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- PDB-6z8r: Copper transporter OprC -

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Basic information

Entry
Database: PDB / ID: 6z8r
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
COPPER (II) ION / Copper transport outer membrane porin OprC
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,9324
Polymers158,8052
Non-polymers1272
Water2,396133
1
A: Putative copper transport outer membrane porin OprC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4662
Polymers79,4021
Non-polymers641
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)79,4662
Polymers79,4021
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.030, 196.860, 165.480
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: 79402.312 Da / Num. of mol.: 2 / Mutation: M147H
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: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 3.98 Å3/Da / Density % sol: 69.06 %
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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.351326 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.351326 Å / Relative weight: 1
ReflectionResolution: 2.38→98.09 Å / Num. obs: 101148 / % possible obs: 100 % / Redundancy: 13.57 % / Biso Wilson estimate: 62.32 Å2 / Rpim(I) all: 0.044 / Net I/σ(I): 11.71
Reflection shellResolution: 2.38→2.42 Å / Num. unique obs: 10029 / CC1/2: 0.3205

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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: 2.38→68.44 Å / SU ML: 0.4031 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.7081
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2518 9709 4.95 %
Rwork0.2169 186342 -
obs0.2186 101122 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.87 Å2
Refinement stepCycle: LAST / Resolution: 2.38→68.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10158 0 2 133 10293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008510412
X-RAY DIFFRACTIONf_angle_d0.991714118
X-RAY DIFFRACTIONf_chiral_restr0.05651457
X-RAY DIFFRACTIONf_plane_restr0.00641885
X-RAY DIFFRACTIONf_dihedral_angle_d13.25411445
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.410.37283640.36336220X-RAY DIFFRACTION99.62
2.41-2.440.39413440.36446076X-RAY DIFFRACTION99.47
2.44-2.470.37643590.35746198X-RAY DIFFRACTION99.85
2.47-2.50.37113380.3456240X-RAY DIFFRACTION99.92
2.5-2.530.35063120.34086190X-RAY DIFFRACTION99.95
2.53-2.560.4083470.34436186X-RAY DIFFRACTION99.98
2.56-2.60.38312940.33526244X-RAY DIFFRACTION100
2.6-2.640.3193160.31776194X-RAY DIFFRACTION99.98
2.64-2.680.32872980.29146257X-RAY DIFFRACTION99.98
2.68-2.720.27873150.28446265X-RAY DIFFRACTION100
2.72-2.770.30433240.26586219X-RAY DIFFRACTION99.97
2.77-2.820.30073100.266152X-RAY DIFFRACTION99.98
2.82-2.880.26973430.24576230X-RAY DIFFRACTION99.95
2.88-2.930.26473140.23566209X-RAY DIFFRACTION100
2.93-30.26923080.23576235X-RAY DIFFRACTION100
3-3.070.27973380.24516224X-RAY DIFFRACTION99.97
3.07-3.150.293580.23896189X-RAY DIFFRACTION99.98
3.15-3.230.27083020.22636209X-RAY DIFFRACTION100
3.23-3.330.26023000.21996204X-RAY DIFFRACTION100
3.33-3.430.25423360.19926214X-RAY DIFFRACTION99.92
3.43-3.560.23243270.19136211X-RAY DIFFRACTION99.97
3.56-3.70.24013050.20476261X-RAY DIFFRACTION99.89
3.7-3.870.26592980.20416222X-RAY DIFFRACTION99.97
3.87-4.070.28642890.21416261X-RAY DIFFRACTION99.97
4.07-4.320.21872830.20256259X-RAY DIFFRACTION100
4.32-4.660.20063090.17916197X-RAY DIFFRACTION100
4.66-5.130.22743660.18096154X-RAY DIFFRACTION100
5.13-5.870.22813730.19286197X-RAY DIFFRACTION100
5.87-7.390.23853440.19396213X-RAY DIFFRACTION100
7.39-68.440.19742950.19786212X-RAY DIFFRACTION99.53
Refinement TLS params.Method: refined / Origin x: 29.1578399318 Å / Origin y: 34.1627283736 Å / Origin z: 40.9670617518 Å
111213212223313233
T0.44032648386 Å2-0.0249529459661 Å2-0.000741021475972 Å2-0.493220451287 Å20.00128313478466 Å2--0.494620994564 Å2
L0.265160179774 °2-0.0335951740457 °2-0.166204715006 °2-0.463176259786 °20.329348199312 °2--0.551217834007 °2
S0.0470516654816 Å °-0.0484345832194 Å °0.0373459532384 Å °0.0480421038336 Å °-0.044475145782 Å °0.0507459128146 Å °-0.053416308679 Å °0.0188608899276 Å °-0.00938053274519 Å °
Refinement TLS groupSelection details: all

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