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- PDB-9eg2: Co-MAHF-9 A8F Metal Alpha-Helix Framework -

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Basic information

Entry
Database: PDB / ID: 9eg2
TitleCo-MAHF-9 A8F Metal Alpha-Helix Framework
ComponentsCo-MAHF-9 A8F
KeywordsDE NOVO PROTEIN / synthetic construct
Function / homology: / METHANOL
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.89 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 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

Downloads & links

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Assembly

Deposited unit
A: Co-MAHF-9 A8F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,1744
Polymers1,0511
Non-polymers1233
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.602, 12.668, 19.348
Angle α, β, γ (deg.)90.000, 118.990, 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-103-

CO

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Components

#1: Protein/peptide Co-MAHF-9 A8F


Mass: 1051.283 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: CH4O
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 1.54 Å3/Da / Density % sol: 19.89 %
Crystal growTemperature: 298 K / Method: slow cooling / Details: acetonitrile, water, cobalt acetate, methanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.688839 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.688839 Å / Relative weight: 1
ReflectionResolution: 0.89→16.92 Å / Num. obs: 14755 / % possible obs: 94.44 % / Redundancy: 3.3 % / CC1/2: 0.968 / Net I/σ(I): 2.61
Reflection shellResolution: 0.89→0.94 Å / Num. unique obs: 1102 / CC1/2: 0.0376 / % possible all: 93.87

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.89→16.92 Å / SU ML: 0.0817 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 24.8997
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1879 914 9.91 %
Rwork0.1742 8313 -
obs0.1755 9227 94.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 6.47 Å2
Refinement stepCycle: LAST / Resolution: 0.89→16.92 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms72 0 9 4 85
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008687
X-RAY DIFFRACTIONf_angle_d2.0696119
X-RAY DIFFRACTIONf_chiral_restr0.082710
X-RAY DIFFRACTIONf_plane_restr0.006914
X-RAY DIFFRACTIONf_dihedral_angle_d24.644129
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.89-0.940.34181320.31661184X-RAY DIFFRACTION93.87
0.94-10.29451250.29561193X-RAY DIFFRACTION93.87
1-1.070.3111260.27291151X-RAY DIFFRACTION91.61
1.07-1.180.25181350.23471194X-RAY DIFFRACTION95.27
1.18-1.350.18741370.20511211X-RAY DIFFRACTION97.33
1.35-1.70.15321300.15081169X-RAY DIFFRACTION93.79
1.7-16.920.11071290.09021211X-RAY DIFFRACTION95.65

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