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- PDB-4kku: Structure of BesA (Selenomethinone derivative - P212121) -

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Basic information

Entry
Database: PDB / ID: 4kku
TitleStructure of BesA (Selenomethinone derivative - P212121)
ComponentsMembrane fusion protein
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


efflux pump complex / efflux transmembrane transporter activity / plasma membrane
Similarity search - Function
: / 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 / : / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Single hybrid motif / Elongation Factor Tu (Ef-tu); domain 3 ...: / 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 / : / 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
Membrane fusion protein
Similarity search - Component
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 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 17, 2013Group: Structure summary
Revision 1.2Jul 31, 2013Group: Database references
Revision 1.3Sep 25, 2013Group: Database references
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Membrane fusion protein
B: Membrane fusion protein
C: Membrane fusion protein
D: Membrane fusion protein


Theoretical massNumber of molelcules
Total (without water)130,9814
Polymers130,9814
Non-polymers00
Water3,207178
1
A: Membrane fusion protein


Theoretical massNumber of molelcules
Total (without water)32,7451
Polymers32,7451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Membrane fusion protein


Theoretical massNumber of molelcules
Total (without water)32,7451
Polymers32,7451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Membrane fusion protein


Theoretical massNumber of molelcules
Total (without water)32,7451
Polymers32,7451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Membrane fusion protein


Theoretical massNumber of molelcules
Total (without water)32,7451
Polymers32,7451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.740, 152.130, 155.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRAA44 - 31723 - 296
21TYRTYRBB44 - 31723 - 296
12ARGARGAA45 - 31724 - 296
22ARGARGCC45 - 31724 - 296
13TYRTYRAA44 - 31723 - 296
23TYRTYRDD44 - 31723 - 296
14ARGARGBB45 - 31724 - 296
24ARGARGCC45 - 31724 - 296
15TYRTYRBB44 - 31723 - 296
25TYRTYRDD44 - 31723 - 296
16ARGARGCC45 - 31724 - 296
26ARGARGDD45 - 31724 - 296

NCS ensembles :
ID
1
2
3
4
5
6
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein
Membrane fusion protein


Mass: 32745.141 Da / Num. of mol.: 4 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.33 Å3/Da / Density % sol: 63.06 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 100 mM phosphate/citrate pH 4.2, 100 mM LiSO4, 16 % (w/v) PEG 1000, VAPOR DIFFUSION, SITTING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9787 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2012
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.35→77.74 Å / Num. all: 72616 / Num. obs: 72616 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.35→2.4 Å / % possible all: 88.5

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.35→77.74 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.918 / SU B: 6.832 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.278 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26359 3644 5 %RANDOM
Rwork0.23557 ---
all0.23698 68894 --
obs0.23698 68894 98.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.892 Å2
Baniso -1Baniso -2Baniso -3
1-2.03 Å20 Å20 Å2
2---1.76 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 2.35→77.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8201 0 0 178 8379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0198376
X-RAY DIFFRACTIONr_bond_other_d0.0080.028642
X-RAY DIFFRACTIONr_angle_refined_deg1.8552.00511304
X-RAY DIFFRACTIONr_angle_other_deg1.271319992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.82951075
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.05425.724297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.021151624
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5481532
X-RAY DIFFRACTIONr_chiral_restr0.1090.21386
X-RAY DIFFRACTIONr_gen_planes_refined0.010.029160
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021596
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A171280.07
12B171280.07
21A168560.08
22C168560.08
31A168230.09
32D168230.09
41B170730.07
42C170730.07
51B171460.08
52D171460.08
61C169310.07
62D169310.07
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 231 -
Rwork0.332 4529 -
obs--88.43 %

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