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- PDB-3ne5: Crystal structure of the CusBA heavy-metal efflux complex from Es... -

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Basic information

Entry
Database: PDB / ID: 3ne5
TitleCrystal structure of the CusBA heavy-metal efflux complex from Escherichia coli
Components
  • Cation efflux system protein cusA
  • Cation efflux system protein cusB
KeywordsMETAL TRANSPORT / Transmembrane helix
Function / homology
Function and homology information


silver ion transport / silver ion transmembrane transporter activity / plasma membrane copper ion transport / copper ion transmembrane transport / response to silver ion / silver ion transmembrane transport / cell envelope / copper ion transmembrane transporter activity / copper ion export / detoxification of copper ion ...silver ion transport / silver ion transmembrane transporter activity / plasma membrane copper ion transport / copper ion transmembrane transport / response to silver ion / silver ion transmembrane transport / cell envelope / copper ion transmembrane transporter activity / copper ion export / detoxification of copper ion / response to copper ion / xenobiotic transmembrane transporter activity / transition metal ion binding / intracellular copper ion homeostasis / response to toxic substance / outer membrane-bounded periplasmic space / copper ion binding / membrane / plasma membrane
Similarity search - Function
Helix Hairpins - #730 / Long alpha hairpin domain of cation efflux system protein, CusB / conserved putative lor/sdh protein from methanococcus maripaludis s2 fold - #20 / conserved putative lor/sdh protein from methanococcus maripaludis s2 fold / Heavy metal binding domain / Heavy metal binding domain / Cation efflux system CzcA/CusA/SilA/NccA/HelA/CnrA / Efflux pump adaptor protein, beta barrel domain / Cation efflux system protein CusB, domain 1 / Cation efflux system protein CusB domain 1 ...Helix Hairpins - #730 / Long alpha hairpin domain of cation efflux system protein, CusB / conserved putative lor/sdh protein from methanococcus maripaludis s2 fold - #20 / conserved putative lor/sdh protein from methanococcus maripaludis s2 fold / Heavy metal binding domain / Heavy metal binding domain / Cation efflux system CzcA/CusA/SilA/NccA/HelA/CnrA / Efflux pump adaptor protein, beta barrel domain / Cation efflux system protein CusB, domain 1 / Cation efflux system protein CusB domain 1 / RND efflux pump, membrane fusion protein / RND efflux pump, membrane fusion protein, barrel-sandwich domain / Barrel-sandwich domain of CusB or HlyD membrane-fusion / Acriflavin resistance protein / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / AcrB/AcrD/AcrF family / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Helix Hairpins / Elongation Factor Tu (Ef-tu); domain 3 / Helix non-globular / Special / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Cation efflux system protein CusA / Cation efflux system protein CusB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.898 Å
AuthorsSu, C.-C.
CitationJournal: Nature / Year: 2011
Title: Crystal structure of the CusBA heavy-metal efflux complex of Escherichia coli.
Authors: Su, C.C. / Long, F. / Zimmermann, M.T. / Rajashankar, K.R. / Jernigan, R.L. / Yu, E.W.
History
DepositionJun 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 18, 2013Group: Derived calculations
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Cation efflux system protein cusB
C: Cation efflux system protein cusB
A: Cation efflux system protein cusA


Theoretical massNumber of molelcules
Total (without water)206,0623
Polymers206,0623
Non-polymers00
Water34219
1
B: Cation efflux system protein cusB
C: Cation efflux system protein cusB
A: Cation efflux system protein cusA

B: Cation efflux system protein cusB
C: Cation efflux system protein cusB
A: Cation efflux system protein cusA

B: Cation efflux system protein cusB
C: Cation efflux system protein cusB
A: Cation efflux system protein cusA


Theoretical massNumber of molelcules
Total (without water)618,1869
Polymers618,1869
Non-polymers00
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area56930 Å2
ΔGint-166 kcal/mol
Surface area185670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.267, 160.267, 682.835
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Cation efflux system protein cusB


Mass: 45179.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: cusB, ylcD, b0574, JW0563 / Production host: Escherichia coli (E. coli) / References: UniProt: P77239
#2: Protein Cation efflux system protein cusA


Mass: 115702.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: cusA, ybdE, b0575, JW0564 / Production host: Escherichia coli (E. coli) / References: UniProt: P38054
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 4.1 Å3/Da / Density % sol: 69.96 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.5
Details: 10 % PEG3350, 0.4M NH4SO4, 1% JM600, 5% Glycerol, 0.1M Bis-tris propane (7.5), EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 9, 2010
RadiationMonochromator: Cryo-Cooled Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.898→39.496 Å / Num. obs: 75498 / % possible obs: 93.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 1.4 % / Rmerge(I) obs: 0.09
Reflection shellResolution: 2.898→3 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 1.5 / % possible all: 90.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.898→39.493 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.783 / SU ML: 0.43 / σ(F): 0.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.267 2975 4.99 %RANDOM
Rwork0.229 ---
obs0.231 59612 78.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.341 Å2 / ksol: 0.286 e/Å3
Displacement parametersBiso max: 305.08 Å2 / Biso mean: 69.29 Å2 / Biso min: 7.72 Å2
Baniso -1Baniso -2Baniso -3
1-3.572 Å2-0 Å2-0 Å2
2--3.572 Å20 Å2
3----7.143 Å2
Refinement stepCycle: LAST / Resolution: 2.898→39.493 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12854 0 0 19 12873
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313097
X-RAY DIFFRACTIONf_angle_d0.68317833
X-RAY DIFFRACTIONf_chiral_restr0.0462123
X-RAY DIFFRACTIONf_plane_restr0.0032267
X-RAY DIFFRACTIONf_dihedral_angle_d17.2234763
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.898-2.9450.428840.3682066215061
2.945-2.9960.3661100.3552170228064
2.996-3.0510.395970.3462151224863
3.051-3.1090.3841120.332222233466
3.109-3.1730.361220.3142288241068
3.173-3.2420.3081540.2932339249370
3.242-3.3170.3741180.2852428254671
3.317-3.40.3141280.2742538266675
3.4-3.4920.3071530.2612561271476
3.492-3.5950.2851180.2582655277378
3.595-3.7110.3131470.2442688283579
3.711-3.8430.2831410.2312748288981
3.843-3.9970.2791450.2162825297083
3.997-4.1790.2221540.1912857301185
4.179-4.3990.231710.1752909308085
4.399-4.6740.2131490.1633035318488
4.674-5.0340.1811600.1583089324990
5.034-5.5390.2431700.1823143331391
5.539-6.3380.2251740.2083181335592
6.338-7.9750.2421740.2093222339692
7.975-39.4960.2241940.2113522371697

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