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- PDB-5icu: The crystal structure of CopC from Methylosinus trichosporium OB3b -

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Basic information

Entry
Database: PDB / ID: 5icu
TitleThe crystal structure of CopC from Methylosinus trichosporium OB3b
ComponentsCopC
KeywordsCHAPERONE / CopC / metal homeostasis / PcoC / cupredoxin
Function / homology
Function and homology information


copper ion transport / response to copper ion / cell envelope / 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 (II) ION / CopC
Similarity search - Component
Biological speciesMethylosinus trichosporium OB3b (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsLawton, T.J. / Hurley, J.D. / Rosenzweig, A.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM58518 United States
CitationJournal: Biochemistry / Year: 2016
Title: The CopC Family: Structural and Bioinformatic Insights into a Diverse Group of Periplasmic Copper Binding Proteins.
Authors: Lawton, T.J. / Kenney, G.E. / Hurley, J.D. / Rosenzweig, A.C.
History
DepositionFeb 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CopC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2095
Polymers10,9261
Non-polymers2834
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.671, 54.125, 65.371
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: 10926.300 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylosinus trichosporium OB3b (bacteria)
Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) star / References: UniProt: A0A158RFT6*PLUS
#2: Chemical ChemComp-CU / COPPER (II) ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.32 Å3/Da / Density % sol: 47.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES sodium salt, 0.8 M sodium phosphate, and 0.8 M potassium phosphate, pH 7.5.

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.46→27.98 Å / Num. obs: 17434 / % possible obs: 99.9 % / Redundancy: 8.6 % / Net I/σ(I): 41.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→27.98 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.908 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.064 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19112 938 5.1 %RANDOM
Rwork0.16512 ---
obs0.1664 17434 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 10.371 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.06 Å2
Refinement stepCycle: 1 / Resolution: 1.46→27.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms771 0 14 88 873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.019802
X-RAY DIFFRACTIONr_bond_other_d0.0030.02771
X-RAY DIFFRACTIONr_angle_refined_deg1.6651.9851084
X-RAY DIFFRACTIONr_angle_other_deg0.96431790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7475103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.74724.19431
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.77415130
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.071153
X-RAY DIFFRACTIONr_chiral_restr0.1080.2124
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021883
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02164
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_it0.5110.726409
X-RAY DIFFRACTIONr_mcbond_other0.4990.726408
X-RAY DIFFRACTIONr_mcangle_it0.8121.091510
X-RAY DIFFRACTIONr_mcangle_other0.8131.091511
X-RAY DIFFRACTIONr_scbond_it1.1680.874393
X-RAY DIFFRACTIONr_scbond_other1.1640.874393
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7951.25574
X-RAY DIFFRACTIONr_long_range_B_refined3.46711.606886
X-RAY DIFFRACTIONr_long_range_B_other3.46711.607886
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded11.86251
LS refinement shellResolution: 1.46→1.495 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.165 66 -
Rwork0.168 1213 -
obs--96.46 %
Refinement TLS params.Method: refined / Origin x: -1.2811 Å / Origin y: -3.3126 Å / Origin z: 5.0738 Å
111213212223313233
T0.0135 Å2-0.0024 Å20.0043 Å2-0.0047 Å20.001 Å2--0.0075 Å2
L0.3986 °20.1753 °20.3126 °2-0.2165 °20.2719 °2--0.71 °2
S-0.0185 Å °0.0114 Å °0.0359 Å °-0.004 Å °0.0162 Å °0.0234 Å °-0.0676 Å °0.0175 Å °0.0023 Å °

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