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- PDB-7mek: Structure of copper bound to Ycnl -

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Basic information

Entry
Database: PDB / ID: 7mek
TitleStructure of copper bound to Ycnl
ComponentsUncharacterized protein YcnI
KeywordsMETAL BINDING PROTEIN / Cupredoxin / Cu-binding
Function / homologyYcnI-like / YcnI-like superfamily / Domain of unkown function (DUF1775) / plasma membrane / COPPER (II) ION / Copper-binding protein CutI
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsDamle, M. / Fisher, O.S.
CitationJournal: J.Biol.Chem. / Year: 2021
Title: The YcnI protein from Bacillus subtilis contains a copper-binding domain.
Authors: Damle, M.S. / Singh, A.N. / Peters, S.C. / Szalai, V.A. / Fisher, O.S.
History
DepositionApr 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 1, 2021Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 15, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein YcnI
B: Uncharacterized protein YcnI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0154
Polymers28,8882
Non-polymers1272
Water2,252125
1
A: Uncharacterized protein YcnI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5072
Polymers14,4441
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein YcnI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5072
Polymers14,4441
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.190, 90.190, 209.120
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Uncharacterized protein YcnI


Mass: 14443.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ycnI, BSU03940 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P94431
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.25 Å3/Da / Density % sol: 71.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M citric acid, 2.17 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.3776 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3776 Å / Relative weight: 1
ReflectionResolution: 2.11→30 Å / Num. obs: 54321 / % possible obs: 99.6 % / Redundancy: 5.3 % / CC1/2: 0.995 / Rrim(I) all: 0.138 / Net I/σ(I): 9.64
Reflection shellResolution: 2.11→2.16 Å / Mean I/σ(I) obs: 2.64 / Num. unique obs: 3960 / CC1/2: 0.569 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ESM

3esm


Resolution: 2.11→29.52 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2175 3670 6.76 %
Rwork0.1953 50651 -
obs0.1968 54321 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.64 Å2 / Biso mean: 47.0486 Å2 / Biso min: 20.71 Å2
Refinement stepCycle: final / Resolution: 2.11→29.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2027 0 2 125 2154
Biso mean--54.78 50.35 -
Num. residues----256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022085
X-RAY DIFFRACTIONf_angle_d0.5262843
X-RAY DIFFRACTIONf_chiral_restr0.045302
X-RAY DIFFRACTIONf_plane_restr0.004368
X-RAY DIFFRACTIONf_dihedral_angle_d14.17747
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.11-2.140.3091360.30841913204997
2.14-2.170.27671440.260919492093100
2.17-2.20.2611390.234319632102100
2.2-2.240.2061420.226719272069100
2.24-2.270.22721420.219519702112100
2.27-2.310.29941390.224219432082100
2.31-2.350.22981390.231319372076100
2.35-2.390.2211390.21719522091100
2.39-2.440.24761420.20619842126100
2.44-2.490.21251420.225119372079100
2.49-2.540.27541380.232519422080100
2.54-2.60.22011470.213219462093100
2.6-2.660.21161400.212719772117100
2.66-2.730.2371450.222519542099100
2.74-2.820.22721420.21819572099100
2.82-2.910.23231440.212919622106100
2.91-3.010.23921410.194719332074100
3.01-3.130.25441410.202519362077100
3.13-3.270.2421430.20719582101100
3.27-3.440.22271430.180519492092100
3.45-3.660.20981380.18611884202297
3.66-3.940.20531480.184219642112100
3.94-4.340.15471380.151319612099100
4.34-4.960.16111440.150719472091100
4.96-6.240.23451350.172419492084100
6.25-29.520.22561390.21521957209699

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