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

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Basic information

Entry
Database: PDB / ID: 4dnt
TitleCrystal structure of the CusBA heavy-metal efflux complex from Escherichia coli, 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
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: 3.1 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 9, 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

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


Theoretical massNumber of molelcules
Total (without water)206,0923
Polymers206,0923
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)618,2769
Polymers618,2769
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 area57490 Å2
ΔGint-166 kcal/mol
Surface area183920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.636, 159.636, 681.098
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, cusA, 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: 115732.883 Da / Num. of mol.: 1 / Mutation: D405A
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: 4.05 Å3/Da / Density % sol: 69.64 %
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: 3.1→113.516 Å / Num. all: 61292 / Num. obs: 61292 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Rsym value: 0.139 / Net I/σ(I): 10.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.1-3.185.50.8720.82472445020.872100
3.18-3.275.50.70912385443640.709100
3.27-3.365.50.5221.42317842310.522100
3.36-3.475.40.4381.42258941500.438100
3.47-3.585.50.3372.12178539890.337100
3.58-3.715.40.2742.62113138910.274100
3.71-3.855.40.233.12024337310.23100
3.85-45.40.1853.71945736130.185100
4-4.185.40.1415.11861034620.141100
4.18-4.385.30.1146.11779833330.114100
4.38-4.625.30.097.61674731560.09100
4.62-4.95.30.088.71595529950.08100
4.9-5.245.20.088.51459228110.0899.9
5.24-5.665.10.08581352426510.08599.8
5.66-6.24.90.1026.41184924130.10299.7
6.2-6.934.60.1016.21034122350.101100
6.93-85.50.0916.41077519610.091100
8-9.85.40.04115.2918016940.041100
9.8-13.865.30.03915.4696213240.039100
13.86-113.5164.60.0428.436407860.04299.7

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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: 3.1→107.327 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8294 / SU ML: 0.32 / σ(F): 0 / Phase error: 23.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2445 2834 5.03 %RANDOM
Rwork0.2191 ---
all0.2203 56385 --
obs0.2203 56385 91.96 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.979 Å2 / ksol: 0.319 e/Å3
Displacement parametersBiso max: 308.31 Å2 / Biso mean: 79.9083 Å2 / Biso min: 14.05 Å2
Baniso -1Baniso -2Baniso -3
1-5.3991 Å20 Å2-0 Å2
2--5.3991 Å2-0 Å2
3----10.7981 Å2
Refinement stepCycle: LAST / Resolution: 3.1→107.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12876 0 0 19 12895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313122
X-RAY DIFFRACTIONf_angle_d0.67517866
X-RAY DIFFRACTIONf_chiral_restr0.0462128
X-RAY DIFFRACTIONf_plane_restr0.0032270
X-RAY DIFFRACTIONf_dihedral_angle_d15.8384812
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.15350.35661350.3532249238479
3.1535-3.21080.38091330.33132289242280
3.2108-3.27260.29051160.31372379249582
3.2726-3.33940.30011240.29282434255885
3.3394-3.4120.33071390.29452483262286
3.412-3.49140.31171400.27142524266488
3.4914-3.57870.31320.26562548268089
3.5787-3.67550.28291260.25172638276491
3.6755-3.78360.27031440.24492686283093
3.7836-3.90580.27571160.22982742285894
3.9058-4.04540.24251490.2042709285894
4.0454-4.20730.22651550.18352780293596
4.2073-4.39880.19541460.16762797294396
4.3988-4.63070.1891650.1622816298197
4.6307-4.92090.18231660.15692814298097
4.9209-5.30080.19771470.17342875302298
5.3008-5.83420.23871300.20452896302698
5.8342-6.67830.23921530.21852867302097
6.6783-8.41350.22571670.20172957312499
8.4135-107.3270.24281510.23183068321998

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