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- PDB-9c14: Structure of the CopC-like domain of YcnJ -

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Basic information

Entry
Database: PDB / ID: 9c14
TitleStructure of the CopC-like domain of YcnJ
ComponentsCopper transport protein YcnJ
KeywordsMETAL BINDING PROTEIN / Copper import / CopC / YcnJ / extracellular domain
Function / homology
Function and homology information


copper ion transport / response to copper ion / periplasmic space / copper ion binding / plasma membrane
Similarity search - Function
Copper resistance protein D / Copper resistance protein D / Copper transport protein C/D / CopC domain / CopC domain / Copper resistance protein CopC/internalin, immunoglobulin-like / Immunoglobulin E-set
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Copper transport protein CutJ
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
Authorsde Oliveira Silva, Y.R. / Zheng, D. / Fisher, O.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2137107 United States
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Copper acquisition in Bacillus subtilis involves Cu(II) exchange between YcnI and YcnJ.
Authors: Rafael de Oliveira Silva, Y. / Barnes, G. / Zheng, D. / Zhitnitsky, D. / Geathers, S.J. / Peters, S.C. / Szalai, V.A. / Helmann, J.D. / Fisher, O.S.
History
DepositionMay 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Copper transport protein YcnJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2654
Polymers10,9231
Non-polymers3423
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.957, 35.957, 165.762
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Copper transport protein YcnJ


Mass: 10923.192 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: ycnJ, BSU03950 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C0SP95
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.45 Å3/Da / Density % sol: 49.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium Sulfate, 39% PEG 8000. Cross-seeding with crystals obtained for YcnI W137F (PDB ID: 8UM6)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.378 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.378 Å / Relative weight: 1
ReflectionResolution: 1.6→55.25 Å / Num. obs: 15495 / % possible obs: 100 % / Redundancy: 24.1 % / Biso Wilson estimate: 24.7 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.858 / Rpim(I) all: 0.177 / Rrim(I) all: 0.876 / Net I/σ(I): 9.6
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 24.6 % / Num. unique obs: 746 / CC1/2: 0.516 / Rpim(I) all: 8.103 / Rrim(I) all: 40.355 / % possible all: 100

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→41.44 Å / SU ML: 0.2796 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.9354
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2327 1533 10.01 %
Rwork0.2107 13780 -
obs0.2129 15313 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.31 Å2
Refinement stepCycle: LAST / Resolution: 1.6→41.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms771 0 20 62 853
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061827
X-RAY DIFFRACTIONf_angle_d0.89851121
X-RAY DIFFRACTIONf_chiral_restr0.066118
X-RAY DIFFRACTIONf_plane_restr0.0058146
X-RAY DIFFRACTIONf_dihedral_angle_d7.0172113
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.650.48551350.4751209X-RAY DIFFRACTION99.85
1.65-1.710.41621380.39011234X-RAY DIFFRACTION99.85
1.71-1.780.30671330.29241198X-RAY DIFFRACTION100
1.78-1.860.25871350.21721223X-RAY DIFFRACTION100
1.86-1.960.24091380.21781234X-RAY DIFFRACTION99.93
1.96-2.080.26121350.23861219X-RAY DIFFRACTION99.93
2.08-2.240.24171390.19781247X-RAY DIFFRACTION99.86
2.24-2.470.24451380.21121241X-RAY DIFFRACTION100
2.47-2.820.2361410.21951278X-RAY DIFFRACTION100
2.82-3.560.23371430.19991289X-RAY DIFFRACTION99.93
3.56-41.440.18161580.17151408X-RAY DIFFRACTION100

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