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- PDB-6fom: Copper transporter OprC -

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Basic information

Entry
Database: PDB / ID: 6fom
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 (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent receptor-like, beta-barrel domain superfamily / TonB-dependent Receptor Plug Domain
Similarity search - Domain/homology
Copper transport outer membrane porin OprC
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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: Data collection / Database references ...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_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_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: Only PDB header information has been changed, in this case Entry authors and citation.
Provider: author / Type: Coordinate replacement
Revision 1.2Dec 1, 2021Group: Advisory / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_validate_close_contact / struct_conn
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 1.3Jan 17, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,8326
Polymers158,6062
Non-polymers1,2264
Water00
1
A: Putative copper transport outer membrane porin OprC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9163
Polymers79,3031
Non-polymers6132
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)79,9163
Polymers79,3031
Non-polymers6132
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.129, 170.556, 197.374
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Putative copper transport outer membrane porin OprC


Mass: 79303.180 Da / Num. of mol.: 2 / Mutation: C143A/M147A
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-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
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: 3.3 Å3/Da / Density % sol: 62.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M sodium chloride 0.15 M ammonium sulfate 0.01 M MES sodium 19% (w/v) PEG1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2.9→49.26 Å / Num. obs: 42339 / % possible obs: 89.1 % / Redundancy: 5.5 % / CC1/2: 0.99 / Net I/σ(I): 7
Reflection shellResolution: 2.9→3.01 Å / Num. unique obs: 0 / CC1/2: 0.5

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FOK

6fok


Resolution: 2.9→49.26 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.27 2023 4.79 %
Rwork0.214 --
obs0.217 42221 88.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→49.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10054 0 75 0 10129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910379
X-RAY DIFFRACTIONf_angle_d1.2914041
X-RAY DIFFRACTIONf_dihedral_angle_d8.7437269
X-RAY DIFFRACTIONf_chiral_restr0.0671448
X-RAY DIFFRACTIONf_plane_restr0.0081862
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-2.97260.33431130.28142229X-RAY DIFFRACTION70
2.9726-3.05290.31921100.28022366X-RAY DIFFRACTION74
3.0529-3.14270.3651460.27362533X-RAY DIFFRACTION80
3.1427-3.24420.37811260.26952646X-RAY DIFFRACTION83
3.2442-3.36010.34411390.2452776X-RAY DIFFRACTION88
3.3601-3.49460.27771450.21782826X-RAY DIFFRACTION88
3.4946-3.65360.30831450.20822966X-RAY DIFFRACTION92
3.6536-3.84610.28281620.20993046X-RAY DIFFRACTION96
3.8461-4.0870.23471330.20463097X-RAY DIFFRACTION96
4.087-4.40240.23721440.18892963X-RAY DIFFRACTION91
4.4024-4.84510.23331610.16512897X-RAY DIFFRACTION90
4.8451-5.54530.23361630.18233109X-RAY DIFFRACTION95
5.5453-6.98340.28921550.21933310X-RAY DIFFRACTION100
6.9834-49.260.23961810.23393434X-RAY DIFFRACTION99

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