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- PDB-6nfq: CopC from Pseudomonas fluorescens -

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Basic information

Entry
Database: PDB / ID: 6nfq
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 / Copper resistance protein CopC/internalin, immunoglobulin-like / Immunoglobulin E-set
Similarity search - Domain/homology
COPPER (II) ION / YTTRIUM (III) ION / Copper resistance protein C
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CopC
B: CopC
C: CopC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2047
Polymers37,9253
Non-polymers2804
Water1,72996
1
A: CopC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7943
Polymers12,6421
Non-polymers1522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CopC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7052
Polymers12,6421
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: CopC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7052
Polymers12,6421
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.730, 111.319, 82.222
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-202-

YT3

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Components

#1: Protein CopC


Mass: 12641.553 Da / Num. of mol.: 3
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: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-YT3 / YTTRIUM (III) ION


Mass: 88.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Y
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.34 Å3/Da / Density % sol: 47.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 2.5 M ammonium sulfate, 0.1 M Bis-Tris propane, pH 6.7, 2 mM yttrium chloride hexahydrate

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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: 2→46 Å / Num. obs: 23030 / % possible obs: 99.5 % / Redundancy: 6 % / Net I/σ(I): 9.7
Reflection shellResolution: 2→2.05 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 2C9Q

2c9q


Resolution: 2→46 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.725 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.035 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25988 1238 5.1 %RANDOM
Rwork0.22791 ---
obs0.2296 23030 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.18 Å2
Baniso -1Baniso -2Baniso -3
1-31.11 Å20 Å20 Å2
2---11.18 Å20 Å2
3----19.93 Å2
Refinement stepCycle: 1 / Resolution: 2→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2122 0 4 96 2222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0142164
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172029
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.6592950
X-RAY DIFFRACTIONr_angle_other_deg0.8691.6544729
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1675286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.52624.875
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.64515340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.394153
X-RAY DIFFRACTIONr_chiral_restr0.0630.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022393
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02379
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_it2.9783.7831153
X-RAY DIFFRACTIONr_mcbond_other2.9633.7811152
X-RAY DIFFRACTIONr_mcangle_it3.8545.6621436
X-RAY DIFFRACTIONr_mcangle_other3.8535.6641437
X-RAY DIFFRACTIONr_scbond_it3.6614.161010
X-RAY DIFFRACTIONr_scbond_other3.664.1621011
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4026.0671513
X-RAY DIFFRACTIONr_long_range_B_refined6.58745.0472179
X-RAY DIFFRACTIONr_long_range_B_other6.58545.0182172
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.002→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 89 -
Rwork0.323 1659 -
obs--98.2 %

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