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- PDB-6zif: The structure of a cytosolic copper storage protein from Methyloc... -

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Basic information

Entry
Database: PDB / ID: 6zif
TitleThe structure of a cytosolic copper storage protein from Methylocystis sp. Strain Rockwell (ATCC 49242)
ComponentsRkCSP3
KeywordsMETAL BINDING PROTEIN / Copper / copper storage / copper homeostasis / methanotroph / methane oxidation / four-helix bundle
Function / homologyCOPPER (I) ION
Function and homology information
Biological speciesMethylocystis sp. ATCC 49242 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBasle, A. / Lee, J. / Dennison, C.
CitationJournal: To Be Published
Title: The importance of sites at the entrance of a copper storage protein for Cu(I) binding and removal
Authors: Lee, J. / Basle, A. / Dennison, C.
History
DepositionJun 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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: RkCSP3
B: RkCSP3
C: RkCSP3
D: RkCSP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,79374
Polymers48,3414
Non-polymers4,45270
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13380 Å2
ΔGint-640 kcal/mol
Surface area20300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.76, 60.76, 231.93
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
RkCSP3


Mass: 12085.321 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylocystis sp. ATCC 49242 (bacteria)
Production host: Escherichia coli (E. coli)
#2: Chemical...
ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 68 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestY

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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: 2.21 Å3/Da / Density % sol: 44.45 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 200 mM MgCl2, 100 mM Hepes pH 7.5 and 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96878 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96878 Å / Relative weight: 1
ReflectionResolution: 2.2→47.772 Å / Num. obs: 22975 / % possible obs: 99.3 % / Redundancy: 11.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.074 / Rrim(I) all: 0.19 / Net I/σ(I): 7.6
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 12.3 % / Num. unique obs: 1957 / CC1/2: 0.567

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
xia2data processing
Aimlessdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LMF

3lmf


Resolution: 2.2→47.77 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.926 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27036 1133 -RANDOM
Rwork0.21071 ---
obs0.21362 21763 99.09 %-
Displacement parametersBiso mean: 48.932 Å2
Baniso -1Baniso -2Baniso -3
1-2.13 Å2-0 Å2-0 Å2
2--2.13 Å2-0 Å2
3----4.25 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3246 0 70 0 3316
LS refinement shellResolution: 2.2→2.27 Å /
Rfactor% reflection
Rfree0.332 -
Rwork0.321 -
obs-100 %

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