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- PDB-6z8u: Copper transporter OprC -

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Basic information

Entry
Database: PDB / ID: 6z8u
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: 2.61 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 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 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

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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)159,3048
Polymers158,6572
Non-polymers6476
Water1,27971
1
A: Putative copper transport outer membrane porin OprC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6524
Polymers79,3281
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)79,6524
Polymers79,3281
Non-polymers3243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.113, 195.716, 165.301
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
Components on special symmetry positions
IDModelComponents
11B-902-

HOH

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Components

#1: Protein Putative copper transport outer membrane porin OprC


Mass: 79328.297 Da / Num. of mol.: 2 / 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)
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.: 71 / 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: 3.95 Å3/Da / Density % sol: 68.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.5 M Potassium chloride 0.05 M HEPES 12-16 % v/v PEG 400

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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: Feb 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.35136 Å / Relative weight: 1
ReflectionResolution: 2.61→63.14 Å / Num. obs: 74873 / % possible obs: 98.01 % / Redundancy: 13.25 % / Biso Wilson estimate: 57.44 Å2 / Rpim(I) all: 0.182 / Net I/σ(I): 5
Reflection shellResolution: 2.61→2.66 Å / Num. unique obs: 7326 / CC1/2: 0.317

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FOK

6fok


Resolution: 2.61→63.14 Å / SU ML: 0.476 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.5925
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2732 7024 5.01 %
Rwork0.2123 133202 -
obs0.2154 73192 94.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.21 Å2
Refinement stepCycle: LAST / Resolution: 2.61→63.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10112 0 6 71 10189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008110361
X-RAY DIFFRACTIONf_angle_d1.028414050
X-RAY DIFFRACTIONf_chiral_restr0.05561455
X-RAY DIFFRACTIONf_plane_restr0.00631875
X-RAY DIFFRACTIONf_dihedral_angle_d15.10291439
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.61-2.640.34371420.31082819X-RAY DIFFRACTION60.1
2.64-2.670.33011760.32933379X-RAY DIFFRACTION72.27
2.67-2.70.381840.33923932X-RAY DIFFRACTION83.47
2.7-2.740.37852000.34684135X-RAY DIFFRACTION88.38
2.74-2.770.39222120.35154348X-RAY DIFFRACTION91.75
2.77-2.810.3732400.32454260X-RAY DIFFRACTION92.02
2.81-2.850.35142260.32464532X-RAY DIFFRACTION96.49
2.85-2.890.41952590.32084479X-RAY DIFFRACTION96.73
2.89-2.940.35882830.29344511X-RAY DIFFRACTION97.26
2.94-2.990.31082490.28924564X-RAY DIFFRACTION97.59
2.99-3.040.38052510.26944561X-RAY DIFFRACTION97.41
3.04-3.090.34842240.27094607X-RAY DIFFRACTION97.69
3.09-3.150.30572540.25634538X-RAY DIFFRACTION97.74
3.15-3.220.3352080.24364621X-RAY DIFFRACTION97.93
3.22-3.290.30222490.23774631X-RAY DIFFRACTION97.99
3.29-3.360.30822610.21784545X-RAY DIFFRACTION98.16
3.36-3.450.25522600.2074586X-RAY DIFFRACTION98.06
3.45-3.540.27342500.19984529X-RAY DIFFRACTION98.25
3.54-3.650.28062670.19274595X-RAY DIFFRACTION98.3
3.65-3.760.25062030.1874696X-RAY DIFFRACTION98.33
3.76-3.90.26362530.18894587X-RAY DIFFRACTION98.53
3.9-4.050.2382180.19724641X-RAY DIFFRACTION98.74
4.05-4.240.26582160.19054594X-RAY DIFFRACTION98.71
4.24-4.460.23332290.17564687X-RAY DIFFRACTION98.87
4.46-4.740.21352760.15694576X-RAY DIFFRACTION99.02
4.74-5.110.20762610.16074618X-RAY DIFFRACTION99.13
5.11-5.620.2352680.17064635X-RAY DIFFRACTION99.13
5.62-6.430.23222520.17294631X-RAY DIFFRACTION99.47
6.44-8.10.25592100.18614695X-RAY DIFFRACTION99.45
8.1-63.140.27322430.23054670X-RAY DIFFRACTION99.27
Refinement TLS params.Method: refined / Origin x: 29.2218016335 Å / Origin y: -34.0148335376 Å / Origin z: -41.1878061852 Å
111213212223313233
T0.528472392407 Å20.0210694110808 Å20.0186265087783 Å2-0.313956734484 Å2-0.0171763956791 Å2--0.280964485496 Å2
L0.165607100572 °20.0518806359434 °20.12796574796 °2-0.433387602055 °20.195534417737 °2--0.395676940871 °2
S0.0172553619083 Å °0.0391082707386 Å °-0.0349936896541 Å °-0.0535616457136 Å °-0.0170643803486 Å °0.0270666372219 Å °0.0466354759547 Å °0.0298411006705 Å °0.000415663983026 Å °
Refinement TLS groupSelection details: all

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