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- PDB-6z91: Copper transporter OprC -

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Basic information

Entry
Database: PDB / ID: 6z91
TitleCopper transporter OprC
ComponentsPutative copper transport outer membrane porin OprC
KeywordsMEMBRANE PROTEIN / copper transporter / TBDT / Pseudomonas aeruginosa / OprC
Function / homology
Function and homology information


siderophore transmembrane transport / siderophore uptake transmembrane transporter activity / cell outer membrane / metal ion binding
Similarity search - Function
TonB-dependent copper receptor / TonB-dependent receptor, beta-barrel domain / Maltoporin; Chain A / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent Receptor Plug Domain ...TonB-dependent copper receptor / TonB-dependent receptor, beta-barrel domain / Maltoporin; Chain A / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent Receptor Plug Domain / TonB-dependent receptor-like, beta-barrel domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
SILVER ION / Copper transport outer membrane porin OprC
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBhamidimarri, S.P. / van den Berg, B.
CitationJournal: Plos Biol. / Year: 2021
Title: Acquisition of ionic copper by the bacterial outer membrane protein OprC through a novel binding site.
Authors: Bhamidimarri, S.P. / Young, T.R. / Shanmugam, M. / Soderholm, S. / Basle, A. / Bumann, D. / van den Berg, B.
History
DepositionJun 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: Advisory / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative copper transport outer membrane porin OprC
B: Putative copper transport outer membrane porin OprC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,3748
Polymers158,7272
Non-polymers6476
Water23413
1
A: Putative copper transport outer membrane porin OprC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6874
Polymers79,3631
Non-polymers3243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative copper transport outer membrane porin OprC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6874
Polymers79,3631
Non-polymers3243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.478, 195.030, 165.473
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 Putative copper transport outer membrane porin OprC


Mass: 79363.297 Da / Num. of mol.: 2 / Mutation: C143A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: oprC, PA3790 / Production host: Escherichia coli (E. coli) / References: UniProt: G3XD89
#2: Chemical
ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ag
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 3.93 Å3/Da / Density % sol: 68.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M Choline chloride 0.1 M Tris 12-16 % w/v PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.407337 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.407337 Å / Relative weight: 1
ReflectionResolution: 2.6→165.47 Å / Num. obs: 76695 / % possible obs: 99.92 % / Redundancy: 13.5 % / Biso Wilson estimate: 61.55 Å2 / Rpim(I) all: 0.055 / Net I/σ(I): 7.56
Reflection shellResolution: 2.6→2.64 Å / Num. unique obs: 7519 / CC1/2: 0.644

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Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FOK

6fok


Resolution: 2.6→82.74 Å / SU ML: 0.4008 / Cross valid method: FREE R-VALUE / σ(F): 0.06 / Phase error: 31.5848
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2618 7433 5.02 %
Rwork0.2219 140774 -
obs0.2239 76648 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.22 Å2
Refinement stepCycle: LAST / Resolution: 2.6→82.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10148 0 6 13 10167
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008310410
X-RAY DIFFRACTIONf_angle_d1.07814118
X-RAY DIFFRACTIONf_chiral_restr0.05771459
X-RAY DIFFRACTIONf_plane_restr0.00691885
X-RAY DIFFRACTIONf_dihedral_angle_d16.47981448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.630.40882170.38244504X-RAY DIFFRACTION96.13
2.63-2.660.42562130.36944728X-RAY DIFFRACTION99.94
2.66-2.690.36742560.33634726X-RAY DIFFRACTION99.78
2.69-2.730.39052440.32694695X-RAY DIFFRACTION99.62
2.73-2.760.35492340.31284765X-RAY DIFFRACTION99.66
2.76-2.80.35962450.30854652X-RAY DIFFRACTION99.88
2.8-2.840.35572780.30064655X-RAY DIFFRACTION99.82
2.84-2.880.35782640.29514640X-RAY DIFFRACTION99.82
2.88-2.930.33662430.28224695X-RAY DIFFRACTION99.8
2.93-2.980.29972480.29134725X-RAY DIFFRACTION99.78
2.98-3.030.38272130.2924760X-RAY DIFFRACTION99.82
3.03-3.080.38032570.29754656X-RAY DIFFRACTION99.92
3.08-3.140.3182620.27024688X-RAY DIFFRACTION99.94
3.14-3.210.3252800.26394645X-RAY DIFFRACTION99.94
3.21-3.280.27862420.24944751X-RAY DIFFRACTION99.96
3.28-3.350.32882510.24054696X-RAY DIFFRACTION100
3.35-3.440.26592850.22184669X-RAY DIFFRACTION99.72
3.44-3.530.28412640.2144638X-RAY DIFFRACTION99.98
3.53-3.630.25632300.21734721X-RAY DIFFRACTION99.96
3.63-3.750.25712220.22974763X-RAY DIFFRACTION99.98
3.75-3.880.26772850.21414673X-RAY DIFFRACTION99.96
3.88-4.040.25922760.21234666X-RAY DIFFRACTION99.94
4.04-4.220.22592520.21454677X-RAY DIFFRACTION99.96
4.22-4.450.26322230.1924761X-RAY DIFFRACTION100
4.45-4.720.20822550.17834677X-RAY DIFFRACTION100
4.72-5.090.17911980.1734750X-RAY DIFFRACTION100
5.09-5.60.19872290.18654741X-RAY DIFFRACTION99.94
5.6-6.410.22762480.1924696X-RAY DIFFRACTION100
6.41-8.080.23622840.19174657X-RAY DIFFRACTION100
8.08-84.010.21292350.19744704X-RAY DIFFRACTION99.34
Refinement TLS params.Method: refined / Origin x: 29.0381004099 Å / Origin y: -33.754867167 Å / Origin z: -41.1155157752 Å
111213212223313233
T0.608817447359 Å20.0165862931977 Å20.0125143855913 Å2-0.412436968017 Å2-0.0196023805645 Å2--0.456453094661 Å2
L0.270650165453 °20.0159234760944 °20.3103504856 °2-0.340996843285 °20.215189845372 °2--0.591325009858 °2
S0.0596813326674 Å °0.0501686827103 Å °-0.0833888928546 Å °-0.0401941026474 Å °-0.0167043156956 Å °0.0319468306035 Å °0.083706602474 Å °0.0538620048071 Å °-0.0503144276124 Å °
Refinement TLS groupSelection details: all

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