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- PDB-3k07: Crystal structure of CusA -

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Basic information

Entry
Database: PDB / ID: 3k07
TitleCrystal structure of CusA
ComponentsCation efflux system protein cusA
KeywordsTRANSPORT PROTEIN / transmembrane helix / Cell inner membrane / Cell membrane / Copper transport / Ion transport / Membrane / Transmembrane / Transport
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 / copper ion export / copper ion transmembrane transporter activity / detoxification of copper ion / response to 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 / copper ion export / copper ion transmembrane transporter activity / detoxification of copper ion / response to copper ion / xenobiotic transmembrane transporter activity / intracellular copper ion homeostasis / response to toxic substance / copper ion binding / membrane / plasma membrane
Similarity search - Function
Cation efflux system CzcA/CusA/SilA/NccA/HelA/CnrA / 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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.521 Å
AuthorsSu, C.-C.
CitationJournal: Nature / Year: 2010
Title: Crystal structures of the CusA efflux pump suggest methionine-mediated metal transport.
Authors: Long, F. / Su, C.C. / Zimmermann, M.T. / Boyken, S.E. / Rajashankar, K.R. / Jernigan, R.L. / Yu, E.W.
History
DepositionSep 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 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
A: Cation efflux system protein cusA


Theoretical massNumber of molelcules
Total (without water)115,8341
Polymers115,8341
Non-polymers00
Water0
1
A: Cation efflux system protein cusA

A: Cation efflux system protein cusA

A: Cation efflux system protein cusA


Theoretical massNumber of molelcules
Total (without water)347,5023
Polymers347,5023
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area15690 Å2
ΔGint-74 kcal/mol
Surface area117670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.393, 178.393, 285.761
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 cusA


Mass: 115833.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b0575, cusA, JW0564, ybdE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-codonPlus-dacrB / References: UniProt: P38054

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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: 3.78 Å3/Da / Density % sol: 67.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10% PEG 3350, 0.1M Na citrate, 0.5M (NH4)2SO4, 10% Glycerol, 1% JM600 pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 30, 2009
RadiationMonochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.52→40 Å / Num. obs: 21591 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rmerge(I) obs: 0.057 / Χ2: 1.257 / Net I/σ(I): 12.2
Reflection shellResolution: 3.52→3.65 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.489 / Num. unique all: 2149 / Χ2: 1.123 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SHARPphasing
RefinementResolution: 3.521→37.285 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.34 / σ(F): 0.1 / Phase error: 27.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.279 1037 5.1 %
Rwork0.237 19316 -
obs0.239 20353 92.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 110.889 Å2 / ksol: 0.295 e/Å3
Displacement parametersBiso max: 515.41 Å2 / Biso mean: 154.211 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-1.411 Å2-0 Å2-0 Å2
2--1.411 Å20 Å2
3----2.822 Å2
Refinement stepCycle: LAST / Resolution: 3.521→37.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7885 0 0 0 7885
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048047
X-RAY DIFFRACTIONf_angle_d0.87410958
X-RAY DIFFRACTIONf_chiral_restr0.061301
X-RAY DIFFRACTIONf_plane_restr0.0041379
X-RAY DIFFRACTIONf_dihedral_angle_d18.0242905
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.521-3.7070.2981300.2952523265386
3.707-3.9390.3181530.2542584273789
3.939-4.2420.2841580.2322735289393
4.242-4.6680.2731380.2052815295395
4.668-5.3420.2741730.212853302697
5.342-6.7240.2881470.252896304396
6.724-37.2870.2411380.2232910304894
Refinement TLS params.Method: refined / Origin x: 4.4948 Å / Origin y: 27.007 Å / Origin z: 76.37 Å
111213212223313233
T1.1824 Å2-0.1172 Å20.1979 Å2-0.5657 Å20.0198 Å2--0.7465 Å2
L0.5342 °20.0755 °2-0.4272 °2-0.3896 °2-0.5184 °2--2.5907 °2
S0.1346 Å °-0.0217 Å °0.2457 Å °-0.0312 Å °0.1708 Å °-0.009 Å °-0.601 Å °-0.0733 Å °-0.2604 Å °
Refinement TLS groupSelection details: all

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