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- PDB-4kkt: Crystal Structure of BesA (P21 form) -

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Basic information

Entry
Database: PDB / ID: 4kkt
TitleCrystal Structure of BesA (P21 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
Membrane fusion protein
Similarity search - Component
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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)130,0434
Polymers130,0434
Non-polymers00
Water2,000111
1
A: Membrane fusion protein


Theoretical massNumber of molelcules
Total (without water)32,5111
Polymers32,5111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Membrane fusion protein


Theoretical massNumber of molelcules
Total (without water)32,5111
Polymers32,5111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Membrane fusion protein


Theoretical massNumber of molelcules
Total (without water)32,5111
Polymers32,5111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Membrane fusion protein


Theoretical massNumber of molelcules
Total (without water)32,5111
Polymers32,5111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.200, 73.740, 152.230
Angle α, β, γ (deg.)90.00, 98.06, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGILEILEAA45 - 31724 - 296
21ARGARGILEILEBB45 - 31724 - 296
12ARGARGILEILEAA45 - 31724 - 296
22ARGARGILEILECC45 - 31724 - 296
13ARGARGILEILEAA45 - 31724 - 296
23ARGARGILEILEDD45 - 31724 - 296
14ARGARGILEILEBB45 - 31724 - 296
24ARGARGILEILECC45 - 31724 - 296
15TYRTYRILEILEBB44 - 31723 - 296
25TYRTYRILEILEDD44 - 31723 - 296
16ARGARGASNASNCC45 - 31624 - 295
26ARGARGASNASNDD45 - 31624 - 295

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: 32510.668 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 / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 3.34 Å3/Da / Density % sol: 63.19 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 4.7
Details: 0.1M phosphate/citrate pH 4.7, 25% PEG 6,000, 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: 2.53→73.74 Å / Num. all: 66687 / Num. obs: 54853 / % possible obs: 95.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.53→2.6 Å / % possible all: 87.3

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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: 2.53→73.27 Å / Cor.coef. Fo:Fc: 0.884 / Cor.coef. Fo:Fc free: 0.863 / SU B: 9.823 / SU ML: 0.219 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.445 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2855 2784 5.1 %RANDOM
Rwork0.25737 ---
all0.25882 52051 --
obs0.25882 52051 95.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20 Å20.13 Å2
2--0.38 Å20 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 2.53→73.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8113 0 0 111 8224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0198248
X-RAY DIFFRACTIONr_bond_other_d0.0060.028514
X-RAY DIFFRACTIONr_angle_refined_deg1.6561.99611126
X-RAY DIFFRACTIONr_angle_other_deg1.127319681
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.89851056
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.07525.729295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.421151647
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2021532
X-RAY DIFFRACTIONr_chiral_restr0.0910.21371
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029010
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021578
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
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A167460.07
12B167460.07
21A168020.08
22C168020.08
31A166950.08
32D166950.08
41B169760.07
42C169760.07
51B170860.06
52D170860.06
61C169060.06
62D169060.06
LS refinement shellResolution: 2.53→2.596 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 178 -
Rwork0.335 3407 -
obs--85.7 %

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