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- PDB-6ei0: Cytosolic copper storage protein Csp from Streptomyces lividans: ... -

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Basic information

Entry
Database: PDB / ID: 6ei0
TitleCytosolic copper storage protein Csp from Streptomyces lividans: apo form
ComponentsCytosolic copper storage protein (Ccsp)
KeywordsMETAL BINDING PROTEIN / Copper storage / cytocolic
Function / homologyProtein of unknown function DUF326 / Domain of Unknown Function (DUF326) / Uncharacterized cysteine-rich protein YhjQ-like / TRIETHYLENE GLYCOL / Uncharacterized protein
Function and homology information
Biological speciesStreptomyces lividans 1326 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.34 Å
AuthorsStraw, M.L. / Chaplin, A.K. / Hough, M.A. / Worrall, J.A.R.
CitationJournal: Metallomics / Year: 2018
Title: A cytosolic copper storage protein provides a second level of copper tolerance in Streptomyces lividans.
Authors: Straw, M.L. / Chaplin, A.K. / Hough, M.A. / Paps, J. / Bavro, V.N. / Wilson, M.T. / Vijgenboom, E. / Worrall, J.A.R.
History
DepositionSep 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.formula_weight
Revision 1.2Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
Q: Cytosolic copper storage protein (Ccsp)
G: Cytosolic copper storage protein (Ccsp)
U: Cytosolic copper storage protein (Ccsp)
N: Cytosolic copper storage protein (Ccsp)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2517
Polymers49,9134
Non-polymers3383
Water7,584421
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8720 Å2
ΔGint-72 kcal/mol
Surface area17420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.576, 93.576, 213.252
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein
Cytosolic copper storage protein (Ccsp)


Mass: 12478.286 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans 1326 (bacteria) / Gene: SAMN05428941_3460 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1H2BDT0
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 421 / 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: 2.7 Å3/Da / Density % sol: 54.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15 mg/ml protein was mixed with an equal volume of reservoir solution containing 1.4 M ammonium sulfate, 0.1 M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.34→81.04 Å / Num. obs: 123798 / % possible obs: 100 % / Redundancy: 18.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.016 / Rrim(I) all: 0.068 / Net I/σ(I): 18.1 / Num. measured all: 2259045 / Scaling rejects: 2225
Reflection shellResolution: 1.34→1.37 Å / Redundancy: 13.3 % / Rmerge(I) obs: 1.452 / Num. unique obs: 8933 / CC1/2: 0.76 / Rpim(I) all: 0.409 / Rrim(I) all: 1.51 / % possible all: 99.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimless0.5.23data scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3lmf

3lmf


Resolution: 1.34→81.04 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.802 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.051 / ESU R Free: 0.051 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.202 6098 5 %RANDOM
Rwork0.169 ---
obs0.171 116755 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å2-0.39 Å20 Å2
2---0.77 Å20 Å2
3---2.5 Å2
Refinement stepCycle: LAST / Resolution: 1.34→81.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3358 0 21 421 3800
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193562
X-RAY DIFFRACTIONr_bond_other_d0.0010.023220
X-RAY DIFFRACTIONr_angle_refined_deg1.5371.9514850
X-RAY DIFFRACTIONr_angle_other_deg2.13937475
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7715510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.36223.826149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.29815590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4221536
X-RAY DIFFRACTIONr_chiral_restr0.0920.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024184
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02688
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr8.2536781
X-RAY DIFFRACTIONr_sphericity_free27.9795249
X-RAY DIFFRACTIONr_sphericity_bonded14.48156914
LS refinement shellResolution: 1.34→1.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 431 -
Rwork0.302 8499 -
obs--99.22 %

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