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- PDB-6z8z: Copper transporter OprC -

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Basic information

Entry
Database: PDB / ID: 6z8z
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 transport outer membrane porin OprC
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 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
Water70339
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)67.019, 171.225, 198.196
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 (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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 3.58 Å3/Da / Density % sol: 65.66 %
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: 1.35131 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: 1.35131 Å / Relative weight: 1
ReflectionResolution: 2.56→129.57 Å / Num. obs: 74440 / % possible obs: 100 % / Redundancy: 12.25 % / Biso Wilson estimate: 68.28 Å2 / Rpim(I) all: 0.096 / Net I/σ(I): 5.4
Reflection shellResolution: 2.56→2.6 Å / Num. unique obs: 7325 / CC1/2: 0.339

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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: 2.56→67.02 Å / SU ML: 0.4808 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 32.9734
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2949 7104 5.02 %
Rwork0.238 134549 -
obs0.2408 74371 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.54 Å2
Refinement stepCycle: LAST / Resolution: 2.56→67.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10144 0 0 39 10183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008410402
X-RAY DIFFRACTIONf_angle_d1.07714108
X-RAY DIFFRACTIONf_chiral_restr0.05581458
X-RAY DIFFRACTIONf_plane_restr0.00661884
X-RAY DIFFRACTIONf_dihedral_angle_d15.21121447
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-2.590.34752040.30754550X-RAY DIFFRACTION99.85
2.59-2.620.34812640.30274404X-RAY DIFFRACTION99.85
2.62-2.650.38712140.31374526X-RAY DIFFRACTION99.96
2.65-2.690.34742630.31994506X-RAY DIFFRACTION99.83
2.69-2.720.43092500.32684416X-RAY DIFFRACTION99.94
2.72-2.760.42632420.32544507X-RAY DIFFRACTION99.89
2.76-2.80.40042300.32924518X-RAY DIFFRACTION99.52
2.8-2.840.36622310.30724422X-RAY DIFFRACTION99.87
2.84-2.880.36332210.30494499X-RAY DIFFRACTION99.52
2.88-2.930.33222250.29494491X-RAY DIFFRACTION99.62
2.93-2.980.3762420.28694466X-RAY DIFFRACTION99.83
2.98-3.040.35392270.2934576X-RAY DIFFRACTION99.52
3.04-3.090.32152410.2894385X-RAY DIFFRACTION99.66
3.09-3.160.3772320.30344515X-RAY DIFFRACTION99.71
3.16-3.230.36262260.31474489X-RAY DIFFRACTION99.68
3.23-3.30.30292530.28114480X-RAY DIFFRACTION99.75
3.3-3.380.33232340.27214489X-RAY DIFFRACTION99.79
3.38-3.470.33312290.24754471X-RAY DIFFRACTION99.72
3.47-3.580.3372460.24344466X-RAY DIFFRACTION99.72
3.58-3.690.30852800.24614448X-RAY DIFFRACTION99.75
3.69-3.820.32792150.24674514X-RAY DIFFRACTION99.83
3.82-3.980.30562450.25094513X-RAY DIFFRACTION99.81
3.98-4.160.32792710.24284428X-RAY DIFFRACTION100
4.16-4.380.2412240.21464494X-RAY DIFFRACTION99.94
4.38-4.650.30192410.20134481X-RAY DIFFRACTION99.89
4.65-5.010.22722380.19444500X-RAY DIFFRACTION99.94
5.01-5.510.25272540.20764496X-RAY DIFFRACTION99.94
5.51-6.310.26042140.19894491X-RAY DIFFRACTION99.94
6.31-7.950.23362190.18674529X-RAY DIFFRACTION99.98
7.95-67.020.21572290.19654479X-RAY DIFFRACTION99.45
Refinement TLS params.Method: refined / Origin x: 10.171718395 Å / Origin y: 44.3424594961 Å / Origin z: 62.3748361336 Å
111213212223313233
T0.574491158583 Å2-0.102530629221 Å2-0.00747932909402 Å2-0.462771604417 Å2-0.0339025064162 Å2--0.524415288803 Å2
L0.124370792647 °2-0.0643845317558 °2-0.111975224085 °2-0.514349852667 °20.549875005371 °2--0.940065998856 °2
S0.0496924030844 Å °-0.0564408590807 Å °0.00421702967454 Å °-0.00763353005318 Å °0.0599690362629 Å °-0.0415018130522 Å °-0.0319028153353 Å °0.183112512956 Å °-0.11296967041 Å °
Refinement TLS groupSelection details: all

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