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- PDB-6q6b: Structure of the copper storage protein, Ccsp, from Streptomyces ... -

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Basic information

Entry
Database: PDB / ID: 6q6b
TitleStructure of the copper storage protein, Ccsp, from Streptomyces lividans loaded with 10 copper equivalents
ComponentsCytosolic copper storage protein
KeywordsMETAL BINDING PROTEIN / Copper / cytosolic / storage / Streptomyces lividans
Function / homologyProtein of unknown function DUF326 / Copper storage protein / Uncharacterized cysteine-rich protein YhjQ-like / metal ion binding / COPPER (II) ION / COPPER (I) ION / Four-helix bundle copper-binding protein
Function and homology information
Biological speciesStreptomyces lividans 1326 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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 10, 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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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
A: Cytosolic copper storage protein
D: Cytosolic copper storage protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,10368
Polymers56,0364
Non-polymers4,06764
Water2,234124
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)60,10368
Polymers56,0364
Non-polymers4,06764
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x-y,x,z+1/61
Buried area8680 Å2
ΔGint-60 kcal/mol
Surface area17730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.398, 93.398, 216.015
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
22A
13B
23D
14C
24A
15C
25D
16A
26D

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
11ASPASPLEULEUBA20 - 13517 - 132
21ASPASPLEULEUCB20 - 13517 - 132
12VALVALLEULEUBA19 - 13516 - 132
22VALVALLEULEUAC19 - 13516 - 132
13ASPASPLEULEUBA20 - 13517 - 132
23ASPASPLEULEUDD20 - 13517 - 132
14ASPASPLEULEUCB20 - 13517 - 132
24ASPASPLEULEUAC20 - 13517 - 132
15ASPASPGLYGLYCB20 - 13617 - 133
25ASPASPGLYGLYDD20 - 13617 - 133
16ASPASPLEULEUAC20 - 13517 - 132
26ASPASPLEULEUDD20 - 13517 - 132

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Cytosolic copper storage protein


Mass: 14008.987 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans 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.: 59 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.43 Å3/Da / Density % sol: 49.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.5 M Ammonium Sulfate, 0.1M MES pH6.0

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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 / 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: 1.9→216.01 Å / Num. obs: 44544 / % possible obs: 99.7 % / Redundancy: 9.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.035 / Rrim(I) all: 0.108 / Net I/σ(I): 12.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.9-1.949.21.81328310.4640.6361.926100
9.11-75.758.80.0694740.9980.0220.07395.6

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Phasing

PhasingMethod: molecular replacement

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Processing

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

6ei0


Resolution: 1.9→216.01 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.645 / SU ML: 0.127 / SU R Cruickshank DPI: 0.1553 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.146
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.255 2266 5.1 %RANDOM
Rwork0.2177 ---
obs0.2195 42261 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 137.88 Å2 / Biso mean: 46.74 Å2 / Biso min: 19.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.09 Å20 Å2
2--0.18 Å20 Å2
3----0.58 Å2
Refinement stepCycle: final / Resolution: 1.9→216.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3466 0 64 124 3654
Biso mean--58.97 42.51 -
Num. residues----485
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193561
X-RAY DIFFRACTIONr_bond_other_d0.0020.023216
X-RAY DIFFRACTIONr_angle_refined_deg1.6391.9474834
X-RAY DIFFRACTIONr_angle_other_deg1.02337437
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1845497
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.73523.667150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.22915584
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4911537
X-RAY DIFFRACTIONr_chiral_restr0.0980.2585
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024167
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02690
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B67820.12
12C67820.12
21B70980.08
22A70980.08
31B67880.12
32D67880.12
41C69320.12
42A69320.12
51C72560.08
52D72560.08
61A69020.12
62D69020.12
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.456 152 -
Rwork0.437 3090 -
all-3242 -
obs--99.82 %

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