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- PDB-6nfs: CopC from Pseudomonas fluorescens -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6nfs
TitleCopC from Pseudomonas fluorescens
ComponentsCopC
KeywordsMETAL BINDING PROTEIN / CopC / metallochaperone / copper binding
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 / Immunoglobulin-like - #1220 / Copper resistance protein CopC/internalin, immunoglobulin-like / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Copper resistance protein C
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMaher, M.J.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP140102746 Australia
Australian Research Council (ARC)DP130100728 Australia
CitationJournal: J. Inorg. Biochem. / Year: 2019
Title: The crystal structure of the CopC protein from Pseudomonas fluorescens reveals amended classifications for the CopC protein family.
Authors: Udagedara, S.R. / Wijekoon, C.J.K. / Xiao, Z. / Wedd, A.G. / Maher, M.J.
History
DepositionDec 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
A: CopC


Theoretical massNumber of molelcules
Total (without water)12,6601
Polymers12,6601
Non-polymers00
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.584, 34.753, 94.679
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CopC


Mass: 12659.606 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: C3JYL7*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O

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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: 1.99 Å3/Da / Density % sol: 38.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.7 M ammonium sulfate, 0.1 M Bis-Tris propane, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.5→32.65 Å / Num. obs: 16697 / % possible obs: 99.77 % / Redundancy: 6.8 % / Net I/σ(I): 20.7
Reflection shellResolution: 1.5→1.54 Å

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Processing

Software
NameVersionClassification
HKL-20005.8.0230data reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6NFR

6nfr


Resolution: 1.5→32.65 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.53 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.073 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21105 837 5 %RANDOM
Rwork0.18279 ---
obs0.18429 15981 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.312 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å20 Å2
2--1.99 Å20 Å2
3----1.48 Å2
Refinement stepCycle: 1 / Resolution: 1.5→32.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms720 0 0 104 824
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.014734
X-RAY DIFFRACTIONr_bond_other_d0.0010.017701
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.663998
X-RAY DIFFRACTIONr_angle_other_deg0.9521.6541634
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.008596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.9724.825
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.39715120
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.748151
X-RAY DIFFRACTIONr_chiral_restr0.070.2103
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02807
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02133
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5511.546387
X-RAY DIFFRACTIONr_mcbond_other1.5241.542386
X-RAY DIFFRACTIONr_mcangle_it2.2822.318482
X-RAY DIFFRACTIONr_mcangle_other2.2862.32483
X-RAY DIFFRACTIONr_scbond_it2.8671.916347
X-RAY DIFFRACTIONr_scbond_other2.8661.918347
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3322.708516
X-RAY DIFFRACTIONr_long_range_B_refined5.52220.383790
X-RAY DIFFRACTIONr_long_range_B_other5.45419.8765
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 66 -
Rwork0.257 1140 -
obs--99.26 %

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