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- PDB-6z8y: Copper transporter OprC -

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Basic information

Entry
Database: PDB / ID: 6z8y
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-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
Similarity search - Domain/homology
Copper transport outer membrane porin OprC
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 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 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: Database references / Category: citation / citation_author / database_2
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


Theoretical massNumber of molelcules
Total (without water)158,7272
Polymers158,7272
Non-polymers00
Water41423
1
A: Putative copper transport outer membrane porin OprC


Theoretical massNumber of molelcules
Total (without water)79,3631
Polymers79,3631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative copper transport outer membrane porin OprC


Theoretical massNumber of molelcules
Total (without water)79,3631
Polymers79,3631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.032, 170.742, 198.043
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-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 PAO1 (bacteria) / Gene: oprC, PA3790 / Production host: Escherichia coli (E. coli) / References: UniProt: G3XD89
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 3.57 Å3/Da / Density % sol: 65.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.34 M Ammonium sulfate 0.1 M Sodium citrate 12 -16 % w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1.40889 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.40889 Å / Relative weight: 1
ReflectionResolution: 2.78→198.04 Å / Num. obs: 58146 / % possible obs: 100 % / Redundancy: 12.66 % / Biso Wilson estimate: 68.57 Å2 / Rpim(I) all: 0.078 / Net I/σ(I): 5.52
Reflection shellResolution: 2.78→2.83 Å / Num. unique obs: 5698 / CC1/2: 0.4

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FOK

6fok


Resolution: 2.78→67.03 Å / SU ML: 0.4453 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 29.2958
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2662 5469 4.96 %
Rwork0.2103 104785 -
obs0.2131 58104 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.39 Å2
Refinement stepCycle: LAST / Resolution: 2.78→67.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10111 0 0 23 10134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008810373
X-RAY DIFFRACTIONf_angle_d1.115814072
X-RAY DIFFRACTIONf_chiral_restr0.05781457
X-RAY DIFFRACTIONf_plane_restr0.00651878
X-RAY DIFFRACTIONf_dihedral_angle_d14.54621443
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.78-2.810.36891630.32173496X-RAY DIFFRACTION100
2.81-2.840.34891910.3133456X-RAY DIFFRACTION99.86
2.84-2.880.39911690.31233508X-RAY DIFFRACTION99.73
2.88-2.920.36081850.30093544X-RAY DIFFRACTION99.79
2.92-2.950.36581600.28943472X-RAY DIFFRACTION99.81
2.95-2.990.3191410.27973518X-RAY DIFFRACTION99.81
2.99-3.040.34431950.2723518X-RAY DIFFRACTION99.73
3.04-3.080.30541800.24623434X-RAY DIFFRACTION99.64
3.08-3.130.29691790.25443496X-RAY DIFFRACTION99.92
3.13-3.180.32291730.25453539X-RAY DIFFRACTION99.73
3.18-3.240.34911910.273487X-RAY DIFFRACTION99.78
3.24-3.30.35521720.27543485X-RAY DIFFRACTION99.84
3.3-3.360.35172110.27473511X-RAY DIFFRACTION99.87
3.36-3.430.31872000.22713427X-RAY DIFFRACTION99.81
3.43-3.50.28591910.22363518X-RAY DIFFRACTION99.84
3.5-3.580.32521970.2173456X-RAY DIFFRACTION99.81
3.58-3.670.32351620.21663543X-RAY DIFFRACTION99.73
3.67-3.770.26641890.20693415X-RAY DIFFRACTION99.75
3.77-3.880.27911880.20543524X-RAY DIFFRACTION99.84
3.88-4.010.28031670.20863512X-RAY DIFFRACTION99.95
4.01-4.150.30762420.22123431X-RAY DIFFRACTION99.86
4.15-4.320.24581540.19493497X-RAY DIFFRACTION99.81
4.32-4.510.25791830.16963547X-RAY DIFFRACTION99.97
4.52-4.750.22032170.15733475X-RAY DIFFRACTION99.92
4.75-5.050.19241800.16363470X-RAY DIFFRACTION100
5.05-5.440.21661890.17183494X-RAY DIFFRACTION99.97
5.44-5.990.23041600.17133534X-RAY DIFFRACTION100
5.99-6.850.24251840.18063496X-RAY DIFFRACTION100
6.85-8.630.18241910.1683481X-RAY DIFFRACTION99.92
8.63-67.030.20951650.22493501X-RAY DIFFRACTION99.27
Refinement TLS params.Method: refined / Origin x: 10.1150720773 Å / Origin y: 44.2192958894 Å / Origin z: 62.1493349337 Å
111213212223313233
T0.449994067037 Å2-0.0861696950527 Å20.00410052968726 Å2-0.388819248299 Å2-0.0268603622824 Å2--0.413029015273 Å2
L0.200531968182 °2-0.0494940663211 °2-0.0445538847291 °2-0.474920376049 °20.530024653445 °2--0.965053610789 °2
S0.0687165866624 Å °-0.0288412540763 Å °-0.0154773582243 Å °0.017886533217 Å °0.0583288804613 Å °-0.0549529975441 Å °-0.0157489256474 Å °0.16552485568 Å °-0.132775761141 Å °
Refinement TLS groupSelection details: all

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