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- PDB-3k0i: Crystal structure of Cu(I)CusA -

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Basic information

Entry
Database: PDB / ID: 3k0i
TitleCrystal structure of Cu(I)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
COPPER (I) ION / Cation efflux system protein CusA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 4.116 Å
AuthorsSu, C.-C.
CitationJournal: To be Published
Title: Crystal structure of CusA
Authors: Long, F. / Su, C.-C. / Routh, M.D. / Rajashankar, K.R. / Yu, E.W.
History
DepositionSep 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _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

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Assembly

Deposited unit
A: Cation efflux system protein cusA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,9613
Polymers115,8341
Non-polymers1272
Water00
1
A: Cation efflux system protein cusA
hetero molecules

A: Cation efflux system protein cusA
hetero molecules

A: Cation efflux system protein cusA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)347,8839
Polymers347,5023
Non-polymers3816
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 area17370 Å2
ΔGint-102.8 kcal/mol
Surface area125500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.256, 179.256, 286.266
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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
Details: Resistance-Nodulation-Cell Division (RND) Heavy-metal Transporter
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
#2: Chemical ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu

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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: 3.82 Å3/Da / Density % sol: 67.81 %
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: 1.3779 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: 1.3779 Å / Relative weight: 1
ReflectionResolution: 4.116→40 Å / Num. obs: 26090 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 8.8
Reflection shellResolution: 4.116→4.27 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.457 / % possible all: 99.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 4.116→38.458 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.56 / σ(F): 0.12 / Phase error: 29 / Stereochemistry target values: ML / Details: The Friedel pairs were used in phasing
RfactorNum. reflection% reflection
Rfree0.3085 635 4.97 %
Rwork0.2685 --
obs0.2705 12766 91.32 %
all-14211 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 130.53 Å2 / ksol: 0.25 e/Å3
Displacement parametersBiso mean: 190.13 Å2
Baniso -1Baniso -2Baniso -3
1-1.628 Å2-0 Å2-0 Å2
2--1.628 Å20 Å2
3----3.424 Å2
Refinement stepCycle: LAST / Resolution: 4.116→38.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7802 0 2 0 7804
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067960
X-RAY DIFFRACTIONf_angle_d1.24810834
X-RAY DIFFRACTIONf_dihedral_angle_d20.1072877
X-RAY DIFFRACTIONf_chiral_restr0.0751288
X-RAY DIFFRACTIONf_plane_restr0.0081362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.116-4.43330.28091240.25622215X-RAY DIFFRACTION85
4.4333-4.87860.22111380.20262349X-RAY DIFFRACTION90
4.8786-5.58270.291300.21142429X-RAY DIFFRACTION92
5.5827-7.02660.36311180.27492537X-RAY DIFFRACTION95
7.0266-38.45990.32351250.29562601X-RAY DIFFRACTION94

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