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- PDB-6i1j: Selective formation of trinuclear transition metal centers in a t... -

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Basic information

Entry
Database: PDB / ID: 6i1j
TitleSelective formation of trinuclear transition metal centers in a trimeric helical peptide
ComponentsA helical peptide containing a trinuclear Cu(II) center: HisAD
KeywordsDE NOVO PROTEIN / Trimeric Coiled Coil / Copper-binding peptide
Function / homologyCOPPER (II) ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsBoyle, A.L. / Pannu, N.S.
Funding support Netherlands, 2items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research91116025 Netherlands
Netherlands Organisation for Scientific Research722.015.006 Netherlands
CitationJournal: Chem Sci / Year: 2019
Title: Selective coordination of three transition metal ions within a coiled-coil peptide scaffold.
Authors: Boyle, A.L. / Rabe, M. / Crone, N.S.A. / Rhys, G.G. / Soler, N. / Voskamp, P. / Pannu, N.S. / Kros, A.
History
DepositionOct 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: A helical peptide containing a trinuclear Cu(II) center: HisAD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,5452
Polymers3,4811
Non-polymers641
Water543
1
A: A helical peptide containing a trinuclear Cu(II) center: HisAD
hetero molecules

A: A helical peptide containing a trinuclear Cu(II) center: HisAD
hetero molecules

A: A helical peptide containing a trinuclear Cu(II) center: HisAD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6346
Polymers10,4433
Non-polymers1913
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area1890 Å2
ΔGint-42 kcal/mol
Surface area7750 Å2
MethodPISA
2
A: A helical peptide containing a trinuclear Cu(II) center: HisAD
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)21,26712
Polymers20,8866
Non-polymers3816
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area8460 Å2
ΔGint-133 kcal/mol
Surface area10820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.517, 30.517, 106.035
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein/peptide A helical peptide containing a trinuclear Cu(II) center: HisAD


Mass: 3481.029 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.05 Å3/Da / Density % sol: 39.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.09 M TRIS pH 8.5, 0.18 M LiSO4, 36% v/v PEG400, 5% v/v Jeffamine M-600

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.34765 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34765 Å / Relative weight: 1
ReflectionResolution: 2.35→23.64 Å / Num. obs: 1493 / % possible obs: 99.9 % / Redundancy: 29.6 % / CC1/2: 1 / Rpim(I) all: 0.011 / Net I/σ(I): 27.2
Reflection shellResolution: 2.35→2.54 Å / Redundancy: 31 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 293 / CC1/2: 0.916 / Rpim(I) all: 0.424 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
Aimlessdata scaling
Arcimboldophasing
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.35→23.64 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / Cross valid method: THROUGHOUT / ESU R: 0.489 / ESU R Free: 0.288 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28441 139 9.4 %RANDOM
Rwork0.26586 ---
obs0.26739 1338 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 119.165 Å2
Baniso -1Baniso -2Baniso -3
1-3.83 Å21.92 Å20 Å2
2--3.83 Å20 Å2
3----12.43 Å2
Refinement stepCycle: 1 / Resolution: 2.35→23.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms229 0 1 3 233
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.015232
X-RAY DIFFRACTIONr_bond_other_d0.0010.018237
X-RAY DIFFRACTIONr_angle_refined_deg1.481.626309
X-RAY DIFFRACTIONr_angle_other_deg1.421.662551
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.781529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.62526.6679
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.1961547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0570.234
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02249
X-RAY DIFFRACTIONr_gen_planes_other0.0110.0239
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_it10.15311.435119
X-RAY DIFFRACTIONr_mcbond_other10.14111.432118
X-RAY DIFFRACTIONr_mcangle_it13.77417.169147
X-RAY DIFFRACTIONr_mcangle_other13.75517.171148
X-RAY DIFFRACTIONr_scbond_it10.16712.463113
X-RAY DIFFRACTIONr_scbond_other10.12212.451114
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other15.37218.201163
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.594 11 -
Rwork0.63 87 -
obs--100 %

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