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- PDB-9eg3: Co-MAHF-9 A8H Metal Alpha-Helix Framework -

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Basic information

Entry
Database: PDB / ID: 9eg3
TitleCo-MAHF-9 A8H Metal Alpha-Helix Framework
ComponentsCo-MAHF-9 A8H
KeywordsDE NOVO PROTEIN / synthetic construct
Function / homologyACETATE ION / :
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 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 A8H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,1603
Polymers1,0421
Non-polymers1182
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)11.033, 30.866, 40.588
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-101-

CO

21A-102-

ACT

31A-205-

HOH

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Components

#1: Protein/peptide Co-MAHF-9 A8H


Mass: 1042.256 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 1.63 Å3/Da / Density % sol: 24.59 %
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: 0.61992 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.61992 Å / Relative weight: 1
ReflectionResolution: 1.04→14.43 Å / Num. obs: 6478 / % possible obs: 95.04 % / Redundancy: 6.4 % / Biso Wilson estimate: 7.35 Å2 / CC1/2: 0.998 / Net I/σ(I): 8.94
Reflection shellResolution: 1.04→1.14 Å / Num. unique obs: 1199 / CC1/2: 0.536

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.04→14.43 Å / SU ML: 0.0642 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 12.6521
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1104 619 10.1 %
Rwork0.1022 5509 -
obs0.1031 6128 95.04 %
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: 1.04→14.43 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms71 0 9 8 88
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008387
X-RAY DIFFRACTIONf_angle_d1.468121
X-RAY DIFFRACTIONf_chiral_restr0.094610
X-RAY DIFFRACTIONf_plane_restr0.004315
X-RAY DIFFRACTIONf_dihedral_angle_d21.061413
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.04-1.140.1931340.21961155X-RAY DIFFRACTION80.56
1.14-1.310.13741570.11711447X-RAY DIFFRACTION99.88
1.31-1.650.09931660.09721463X-RAY DIFFRACTION99.63
1.65-14.430.0951620.08241444X-RAY DIFFRACTION99.94

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