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- PDB-6z99: Copper transporter OprC -

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Basic information

Entry
Database: PDB / ID: 6z99
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
SILVER ION / Copper transport outer membrane porin OprC
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 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 3, 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

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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)159,3748
Polymers158,7272
Non-polymers6476
Water1448
1
A: Putative copper transport outer membrane porin OprC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6874
Polymers79,3631
Non-polymers3243
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)79,6874
Polymers79,3631
Non-polymers3243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.644, 195.506, 165.629
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-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: Chemical
ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ag
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 4.34 Å3/Da / Density % sol: 71.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M Choline chloride 0.1 M Tris 12-16 % w/v PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.35132 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.35132 Å / Relative weight: 1
ReflectionResolution: 2.68→84.18 Å / Num. obs: 70434 / % possible obs: 99.88 % / Redundancy: 13.51 % / Biso Wilson estimate: 66.43 Å2 / Rpim(I) all: 0.056 / Net I/σ(I): 0.996
Reflection shellResolution: 2.68→2.73 Å / Num. unique obs: 6894 / CC1/2: 0.575

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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: 2.68→84.18 Å / SU ML: 0.3836 / Cross valid method: FREE R-VALUE / σ(F): 0.09 / Phase error: 30.3472
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2524 6661 4.9 %
Rwork0.2147 129390 -
obs0.2166 70402 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.81 Å2
Refinement stepCycle: LAST / Resolution: 2.68→84.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10170 0 6 8 10184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008810438
X-RAY DIFFRACTIONf_angle_d1.121314159
X-RAY DIFFRACTIONf_chiral_restr0.05981465
X-RAY DIFFRACTIONf_plane_restr0.00621890
X-RAY DIFFRACTIONf_dihedral_angle_d15.05631454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.68-2.710.40812110.34994148X-RAY DIFFRACTION94.91
2.71-2.740.36572050.34444271X-RAY DIFFRACTION99.75
2.74-2.770.37582180.32354341X-RAY DIFFRACTION99.8
2.77-2.810.37972310.31884324X-RAY DIFFRACTION99.85
2.81-2.850.34592060.3154321X-RAY DIFFRACTION100
2.85-2.890.36291870.30614338X-RAY DIFFRACTION99.89
2.89-2.930.35432090.2984355X-RAY DIFFRACTION99.83
2.93-2.970.33992140.29664347X-RAY DIFFRACTION99.96
2.97-3.020.33942080.29784287X-RAY DIFFRACTION99.93
3.02-3.070.37382190.29874317X-RAY DIFFRACTION99.96
3.07-3.120.29721950.27794360X-RAY DIFFRACTION99.98
3.12-3.180.28982080.27554343X-RAY DIFFRACTION99.96
3.18-3.240.26262370.24874346X-RAY DIFFRACTION99.98
3.24-3.30.33842550.2474253X-RAY DIFFRACTION99.98
3.3-3.380.25122580.22644324X-RAY DIFFRACTION99.93
3.38-3.450.2262220.20974327X-RAY DIFFRACTION99.8
3.45-3.540.24192240.2094271X-RAY DIFFRACTION99.91
3.54-3.640.2782000.21164331X-RAY DIFFRACTION99.93
3.64-3.740.23961880.22454362X-RAY DIFFRACTION99.98
3.74-3.860.25092220.22174331X-RAY DIFFRACTION100
3.86-40.29792450.21264314X-RAY DIFFRACTION99.91
4-4.160.23362180.20544366X-RAY DIFFRACTION100
4.16-4.350.23992280.19264252X-RAY DIFFRACTION99.93
4.35-4.580.19552220.17054339X-RAY DIFFRACTION100
4.58-4.870.19252290.15754301X-RAY DIFFRACTION100
4.87-5.240.20182430.16664310X-RAY DIFFRACTION100
5.24-5.770.2282090.1774331X-RAY DIFFRACTION99.96
5.77-6.610.22262440.19544316X-RAY DIFFRACTION100
6.61-8.320.2432390.19154332X-RAY DIFFRACTION99.93
8.32-84.180.23032670.214232X-RAY DIFFRACTION99.4
Refinement TLS params.Method: refined / Origin x: 29.0582484109 Å / Origin y: -33.8844889936 Å / Origin z: -41.1836828077 Å
111213212223313233
T0.461006414412 Å20.0253419696514 Å20.00655823675098 Å2-0.409092933456 Å2-0.00431752666138 Å2--0.431037233666 Å2
L0.401816524096 °20.0389523181608 °20.328335051469 °2-0.641988860388 °20.303482454989 °2--0.779694879253 °2
S0.0866700686887 Å °0.0874397620394 Å °-0.115976674946 Å °-0.0721148747725 Å °-0.0297998275247 Å °0.00087027487178 Å °0.116297139876 Å °0.0604744023663 Å °-0.0596943207856 Å °
Refinement TLS groupSelection details: all

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