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- PDB-6fok: Copper transporter OprC -

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Basic information

Entry
Database: PDB / ID: 6fok
TitleCopper transporter OprC
ComponentsPutative copper transport outer membrane porin OprC
KeywordsMEMBRANE PROTEIN / metalloprotein / TonB dependent transporter / outer membrane protein / copper / Pseudomonas aeruginosa
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 / SAD / Resolution: 1.97 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
DepositionFeb 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / computing / diffrn / entity_src_gen / pdbx_database_related / pdbx_entity_instance_feature / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_struct_assembly / refine / refine_hist / refine_ls_shell / reflns / reflns_shell
Item: _audit_author.name / _citation.title ..._audit_author.name / _citation.title / _diffrn.pdbx_serial_crystal_experiment / _entity_src_gen.gene_src_strain / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_percent_reflns_obs / _refine_hist.d_res_low / _refine_ls_shell.d_res_low / _reflns.pdbx_CC_half / _reflns.pdbx_Rpim_I_all / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_CC_half
Description: Ligand identity
Details: Information has been replaced in the header only for: 1. Entry authors and title 2. Ligand ID: Cu(I) instead of Cu(II)
Provider: author / Type: Coordinate replacement
Revision 1.2Dec 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 1.3Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)162,59516
Polymers158,7912
Non-polymers3,80414
Water10,016556
1
A: Putative copper transport outer membrane porin OprC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,6856
Polymers79,3951
Non-polymers1,2895
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)81,91010
Polymers79,3951
Non-polymers2,5159
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.370, 196.720, 166.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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)
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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 556 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.03 Å3/Da / Density % sol: 69.47 %
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 3 mM CuCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.3785 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3785 Å / Relative weight: 1
ReflectionResolution: 1.97→84.67 Å / Num. obs: 178934 / % possible obs: 99.5 % / Redundancy: 25.4 % / CC1/2: 0.99 / Net I/σ(I): 15.8
Reflection shellResolution: 1.97→2.02 Å / Num. unique obs: 0 / CC1/2: 0.5

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.97→84.67 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.232 8963 5.01 %
Rwork0.21 --
obs0.211 178784 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.97→84.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10011 0 151 556 10718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710439
X-RAY DIFFRACTIONf_angle_d0.92514095
X-RAY DIFFRACTIONf_dihedral_angle_d16.0126160
X-RAY DIFFRACTIONf_chiral_restr0.0581444
X-RAY DIFFRACTIONf_plane_restr0.0061860
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-1.99240.33012910.29925628X-RAY DIFFRACTION100
1.9924-2.01580.3283100.28715620X-RAY DIFFRACTION100
2.0158-2.04040.28352880.2775667X-RAY DIFFRACTION100
2.0404-2.06620.28923190.26995676X-RAY DIFFRACTION100
2.0662-2.09340.31763010.2745647X-RAY DIFFRACTION100
2.0934-2.12210.26462910.25475616X-RAY DIFFRACTION100
2.1221-2.15240.26393120.24095649X-RAY DIFFRACTION100
2.1524-2.18460.24823210.23615612X-RAY DIFFRACTION100
2.1846-2.21870.27093030.2295672X-RAY DIFFRACTION100
2.2187-2.25510.28742650.25915661X-RAY DIFFRACTION100
2.2551-2.2940.29462650.24385708X-RAY DIFFRACTION100
2.294-2.33570.27732890.2325664X-RAY DIFFRACTION100
2.3357-2.38060.27323020.23375650X-RAY DIFFRACTION100
2.3806-2.42920.26233190.2325661X-RAY DIFFRACTION100
2.4292-2.4820.29453050.24575673X-RAY DIFFRACTION100
2.482-2.53980.33612640.30025463X-RAY DIFFRACTION96
2.5398-2.60330.52480.44545022X-RAY DIFFRACTION88
2.6033-2.67370.25162840.23275714X-RAY DIFFRACTION100
2.6737-2.75240.24643130.20275636X-RAY DIFFRACTION100
2.7524-2.84120.25562660.19535727X-RAY DIFFRACTION100
2.8412-2.94280.23912960.19725688X-RAY DIFFRACTION100
2.9428-3.06060.22872900.19375709X-RAY DIFFRACTION100
3.0606-3.19990.23682980.19875698X-RAY DIFFRACTION100
3.1999-3.36860.22293170.18835672X-RAY DIFFRACTION100
3.3686-3.57970.19922960.1855756X-RAY DIFFRACTION100
3.5797-3.8560.21173410.18885680X-RAY DIFFRACTION100
3.856-4.24410.20253090.19175738X-RAY DIFFRACTION100
4.2441-4.85820.17722900.17065786X-RAY DIFFRACTION100
4.8582-6.12050.193460.17995762X-RAY DIFFRACTION100
6.1205-84.670.22773240.21845966X-RAY DIFFRACTION100

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