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- PDB-9eg5: Co-MAHF-9 A8S Metal Alpha-Helix Framework -

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Basic information

Entry
Database: PDB / ID: 9eg5
TitleCo-MAHF-9 A8S Metal Alpha-Helix Framework
ComponentsCo-MAHF-9 A8S
KeywordsDE NOVO PROTEIN / synthetic construct
Function / homologyACETONITRILE / : / METHANOL
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.98 Å
AuthorsRichardson-Matthews, R.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM15479301 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 20, 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

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Assembly

Deposited unit
A: Co-MAHF-9 A8S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,1234
Polymers9911
Non-polymers1323
Water1086
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.174, 10.726, 21.116
Angle α, β, γ (deg.)90.000, 104.140, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-101-

CO

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Components

#1: Protein/peptide Co-MAHF-9 A8S


Mass: 991.187 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4O
#4: Chemical ChemComp-CCN / ACETONITRILE


Mass: 41.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3N
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 1.7 Å3/Da / Density % sol: 27.55 %
Crystal growTemperature: 298 K / Method: slow cooling / Details: water, acetonitrile, methanol, cobalt acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.729405 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.729405 Å / Relative weight: 1
ReflectionResolution: 0.98→20.48 Å / Num. obs: 6822 / % possible obs: 89.47 % / Redundancy: 3.3 % / Biso Wilson estimate: 7.68 Å2 / CC1/2: 0.995 / Net I/σ(I): 10.25
Reflection shellResolution: 0.98→1.06 Å / Num. unique obs: 834 / CC1/2: 0.971

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.98→20.48 Å / SU ML: 0.0635 / Cross valid method: FREE R-VALUE / σ(F): 1.56 / Phase error: 18.5158
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1378 683 10.03 %
Rwork0.114 6125 -
obs0.1163 3646 89.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 10.4 Å2
Refinement stepCycle: LAST / Resolution: 0.98→20.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms67 0 10 6 83
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008172
X-RAY DIFFRACTIONf_angle_d1.729797
X-RAY DIFFRACTIONf_chiral_restr0.09279
X-RAY DIFFRACTIONf_plane_restr0.005610
X-RAY DIFFRACTIONf_dihedral_angle_d24.878211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.98-1.060.163890.1518792X-RAY DIFFRACTION58.81
1.06-1.160.1591440.13391315X-RAY DIFFRACTION94.74
1.16-1.330.16691460.13611345X-RAY DIFFRACTION98.48
1.33-1.670.13581540.11241326X-RAY DIFFRACTION97.11
1.68-20.480.12431500.10161347X-RAY DIFFRACTION97.91

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