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- PDB-9eju: Co-MAHF-9 A8N Metal Alpha-Helix Framework -

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Basic information

Entry
Database: PDB / ID: 9eju
TitleCo-MAHF-9 A8N Metal Alpha-Helix Framework
ComponentsCo-MAHF-9 A8N
KeywordsDE NOVO PROTEIN / synthetic construct
Function / homologyACETONITRILE / :
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 Å
AuthorsRichardson-Matthews, R.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM15479301 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Metal-alpha-Helix Peptide Frameworks.
Authors: Richardson-Matthews, R. / Velko, K. / Bhunia, B. / Ghosh, S. / Oktawiec, J. / Brunzelle, J.S. / Dang, V.T. / Nguyen, A.I.
History
DepositionNov 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Co-MAHF-9 A8N
B: Co-MAHF-9 A8N
C: Co-MAHF-9 A8N
D: Co-MAHF-9 A8N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,35510
Polymers4,0734
Non-polymers2826
Water1,17165
1
A: Co-MAHF-9 A8N
hetero molecules


  • defined by author&software
  • 1.16 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,1594
Polymers1,0181
Non-polymers1413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Co-MAHF-9 A8N


Theoretical massNumber of molelcules
Total (without water)1,0181
Polymers1,0181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Co-MAHF-9 A8N
hetero molecules


  • defined by author&software
  • 1.08 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,0772
Polymers1,0181
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Co-MAHF-9 A8N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,1003
Polymers1,0181
Non-polymers822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)10.024, 16.241, 48.919
Angle α, β, γ (deg.)89.950, 89.830, 72.590
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein/peptide
Co-MAHF-9 A8N


Mass: 1018.212 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical
ChemComp-CCN / ACETONITRILE


Mass: 41.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3N
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 1.84 Å3/Da / Density % sol: 32.98 %
Crystal growTemperature: 298 K / Method: slow cooling
Details: water, acetonitrile, cobalt acetate, sodium hydroxide, methanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.68879 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.68879 Å / Relative weight: 1
ReflectionResolution: 1.17→48.92 Å / Num. obs: 9568 / % possible obs: 96.09 % / Redundancy: 3.5 % / CC1/2: 0.994 / Net I/σ(I): 7.59
Reflection shellResolution: 1.17→1.212 Å / Num. unique obs: 918 / CC1/2: 0.886

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.17→48.92 Å / Cross valid method: FREE R-VALUE / σ(F): 47.01 / Phase error: 37.5492
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2627 2050 10.92 %
Rwork0.2132 16725 -
obs0.2211 9568 94.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.32 Å2
Refinement stepCycle: LAST / Resolution: 1.17→48.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms276 0 30 65 371
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081292
X-RAY DIFFRACTIONf_angle_d1.627400
X-RAY DIFFRACTIONf_chiral_restr0.062936
X-RAY DIFFRACTIONf_plane_restr0.006544
X-RAY DIFFRACTIONf_dihedral_angle_d21.627296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.17-1.20.36721420.32841174X-RAY DIFFRACTION81.98
1.2-1.230.37141460.32471219X-RAY DIFFRACTION83.04
1.23-1.270.36331370.321185X-RAY DIFFRACTION82.75
1.27-1.310.30051380.30791072X-RAY DIFFRACTION82.72
1.31-1.360.33561460.2981296X-RAY DIFFRACTION84.05
1.36-1.410.44231250.2971173X-RAY DIFFRACTION85
1.41-1.470.28491380.2771248X-RAY DIFFRACTION85.25
1.47-1.550.29071260.26121140X-RAY DIFFRACTION84.57
1.55-1.650.28451560.24341276X-RAY DIFFRACTION85.64
1.65-1.780.25041290.22371181X-RAY DIFFRACTION86.58
1.78-1.950.26551390.22241232X-RAY DIFFRACTION85.79
1.96-2.240.2351250.18391184X-RAY DIFFRACTION85.55
2.24-2.820.19241270.15781258X-RAY DIFFRACTION87.6
2.82-48.920.21871450.16211218X-RAY DIFFRACTION85.17

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