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- PDB-6z9n: Copper transporter OprC -

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Basic information

Entry
Database: PDB / ID: 6z9n
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 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 4, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)317,5678
Polymers317,3134
Non-polymers2544
Water1,20767
1
A: Putative copper transport outer membrane porin OprC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,3922
Polymers79,3281
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)79,3922
Polymers79,3281
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative copper transport outer membrane porin OprC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,3922
Polymers79,3281
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putative copper transport outer membrane porin OprC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,3922
Polymers79,3281
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.325, 197.274, 172.119
Angle α, β, γ (deg.)90.000, 91.424, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Putative copper transport outer membrane porin OprC


Mass: 79328.297 Da / Num. of mol.: 4 / Mutation: H323A
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)
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.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 3.6 Å3/Da / Density % sol: 65.84 %
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 2 mM CuSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1.35136 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: 1.35136 Å / Relative weight: 1
ReflectionResolution: 2.73→197.27 Å / Num. obs: 118817 / % possible obs: 100 % / Redundancy: 6.64 % / Biso Wilson estimate: 67.15 Å2 / Rpim(I) all: 0.056 / Net I/σ(I): 7.82
Reflection shellResolution: 2.73→2.78 Å / Num. unique obs: 11858 / CC1/2: 0.674

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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: 2.73→67.3 Å / SU ML: 0.4039 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 28.9201
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2666 11579 5.01 %
Rwork0.2162 219750 -
obs0.2188 118703 98.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.32 Å2
Refinement stepCycle: LAST / Resolution: 2.73→67.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20205 0 4 67 20276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009520722
X-RAY DIFFRACTIONf_angle_d1.14428104
X-RAY DIFFRACTIONf_chiral_restr0.05942911
X-RAY DIFFRACTIONf_plane_restr0.00673751
X-RAY DIFFRACTIONf_dihedral_angle_d16.54752884
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.73-2.760.30983710.26657283X-RAY DIFFRACTION98.32
2.76-2.790.32284500.26857355X-RAY DIFFRACTION98.6
2.79-2.830.30383740.26287345X-RAY DIFFRACTION98.32
2.83-2.860.34513890.27637263X-RAY DIFFRACTION97.98
2.86-2.90.39663780.29997356X-RAY DIFFRACTION98.11
2.9-2.940.31753870.28737310X-RAY DIFFRACTION98.09
2.94-2.980.36693460.28247311X-RAY DIFFRACTION98.32
2.98-3.030.32333900.27127297X-RAY DIFFRACTION98.14
3.03-3.070.32033490.25777412X-RAY DIFFRACTION98.13
3.07-3.130.30923400.24537267X-RAY DIFFRACTION98.27
3.13-3.180.27913360.24617406X-RAY DIFFRACTION98.1
3.18-3.240.30733770.2517307X-RAY DIFFRACTION98.14
3.24-3.30.31323950.24347275X-RAY DIFFRACTION98.38
3.3-3.370.27694130.25017459X-RAY DIFFRACTION98.22
3.37-3.440.31873930.23697197X-RAY DIFFRACTION98.42
3.44-3.520.29214190.22657349X-RAY DIFFRACTION98.38
3.52-3.610.24264030.20897229X-RAY DIFFRACTION98.57
3.61-3.710.27194130.21357383X-RAY DIFFRACTION98.51
3.71-3.810.24033800.21617297X-RAY DIFFRACTION98.54
3.81-3.940.29323430.22547411X-RAY DIFFRACTION98.28
3.94-4.080.29183770.23537259X-RAY DIFFRACTION97.95
4.08-4.240.27963650.20857403X-RAY DIFFRACTION98.42
4.24-4.430.23414080.18687354X-RAY DIFFRACTION98.43
4.43-4.670.22134970.18077137X-RAY DIFFRACTION98.81
4.67-4.960.24973630.17747413X-RAY DIFFRACTION98.68
4.96-5.340.22963520.18467345X-RAY DIFFRACTION98.24
5.34-5.880.24784200.18347308X-RAY DIFFRACTION98.99
5.88-6.730.24043670.19277445X-RAY DIFFRACTION98.41
6.73-8.480.24753800.18427332X-RAY DIFFRACTION98.64
8.48-67.30.24294040.23117242X-RAY DIFFRACTION97.82
Refinement TLS params.Method: refined / Origin x: 30.4798601851 Å / Origin y: 73.7941088 Å / Origin z: 127.50382686 Å
111213212223313233
T0.43784662397 Å2-0.0343206360182 Å20.0107557018033 Å2-0.512083300844 Å20.0204500392575 Å2--0.480323448032 Å2
L0.051433579419 °2-0.0208711637311 °20.00209967059955 °2-0.0979897791821 °20.031255740677 °2--0.120645208974 °2
S0.0184411414408 Å °-0.0149070139861 Å °-0.0240724373494 Å °-0.0152431686136 Å °-0.0292268931794 Å °0.0507618565277 Å °0.0106293352 Å °-0.0359417540425 Å °0.0130775796065 Å °
Refinement TLS groupSelection details: all

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