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- PDB-4kks: Crystal Structure of BesA (C2 form) -

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Basic information

Entry
Database: PDB / ID: 4kks
TitleCrystal Structure of BesA (C2 form)
ComponentsMembrane fusion protein
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


efflux pump complex / efflux transmembrane transporter activity
Similarity search - Function
Membrane fusion protein, biotin-lipoyl like domain / Biotin-lipoyl like / conserved putative lor/sdh protein from methanococcus maripaludis s2 fold - #20 / conserved putative lor/sdh protein from methanococcus maripaludis s2 fold / Efflux pump adaptor protein, beta barrel domain / RND efflux pump, membrane fusion protein / RND efflux pump, membrane fusion protein, barrel-sandwich domain / Barrel-sandwich domain of CusB or HlyD membrane-fusion / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Single hybrid motif ...Membrane fusion protein, biotin-lipoyl like domain / Biotin-lipoyl like / conserved putative lor/sdh protein from methanococcus maripaludis s2 fold - #20 / conserved putative lor/sdh protein from methanococcus maripaludis s2 fold / Efflux pump adaptor protein, beta barrel domain / RND efflux pump, membrane fusion protein / RND efflux pump, membrane fusion protein, barrel-sandwich domain / Barrel-sandwich domain of CusB or HlyD membrane-fusion / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Single hybrid motif / Elongation Factor Tu (Ef-tu); domain 3 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Membrane fusion protein
Similarity search - Component
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGreene, N.P. / Hinchliffe, P. / Crow, A. / Ababou, A. / Hughes, C. / Koronakis, V.
CitationJournal: Febs Lett. / Year: 2013
Title: Structure of an atypical periplasmic adaptor from a multidrug efflux pump of the spirochete Borrelia burgdorferi.
Authors: Greene, N.P. / Hinchliffe, P. / Crow, A. / Ababou, A. / Hughes, C. / Koronakis, V.
History
DepositionMay 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 1.2Sep 25, 2013Group: Database references
Revision 1.3Sep 20, 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

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Assembly

Deposited unit
A: Membrane fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6062
Polymers32,5111
Non-polymers951
Water32418
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.200, 52.500, 76.530
Angle α, β, γ (deg.)90.00, 98.04, 90.00
Int Tables number5
Space group name H-MC121
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein Membrane fusion protein /


Mass: 32510.668 Da / Num. of mol.: 1 / Fragment: UNP residues 26-317
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Strain: ATCC 35210 / B31 / CIP 102532 / DSM 4680 / Gene: BB_0141 / Production host: Escherichia coli (E. coli) / References: UniProt: O51166
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.68 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1M citrate, 30% PEG 300, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 11, 2012
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→44.3 Å / Num. all: 10793 / Num. obs: 9732 / % possible obs: 95.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.6→2.72 Å / % possible all: 80.8

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KKU

4kku


Resolution: 2.6→44.3 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.876 / SU B: 13.917 / SU ML: 0.295 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.013 / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28626 462 4.7 %RANDOM
Rwork0.2057 ---
all0.20955 9270 --
obs0.20955 9270 95.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.302 Å2
Baniso -1Baniso -2Baniso -3
1--3.44 Å20 Å21.02 Å2
2--7.29 Å20 Å2
3----3.84 Å2
Refinement stepCycle: LAST / Resolution: 2.6→44.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2119 0 5 18 2142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192166
X-RAY DIFFRACTIONr_bond_other_d0.0010.022217
X-RAY DIFFRACTIONr_angle_refined_deg1.5881.9992926
X-RAY DIFFRACTIONr_angle_other_deg0.75735130
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.775278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.70725.45577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.52115427
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.537159
X-RAY DIFFRACTIONr_chiral_restr0.0860.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212369
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02416
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: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 22 -
Rwork0.338 525 -
obs--75.97 %

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