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- PDB-6q58: Copper loading to a cytosolic copper storage protein from Strepto... -

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Basic information

Entry
Database: PDB / ID: 6q58
TitleCopper loading to a cytosolic copper storage protein from Streptomyces lividans (five coppers)
ComponentsCytosolic copper storage protein
KeywordsMETAL BINDING PROTEIN / Copper / cytosolic / storage protein / Streptomyces livdians
Function / homologyProtein of unknown function DUF326 / Domain of Unknown Function (DUF326) / Uncharacterized cysteine-rich protein YhjQ-like / metal ion binding / COPPER (I) ION / Four-helix bundle copper-binding protein
Function and homology information
Biological speciesStreptomyces coelicolor 1326 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsStraw, M.L. / Hough, M.A. / Worrall, J.A.R.
CitationJournal: Chemistry / Year: 2019
Title: A Histidine Residue and a Tetranuclear Cuprous-thiolate Cluster Dominate the Copper Loading Landscape of a Copper Storage Protein from Streptomyces lividans.
Authors: Straw, M.L. / Hough, M.A. / Wilson, M.T. / Worrall, J.A.R.
History
DepositionDec 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 24, 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 / struct_ncs_dom_lim
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_asym_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_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Cytosolic copper storage protein
C: Cytosolic copper storage protein
D: Cytosolic copper storage protein
A: Cytosolic copper storage protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,09519
Polymers50,1414
Non-polymers95315
Water7,620423
1
B: Cytosolic copper storage protein
C: Cytosolic copper storage protein
A: Cytosolic copper storage protein
hetero molecules

D: Cytosolic copper storage protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,09519
Polymers50,1414
Non-polymers95315
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x-y,x,z+1/61
Buried area8920 Å2
ΔGint-133 kcal/mol
Surface area17900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.051, 93.051, 212.340
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21C
12B
22D
13B
23A
14C
24D
15C
25A
16D
26A

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALGLYGLYBA19 - 1363 - 120
21VALVALGLYGLYCB19 - 1363 - 120
12ASPASPLEULEUBA20 - 1354 - 119
22ASPASPLEULEUDC20 - 1354 - 119
13VALVALLEULEUBA19 - 1353 - 119
23VALVALLEULEUAD19 - 1353 - 119
14ASPASPLEULEUCB20 - 1354 - 119
24ASPASPLEULEUDC20 - 1354 - 119
15VALVALLEULEUCB19 - 1353 - 119
25VALVALLEULEUAD19 - 1353 - 119
16ASPASPLEULEUDC20 - 1354 - 119
26ASPASPLEULEUAD20 - 1354 - 119

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Cytosolic copper storage protein


Mass: 12535.339 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor 1326 (bacteria)
Gene: SCO3281 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X8F4
#2: Chemical
ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / 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: 2.65 Å3/Da / Density % sol: 53.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.5 M Ammonium Sulfate 0.1M MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.33 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.33 Å / Relative weight: 1
ReflectionResolution: 1.5→212.34 Å / Num. obs: 85587 / % possible obs: 98 % / Redundancy: 8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.02 / Rrim(I) all: 0.06 / Net I/σ(I): 19.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.5-1.532.90.65934920.4480.4470.80182.5
8.22-75.348.70.0546280.9940.0180.05896.2

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Processing

Software
NameVersionClassification
Aimless0.6.2data scaling
REFMACrefinement
PDB_EXTRACT3.24data extraction
DIALSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EI0

6ei0


Resolution: 1.5→212.34 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.463 / SU ML: 0.053 / SU R Cruickshank DPI: 0.0724 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.072
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2135 4291 5 %RANDOM
Rwork0.1945 ---
obs0.1955 81253 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 97.19 Å2 / Biso mean: 27.975 Å2 / Biso min: 13.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.08 Å20 Å2
2--0.15 Å20 Å2
3----0.5 Å2
Refinement stepCycle: final / Resolution: 1.5→212.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3367 0 15 423 3805
Biso mean--35.42 36.62 -
Num. residues----473
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193446
X-RAY DIFFRACTIONr_bond_other_d0.0020.023105
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.9464673
X-RAY DIFFRACTIONr_angle_other_deg0.99137182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7175483
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.98623.699146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.36115566
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1631536
X-RAY DIFFRACTIONr_chiral_restr0.0840.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024033
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02667
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B69500.13
12C69500.13
21B71560.08
22D71560.08
31B68480.13
32A68480.13
41C68620.13
42D68620.13
51C71600.08
52A71600.08
61D69720.12
62A69720.12
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 269 -
Rwork0.278 4993 -
all-5262 -
obs--82.85 %

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