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

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Basic information

Entry
Database: PDB / ID: 4dnr
TitleCrystal structure of the CusBA heavy-metal efflux complex from Escherichia coli, E716F 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 / 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 ...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
COPPER (II) ION / 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: 3.68 Å
AuthorsSu, C.-C. / Long, F. / Yu, E.
CitationJournal: To be Published
Title: Crystal structures of the pre-extrusion and extrusion states of the CusBA adaptor-transporter complex
Authors: Su, C.-C. / Long, F. / Yu, E.
History
DepositionFeb 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,2184
Polymers206,1543
Non-polymers641
Water905
1
B: Cation efflux system protein CusB
C: Cation efflux system protein CusB
A: Cation efflux system protein CusA
hetero molecules

B: Cation efflux system protein CusB
C: Cation efflux system protein CusB
A: Cation efflux system protein CusA
hetero molecules

B: Cation efflux system protein CusB
C: Cation efflux system protein CusB
A: Cation efflux system protein CusA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)618,65312
Polymers618,4629
Non-polymers1913
Water1086
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 area61840 Å2
ΔGint-240 kcal/mol
Surface area194200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.594, 159.594, 689.652
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 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P77239
#2: Protein Cation efflux system protein CusA


Mass: 115794.945 Da / Num. of mol.: 1 / Mutation: E716F
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: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 70 %
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: 3.68→114.942 Å / Num. all: 37324 / Num. obs: 37324 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Net I/σ(I): 6.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.68-3.7840.6251.11082427150.625100
3.78-3.8840.5571.21056426620.557100
3.88-3.9940.4421.61026225950.44299.9
3.99-4.113.90.3542981524850.354100
4.11-4.253.90.3082.3955524270.308100
4.25-4.43.90.2433940923940.243100
4.4-4.563.90.1923.8887222670.192100
4.56-4.753.90.1594.5858121980.159100
4.75-4.963.90.1534.7819421160.153100
4.96-5.23.90.164.5775020100.16100
5.2-5.493.90.1664.3749719410.166100
5.49-5.823.80.1744.1684818070.174100
5.82-6.223.70.1654.4651117380.16599.9
6.22-6.723.70.145.2588916080.1499.6
6.72-7.363.40.1116.4505114710.11199.1
7.36-8.233.70.0887.7494313380.08899.1
8.23-9.53.90.05910.5476112140.059100
9.5-11.643.90.03519396110260.035100
11.64-16.463.80.03617.930998260.03699.9
16.46-114.9423.30.0682.516094860.06898.9

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.68→97.6654 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.36 / σ(F): 0 / Phase error: 26.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2719 1703 5.07 %RANDOM
Rwork0.2443 ---
all0.2457 33612 --
obs0.2457 33612 89.93 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.491 Å2 / ksol: 0.318 e/Å3
Displacement parametersBiso max: 505.87 Å2 / Biso mean: 95.6005 Å2 / Biso min: 4.54 Å2
Baniso -1Baniso -2Baniso -3
1-4.2364 Å20 Å2-0 Å2
2--4.2364 Å2-0 Å2
3----8.4729 Å2
Refinement stepCycle: LAST / Resolution: 3.68→97.6654 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12881 0 1 5 12887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313128
X-RAY DIFFRACTIONf_angle_d0.63517874
X-RAY DIFFRACTIONf_chiral_restr0.0412128
X-RAY DIFFRACTIONf_plane_restr0.0032271
X-RAY DIFFRACTIONf_dihedral_angle_d13.9554813
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.68-3.78830.38181300.35242296242679
3.7883-3.91060.32741150.31792350246580
3.9106-4.05040.27441310.28772457258885
4.0504-4.21250.2961560.25992546270287
4.2125-4.40430.25881530.23252598275189
4.4043-4.63650.2171380.20692710284892
4.6365-4.92690.26711460.1972756290294
4.9269-5.30730.26851370.22422760289793
5.3073-5.84140.30091360.24022740287693
5.8414-6.68650.32341540.24152784293893
6.6865-8.42350.23851620.21352813297594
8.4235-97.66540.22771450.24773099324498

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