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- PDB-6z9y: Copper transporter OprC -

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Basic information

Entry
Database: PDB / ID: 6z9y
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 (II) ION / Copper transport outer membrane porin OprC
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 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: 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

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
Water00
1
A: Putative copper transport outer membrane porin OprC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,3922
Polymers79,3281
Non-polymers641
Water0
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
Water0
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
Water0
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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.341, 197.668, 171.749
Angle α, β, γ (deg.)90.000, 88.748, 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
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: 65.85 %
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: 1.40889 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: 2.95→197.67 Å / Num. obs: 94129 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 69.46 Å2 / Rpim(I) all: 0.081 / Net I/σ(I): 5.56
Reflection shellResolution: 2.95→3 Å / Num. unique obs: 9369 / CC1/2: 0.551

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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: 2.95→85.85 Å / SU ML: 0.4697 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 33.2231
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3022 8963 4.91 %
Rwork0.2421 173642 -
obs0.2451 93985 97.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.95 Å2
Refinement stepCycle: LAST / Resolution: 2.95→85.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20150 0 4 0 20154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00920650
X-RAY DIFFRACTIONf_angle_d1.163128000
X-RAY DIFFRACTIONf_chiral_restr0.05632898
X-RAY DIFFRACTIONf_plane_restr0.00733737
X-RAY DIFFRACTIONf_dihedral_angle_d17.79212867
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-2.980.35193380.29865690X-RAY DIFFRACTION97.83
2.98-3.020.34842770.29675736X-RAY DIFFRACTION97.72
3.02-3.060.35133120.29225847X-RAY DIFFRACTION97.65
3.06-3.090.33973100.2775696X-RAY DIFFRACTION97.8
3.09-3.130.34333180.27995737X-RAY DIFFRACTION97.74
3.13-3.180.32733080.28355785X-RAY DIFFRACTION97.79
3.18-3.220.3352840.28765886X-RAY DIFFRACTION98
3.22-3.270.35622470.28275789X-RAY DIFFRACTION98.29
3.27-3.320.36773230.27485818X-RAY DIFFRACTION97.94
3.32-3.380.31693580.295750X-RAY DIFFRACTION97.82
3.38-3.440.34273120.25215686X-RAY DIFFRACTION97.96
3.44-3.50.29652810.24785814X-RAY DIFFRACTION97.96
3.5-3.560.30122930.23845841X-RAY DIFFRACTION97.83
3.56-3.640.34392500.24245750X-RAY DIFFRACTION98.15
3.64-3.720.30862880.25265913X-RAY DIFFRACTION97.93
3.72-3.80.34882600.25325808X-RAY DIFFRACTION98.2
3.8-3.90.31692770.25045781X-RAY DIFFRACTION97.57
3.9-40.30973020.25555749X-RAY DIFFRACTION97.55
4-4.120.28213300.25155738X-RAY DIFFRACTION97.67
4.12-4.250.31222930.23345803X-RAY DIFFRACTION98.01
4.25-4.410.27192680.22735794X-RAY DIFFRACTION97.87
4.41-4.580.29552890.22655847X-RAY DIFFRACTION98.65
4.58-4.790.25923410.21975842X-RAY DIFFRACTION98.28
4.79-5.040.30052540.21755782X-RAY DIFFRACTION97.88
5.04-5.360.31722330.21865853X-RAY DIFFRACTION98.34
5.36-5.770.29333340.2165781X-RAY DIFFRACTION98.69
5.77-6.350.26442960.21985822X-RAY DIFFRACTION98.23
6.35-7.270.30763270.21745785X-RAY DIFFRACTION98.01
7.28-9.160.24922870.21535833X-RAY DIFFRACTION98.79
9.16-85.850.28573730.25395686X-RAY DIFFRACTION97.18
Refinement TLS params.Method: refined / Origin x: 34.5943028852 Å / Origin y: 48.0451114178 Å / Origin z: 44.3852856507 Å
111213212223313233
T0.381966758528 Å20.0423945282513 Å2-0.126130973103 Å2-0.579134220279 Å20.038983281338 Å2--0.488740669785 Å2
L0.0474323558399 °20.0457985679615 °2-0.00440216813993 °2-0.152289042855 °20.0751104928879 °2--0.22304678005 °2
S0.0152798815591 Å °0.0117776803573 Å °0.0277156640563 Å °-0.0238863463551 Å °-0.0471368721637 Å °0.0441520604453 Å °0.0156923868701 Å °-0.0441254637153 Å °0.0340104041756 Å °
Refinement TLS groupSelection details: all

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