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- PDB-7bk7: PfCopC mutant - D83N -

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Basic information

Entry
Database: PDB / ID: 7bk7
TitlePfCopC mutant - D83N
ComponentsPutative copper resistance protein
KeywordsMETAL BINDING PROTEIN / Copper binding / copper transport
Function / homology
Function and homology information


copper ion transport / response to copper ion / periplasmic space / copper ion binding / plasma membrane
Similarity search - Function
Copper transport protein C/D / : / CopC domain / CopC domain / Copper resistance protein CopC/internalin, immunoglobulin-like / Immunoglobulin E-set
Similarity search - Domain/homology
ACETATE ION / COPPER (II) ION / Copper resistance protein C
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMuderspach, S.J. / Ipsen, J. / Rollan, C.H. / Bertelsen, A.B. / Norholm, M.H.H. / Johansen, K.S. / Lo Leggio, L.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF17SA0027704 Denmark
CitationJournal: Febs Lett. / Year: 2021
Title: Copper binding and reactivity at the histidine brace motif: insights from mutational analysis of the Pseudomonas fluorescens copper chaperone CopC.
Authors: Ipsen, J.O. / Hernandez-Rollan, C. / Muderspach, S.J. / Brander, S. / Bertelsen, A.B. / Jensen, P.E. / Norholm, M.H.H. / Lo Leggio, L. / Johansen, K.S.
History
DepositionJan 15, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Putative copper resistance protein
BBB: Putative copper resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6039
Polymers20,2192
Non-polymers3847
Water1,33374
1
AAA: Putative copper resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3996
Polymers10,1091
Non-polymers2905
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Putative copper resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2043
Polymers10,1091
Non-polymers942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.300, 80.300, 89.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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Components

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Protein , 1 types, 2 molecules AAABBB

#1: Protein Putative copper resistance protein


Mass: 10109.310 Da / Num. of mol.: 2 / Mutation: D83N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: SBW25 / Gene: PFLU_3946
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: C3JYL7

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Non-polymers , 5 types, 81 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.58 Å3/Da / Density % sol: 65.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 2.9 M ammonium sulphate, 0.1 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Oct 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 12725 / % possible obs: 99.8 % / Redundancy: 5.64 % / CC1/2: 0.998 / Rrim(I) all: 0.102 / Net I/σ(I): 10.52
Reflection shellResolution: 2.3→2.36 Å / Num. unique obs: 1884 / CC1/2: 0.457 / Rrim(I) all: 1.962

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSVERSION Jan 31, 2020data reduction
XSCALEVERSION Jan 31, 2020data scaling
MOLREPVers 11.6.03; 30.04.2018phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NFQ

6nfq


Resolution: 2.3→35.266 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.289 / WRfactor Rwork: 0.22 / SU B: 8.819 / SU ML: 0.211 / Average fsc free: 0.8515 / Average fsc work: 0.8713 / Cross valid method: FREE R-VALUE / ESU R: 0.255 / ESU R Free: 0.226
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2676 647 5.088 %
Rwork0.2082 12068 -
all0.212 --
obs-12715 99.882 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 70.442 Å2
Baniso -1Baniso -2Baniso -3
1--0.533 Å2-0 Å20 Å2
2---0.533 Å20 Å2
3---1.066 Å2
Refinement stepCycle: LAST / Resolution: 2.3→35.266 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1398 0 17 74 1489
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0131527
X-RAY DIFFRACTIONr_bond_other_d0.0030.0171457
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.6442092
X-RAY DIFFRACTIONr_angle_other_deg1.221.5833379
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.175206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.7524.3453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.39515239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.008153
X-RAY DIFFRACTIONr_chiral_restr0.0630.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021739
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02295
X-RAY DIFFRACTIONr_nbd_refined0.2050.2278
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.21193
X-RAY DIFFRACTIONr_nbtor_refined0.1580.2638
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.2608
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.289
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2460.210
X-RAY DIFFRACTIONr_nbd_other0.2920.29
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2530.24
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0120.21
X-RAY DIFFRACTIONr_mcbond_it6.2177.307814
X-RAY DIFFRACTIONr_mcbond_other6.2157.296812
X-RAY DIFFRACTIONr_mcangle_it9.28710.9171022
X-RAY DIFFRACTIONr_mcangle_other9.28810.9211023
X-RAY DIFFRACTIONr_scbond_it6.317.792713
X-RAY DIFFRACTIONr_scbond_other6.2767.758710
X-RAY DIFFRACTIONr_scangle_it9.49211.4831070
X-RAY DIFFRACTIONr_scangle_other9.48311.4251065
X-RAY DIFFRACTIONr_lrange_it14.0886.4591523
X-RAY DIFFRACTIONr_lrange_other14.04386.3471512
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.324300.307924X-RAY DIFFRACTION100
2.36-2.4240.317330.296866X-RAY DIFFRACTION100
2.424-2.4940.38660.357841X-RAY DIFFRACTION100
2.494-2.5710.358380.278820X-RAY DIFFRACTION100
2.571-2.6550.406310.283793X-RAY DIFFRACTION100
2.655-2.7480.333400.278756X-RAY DIFFRACTION100
2.748-2.8520.403290.248755X-RAY DIFFRACTION100
2.852-2.9680.325430.232708X-RAY DIFFRACTION100
2.968-3.0990.248520.214670X-RAY DIFFRACTION100
3.099-3.250.272300.236654X-RAY DIFFRACTION100
3.25-3.4260.326450.237616X-RAY DIFFRACTION100
3.426-3.6330.319280.236602X-RAY DIFFRACTION100
3.633-3.8820.321300.22548X-RAY DIFFRACTION100
3.882-4.1920.306300.192518X-RAY DIFFRACTION100
4.192-4.590.205310.167459X-RAY DIFFRACTION100
4.59-5.1280.227280.158433X-RAY DIFFRACTION100
5.128-5.9140.244200.187385X-RAY DIFFRACTION100
5.914-7.2260.282140.187339X-RAY DIFFRACTION100
7.226-10.1450.153220.149246X-RAY DIFFRACTION100
10.145-350.24670.184135X-RAY DIFFRACTION91.6129

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