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- PDB-4dop: Crystal structure of the CusBA heavy-metal efflux complex from Es... -

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Basic information

Entry
Database: PDB / ID: 4dop
TitleCrystal structure of the CusBA heavy-metal efflux complex from Escherichia coli, R mutant
Components
  • Cation efflux system protein CusA
  • Cation efflux system protein CusB
KeywordsTRANSPORT PROTEIN / beta barrel
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 export / copper ion transmembrane transporter activity / 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 export / copper ion transmembrane transporter activity / detoxification of copper ion / response to copper ion / xenobiotic transmembrane transporter activity / intracellular copper ion homeostasis / transition metal ion binding / response to toxic substance / outer membrane-bounded periplasmic space / copper ion binding / membrane / plasma membrane
Similarity search - Function
Long alpha hairpin domain of cation efflux system protein, CusB / Heavy metal binding domain / Heavy metal binding domain / Cation efflux system CzcA/CusA/SilA/NccA/HelA/CnrA / 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 ...Long alpha hairpin domain of cation efflux system protein, CusB / Heavy metal binding domain / Heavy metal binding domain / Cation efflux system CzcA/CusA/SilA/NccA/HelA/CnrA / 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
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 / Resolution: 4.2 Å
AuthorsSu, C.-C. / Long, F. / Yu, E.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Charged Amino Acids (R83, E567, D617, E625, R669, and K678) of CusA Are Required for Metal Ion Transport in the Cus Efflux System.
Authors: Su, C.C. / Long, F. / Lei, H.T. / Bolla, J.R. / Do, S.V. / Rajashankar, K.R. / Yu, E.W.
History
DepositionFeb 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2012Group: Database references
Revision 1.2Sep 5, 2012Group: Database references
Revision 1.3Feb 28, 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)206,0503
Polymers206,0503
Non-polymers00
Water32418
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)618,1509
Polymers618,1509
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 area57700 Å2
ΔGint-167 kcal/mol
Surface area185940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.517, 160.517, 681.326
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: b0574, cusB, JW0563, ylcD / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P77239
#2: Protein Cation efflux system protein CusA


Mass: 115690.773 Da / Num. of mol.: 1 / Mutation: R669A
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 / 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: 4.1 Å3/Da / Density % sol: 69.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: PEG3350, NH4SO4, JM600, pH 7, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2011
RadiationMonochromator: Cryogenically-cooled double crystal Si(111) monochromator. Triple striped vertical and horizantal focussing mirrors in Kirkpatrick-Baez geometry.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 4.2→136.206 Å / Num. all: 25305 / Num. obs: 25305 / % possible obs: 100 % / Redundancy: 6.9 % / Rsym value: 0.332 / Net I/σ(I): 6.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
4.2-4.317.20.8680.91327918550.868100
4.31-4.437.20.72111276417830.721100
4.43-4.567.10.6021.21247817560.602100
4.56-4.77.10.5381.41208016940.538100
4.7-4.857.10.481.51168616510.4899.9
4.85-5.027.10.491.51133516030.4999.9
5.02-5.2170.4831.51079215320.483100
5.21-5.4270.5141.41036914790.514100
5.42-5.6670.5321.41012014530.532100
5.66-5.9470.5281.4951213680.528100
5.94-6.266.90.5031.5885512840.503100
6.26-6.646.70.41.9842412490.4100
6.64-7.16.70.3262.3774811580.326100
7.1-7.676.50.2223.3709010920.22299.9
7.67-8.460.1664.3604310130.16699.9
8.4-9.396.70.1036.962419290.103100
9.39-10.8470.076957438150.076100
10.84-13.2870.06210.948777010.062100
13.28-18.786.70.06211.137125550.06299.9
18.78-136.2065.80.0772.719273350.07799.2

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.2→97.311 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8362 / SU ML: 0.54 / σ(F): 0 / Phase error: 23.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1188 5.09 %RANDOM
Rwork0.2219 ---
all0.2241 23337 --
obs0.2241 23337 92.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 101.314 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso max: 449.28 Å2 / Biso mean: 111.4877 Å2 / Biso min: 5.44 Å2
Baniso -1Baniso -2Baniso -3
1-4.9741 Å2-0 Å2-0 Å2
2--4.9741 Å2-0 Å2
3----9.9481 Å2
Refinement stepCycle: LAST / Resolution: 4.2→97.311 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12873 0 0 18 12891
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313125
X-RAY DIFFRACTIONf_angle_d0.61717870
X-RAY DIFFRACTIONf_chiral_restr0.0412128
X-RAY DIFFRACTIONf_plane_restr0.0032271
X-RAY DIFFRACTIONf_dihedral_angle_d14.1184814
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.2-4.39130.33921330.28392582271587
4.3913-4.62280.27571540.22062640279490
4.6228-4.91240.22611620.18832689285191
4.9124-5.29170.25981450.20952714285992
5.2917-5.82410.28011250.25082720284590
5.8241-6.66670.2961580.23522793295193
6.6667-8.39860.27561610.20092891305296
8.3986-97.3110.23631500.21363120327098

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