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- PDB-7pge: copper transporter PcoB -

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Basic information

Entry
Database: PDB / ID: 7pge
Titlecopper transporter PcoB
ComponentsCopper resistance protein B
KeywordsTRANSPORT PROTEIN / transporter
Function / homologyCopper resistance B precursor / Copper resistance protein B precursor (CopB) / intracellular copper ion homeostasis / cell outer membrane / copper ion binding / THIOCYANATE ION / Copper resistance protein B
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsLi, P. / Gourdon, P.E.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Citation
Journal: Protein Sci. / Year: 2022
Title: PcoB is a defense outer membrane protein that facilitates cellular uptake of copper.
Authors: Li, P. / Nayeri, N. / Gorecki, K. / Becares, E.R. / Wang, K. / Mahato, D.R. / Andersson, M. / Abeyrathna, S.S. / Lindkvist-Petersson, K. / Meloni, G. / Missel, J.W. / Gourdon, P.
#1: Journal: To Be Published
Title: PcoB is a defense outer membrane protein that facilitate cellular uptake of copper
Authors: Ping, L. / Pontus, G.
History
DepositionAug 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Copper resistance protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9704
Polymers24,3761
Non-polymers5943
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-5 kcal/mol
Surface area11220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.489, 75.538, 91.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Copper resistance protein B


Mass: 24375.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pcoB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q47453
#2: Chemical ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Chemical ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#4: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.51 Å3/Da / Density % sol: 50.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG4000, NaSCN, sodium acetate

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: May 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→43.53 Å / Num. obs: 30731 / % possible obs: 99.3 % / Redundancy: 6.6 % / Biso Wilson estimate: 38.19 Å2 / CC1/2: 0.99 / Net I/σ(I): 11.47
Reflection shellResolution: 1.972→2.043 Å / Num. unique obs: 4965 / CC1/2: 0.67

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2→43.53 Å / SU ML: 0.2399 / Cross valid method: FREE R-VALUE / σ(F): 1.21 / Phase error: 27.0962
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2531 1482 5.04 %RANDOM
Rwork0.2205 27935 --
obs0.2221 29417 99.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.02 Å2
Refinement stepCycle: LAST / Resolution: 2→43.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1599 0 40 47 1686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00791677
X-RAY DIFFRACTIONf_angle_d1.0762263
X-RAY DIFFRACTIONf_chiral_restr0.0669229
X-RAY DIFFRACTIONf_plane_restr0.0068288
X-RAY DIFFRACTIONf_dihedral_angle_d17.9738247
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.060.2851310.30482532X-RAY DIFFRACTION99.78
2.06-2.140.32311360.27362538X-RAY DIFFRACTION99.93
2.14-2.220.27081380.2712577X-RAY DIFFRACTION99.67
2.22-2.330.31381250.2832507X-RAY DIFFRACTION98.58
2.33-2.450.25541350.242551X-RAY DIFFRACTION99.08
2.45-2.60.27991320.24112514X-RAY DIFFRACTION98.69
2.6-2.80.21451390.23222568X-RAY DIFFRACTION100
2.8-3.080.29051390.23432556X-RAY DIFFRACTION99.81
3.08-3.530.26111340.20422545X-RAY DIFFRACTION99.89
3.53-4.450.27511340.1932534X-RAY DIFFRACTION99.29
4.45-43.530.20071390.20512513X-RAY DIFFRACTION97.82
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.637536815621.731783176941.011592066324.88931213431.826437372813.1003647386-0.00850296347779-0.04952429752080.00922822240984-0.724578881512-0.5454569693330.785262400972-0.535804945533-1.057660545640.0921289056630.465581634018-0.0672047084657-0.004296025103830.3578170726150.04416239719740.464384782791-2.26047295512-19.8143431052-0.299755360739
21.660142563480.1861735885571.077856513071.988613677360.9793057414590.013620283935-0.202520543161-0.624926458195-0.422467515984-0.197263257679-0.06643978013250.0694211887529-0.476077226679-0.2723713839850.1359883972130.596564382416-0.093240462633-0.01106251112720.5917783082010.02339862828510.652563342481-3.07139700586-18.69923918836.75610117465
34.549718475282.373364914620.5945655594564.90092557021.546662942932.4542974682-0.0158780585846-0.2358522818930.008741623192980.322599150338-0.254021926959-0.389652952085-0.7740556897980.2079469202840.07813103036090.677292852249-0.118084994086-0.04097182139070.427606691550.08231764714840.568244348053-6.36178072104-25.77119335354.71437133556
44.239878386281.2984996017-1.144764731453.10443938706-0.104356367232.571058377050.0346820439343-0.245352012058-0.5070547745620.1556120410810.0624768247416-0.30491503243-0.2448581597470.5646277281260.05058021898940.374019439801-0.056171723008-0.01239350540070.2645467111450.003773469224980.289188698303-15.4722512517-27.68459555144.27559178358
52.483683673832.81366721827-1.831106993263.1048120154-2.409339888750.739976339032-0.0404885825799-0.129681812615-0.209705118489-0.248629645511-0.146949083401-0.1634665465330.1739894042090.3327834797520.05234543807310.464287460758-0.04764864256510.009540221191170.357324429323-0.005420132989440.294827041509-14.5740510392-17.15771808530.516158987887
64.348923358951.35741447795-2.566578856612.92706923465-0.6937893752831.082713507370.31185055567-0.4446203142490.3709404455390.342777963402-0.0442086064440.449725618373-0.1651468075320.3083373631910.03055656942940.373148131234-0.0588974469676-0.005901775905870.284949781738-0.05060110669770.19857506087-14.9793027593-13.68326533336.66425546975
74.209807372740.326706144923-0.7080140620082.38269835371-0.07586612158921.059069129250.1000360919510.10075887381-0.0894277269524-0.102972755904-0.148087594530.168319470358-0.03795741996280.08193950708420.008040636984950.359340893444-0.021352723039-0.02122499169230.2120620441430.0262697307160.211760285874-5.17462368378-10.02845312811.72363729101
80.404988367337-0.3961088025150.5086934472650.9093634385670.09816429192622.244200178860.41564822558-0.622054264924-0.173715048140.785004809822-0.7008362187040.258815215545-0.5297508675520.910263045424-0.04916850006040.676736391398-0.2861044566130.08734623054390.676511228919-0.05878382759410.341161634915-13.9466848905-9.6580208826824.9520041282
93.620183073921.08369326396-0.7384864752252.8159377937-0.4246410074990.681955368994-0.209348902393-0.01115171132670.05044899625550.3575620815740.2243539408240.0840320926260.410946763440.5193663427160.07359056714070.362211015856-0.0400337139808-0.04711907140510.3263518156820.06944117707420.191526331528-2.54460449827-11.94995666943.6563179832
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: B / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'B' and (resid 90 through 103 )90 - 1031 - 14
22chain 'B' and (resid 104 through 119 )104 - 11915 - 30
33chain 'B' and (resid 120 through 139 )120 - 13931 - 50
44chain 'B' and (resid 140 through 182 )140 - 18251 - 93
55chain 'B' and (resid 183 through 215 )183 - 21594 - 126
66chain 'B' and (resid 216 through 239 )216 - 239127 - 141
77chain 'B' and (resid 240 through 268 )240 - 268142 - 170
88chain 'B' and (resid 269 through 283 )269 - 283171 - 185
99chain 'B' and (resid 284 through 296 )284 - 296186 - 198

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