q8GNY5
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M magnesium chloride, 0.1 M Tris-HCl, 45% (v/v) PEG 400, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.2837 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2837 Å / Relative weight: 1
ReflectionResolution: 2.8→47.03 Å / Num. all: 6782 / Num. obs: 6519 / % possible obs: 99.78 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 9.7

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
PHASERphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2YB5

2yb5


Resolution: 2.8→47.03 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.919 / SU B: 50.566 / SU ML: 0.447 / Cross valid method: THROUGHOUT / ESU R Free: 0.468 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.31422 324 4.7 %RANDOM
Rwork0.24108 ---
obs0.24451 6519 99.58 %-
all-6782 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 109.01 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å2-0 Å20 Å2
2---4.06 Å20 Å2
3---2.85 Å2
Refinement stepCycle: LAST / Resolution: 2.8→47.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1765 0 1 12 1778
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.021798
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0611.9642417
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5125212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.37925.68288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.85715358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.919155
X-RAY DIFFRACTIONr_chiral_restr0.0890.2265
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021323
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.485 19 -
Rwork0.443 432 -
obs--99.56 %

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