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- PDB-6ek9: Cytosolic copper storage protein Csp from Streptomyces lividans: ... -

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Basic information

Entry
Database: PDB / ID: 6ek9
TitleCytosolic copper storage protein Csp from Streptomyces lividans: Cu loaded form
ComponentsCytosolic copper storage protein
KeywordsMETAL BINDING PROTEIN / Copper storage / cytocolic
Function / homologyProtein of unknown function DUF326 / Domain of Unknown Function (DUF326) / Uncharacterized cysteine-rich protein YhjQ-like / metal ion binding / COPPER (I) ION / Ferredoxin
Function and homology information
Biological speciesStreptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytosolic copper storage protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,88921
Polymers12,6181
Non-polymers1,27120
Water77543
1
A: Cytosolic copper storage protein
hetero molecules

A: Cytosolic copper storage protein
hetero molecules

A: Cytosolic copper storage protein
hetero molecules

A: Cytosolic copper storage protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,55884
Polymers50,4744
Non-polymers5,08480
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area7830 Å2
ΔGint-61 kcal/mol
Surface area17600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.081, 64.138, 66.003
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Cytosolic copper storage protein


Mass: 12618.470 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Gene: SLIV_21385 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D6ES11
#2: Chemical
ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.6 Å3/Da / Density % sol: 52.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 15 mg/ml protein. 1.4 M ammonium sulfate, 0.1 M MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2016 / Details: Mirrors
RadiationMonochromator: Si monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.945
11-H, L, K20.055
ReflectionResolution: 1.5→45.23 Å / Num. obs: 20701 / % possible obs: 96.4 % / Redundancy: 3.6 % / CC1/2: 0.992 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.045 / Net I/σ(I): 9.7
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.161 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 990 / CC1/2: 0.958 / Rpim(I) all: 0.097 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
Aimlessdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EIO

6eio


Resolution: 1.5→45.22 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.505 / SU ML: 0.072 / SU R Cruickshank DPI: 0.0193 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.019 / ESU R Free: 0.016
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED TWIN REFINEMENT USED
RfactorNum. reflection% reflectionSelection details
Rfree0.2308 1228 5.9 %RANDOM
Rwork0.2056 ---
obs0.2071 19471 89.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 81.35 Å2 / Biso mean: 37.874 Å2 / Biso min: 9.72 Å2
Baniso -1Baniso -2Baniso -3
1--7.89 Å20 Å20 Å2
2--0.64 Å20 Å2
3---7.25 Å2
Refinement stepCycle: final / Resolution: 1.5→45.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms859 0 20 43 922
Biso mean--28.76 17.42 -
Num. residues----121
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.019864
X-RAY DIFFRACTIONr_bond_other_d0.0020.02783
X-RAY DIFFRACTIONr_angle_refined_deg2.0561.9481168
X-RAY DIFFRACTIONr_angle_other_deg1.24731808
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5535120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.19823.61136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.07515139
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.717159
X-RAY DIFFRACTIONr_chiral_restr0.1270.2141
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021006
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02167
X-RAY DIFFRACTIONr_rigid_bond_restr3.94731647
X-RAY DIFFRACTIONr_sphericity_free5.045541
X-RAY DIFFRACTIONr_sphericity_bonded4.04951664
LS refinement shellHighest resolution: 1.5 Å
Refinement TLS params.Method: refined / Origin x: 5.376 Å / Origin y: 9.578 Å / Origin z: 23.911 Å
111213212223313233
T0.3126 Å20.0264 Å2-0.0554 Å2-0.1139 Å20.1207 Å2--0.1717 Å2
L5.3424 °2-0.3557 °2-0.5281 °2-5.8516 °20.546 °2--4.1336 °2
S-0.1061 Å °0.1854 Å °0.242 Å °-1.0331 Å °-0.4859 Å °-0.4107 Å °-0.7848 Å °0.1937 Å °0.5921 Å °

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