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- PDB-6z8q: Copper transporter OprC -

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Basic information

Entry
Database: PDB / ID: 6z8q
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: 2.71 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: 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)159,4388
Polymers158,7912
Non-polymers6476
Water23413
1
A: Putative copper transport outer membrane porin OprC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7194
Polymers79,3951
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)79,7194
Polymers79,3951
Non-polymers3243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.200, 195.290, 167.340
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: 79395.367 Da / Num. of mol.: 2
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: 4.02 Å3/Da / Density % sol: 69.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M NaCl 0.15 M NH4SO4 0.1 M MES 18-22% PEG1000 2 mM AgNO3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1.54977 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54977 Å / Relative weight: 1
ReflectionResolution: 2.71→121.98 Å / Num. obs: 69478 / % possible obs: 99.99 % / Redundancy: 35.5 % / Biso Wilson estimate: 75.71 Å2 / Rpim(I) all: 0.028 / Net I/σ(I): 20.12
Reflection shellResolution: 2.71→2.76 Å / Num. unique obs: 6843 / CC1/2: 0.653 / % possible all: 100

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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: 2.71→97.65 Å / SU ML: 0.3698 / Cross valid method: FREE R-VALUE / σ(F): 0.34 / Phase error: 27.1843
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2539 6744 5.03 %
Rwork0.2156 127458 -
obs0.2174 69472 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.33 Å2
Refinement stepCycle: LAST / Resolution: 2.71→97.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10046 0 6 13 10065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008410304
X-RAY DIFFRACTIONf_angle_d1.046913972
X-RAY DIFFRACTIONf_chiral_restr0.05791446
X-RAY DIFFRACTIONf_plane_restr0.0061862
X-RAY DIFFRACTIONf_dihedral_angle_d10.56791429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.71-2.740.31292020.31414235X-RAY DIFFRACTION100
2.74-2.770.36281980.29924272X-RAY DIFFRACTION100
2.77-2.810.31622560.30044203X-RAY DIFFRACTION100
2.81-2.840.29552660.27954272X-RAY DIFFRACTION99.96
2.84-2.880.29422300.27574164X-RAY DIFFRACTION99.98
2.88-2.920.30482390.28214274X-RAY DIFFRACTION100
2.92-2.960.31192220.2764257X-RAY DIFFRACTION99.98
2.96-3.010.32682520.26944232X-RAY DIFFRACTION100
3.01-3.050.32461900.26564343X-RAY DIFFRACTION100
3.05-3.10.30672130.28044198X-RAY DIFFRACTION99.95
3.1-3.160.33512230.28074242X-RAY DIFFRACTION100
3.16-3.210.34352280.27084296X-RAY DIFFRACTION99.78
3.21-3.270.33312570.2614196X-RAY DIFFRACTION99.96
3.27-3.340.27742170.23474266X-RAY DIFFRACTION100
3.34-3.410.24872220.21114213X-RAY DIFFRACTION99.91
3.41-3.490.25081980.21324309X-RAY DIFFRACTION99.78
3.49-3.580.26262520.20324207X-RAY DIFFRACTION99.87
3.58-3.680.28541810.21464324X-RAY DIFFRACTION99.91
3.68-3.790.28292170.21884239X-RAY DIFFRACTION99.96
3.79-3.910.22362310.22074244X-RAY DIFFRACTION99.93
3.91-4.050.28072220.21954240X-RAY DIFFRACTION100
4.05-4.210.23572190.21164207X-RAY DIFFRACTION99.93
4.21-4.40.23812170.19894295X-RAY DIFFRACTION100
4.4-4.630.23652160.18284265X-RAY DIFFRACTION99.73
4.63-4.920.19992480.17484217X-RAY DIFFRACTION100
4.92-5.30.22092360.17434221X-RAY DIFFRACTION100
5.3-5.840.21242110.18314270X-RAY DIFFRACTION100
5.84-6.680.27472330.19824282X-RAY DIFFRACTION100
6.68-8.420.1882160.19474256X-RAY DIFFRACTION99.93
8.42-97.650.25512320.23314219X-RAY DIFFRACTION99.49

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