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- PDB-9ehp: Co-MAHF-9 A8C Metal Alpha-Helix Framework -

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Basic information

Entry
Database: PDB / ID: 9ehp
TitleCo-MAHF-9 A8C Metal Alpha-Helix Framework
ComponentsCo-MAHF-9 A8C
KeywordsDE NOVO PROTEIN / synthetic construct
Function / homology:
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 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 24, 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
B: Co-MAHF-9 A8C
A: Co-MAHF-9 A8C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,0733
Polymers2,0152
Non-polymers591
Water1086
1
B: Co-MAHF-9 A8C


Theoretical massNumber of molelcules
Total (without water)1,0071
Polymers1,0071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Co-MAHF-9 A8C
hetero molecules


  • defined by author
  • 1.07 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,0662
Polymers1,0071
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)9.917, 16.292, 20.160
Angle α, β, γ (deg.)81.610, 81.500, 72.510
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 A8C


Mass: 1007.252 Da / Num. of mol.: 2 / 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: 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

Crystal growTemperature: 298 K / Method: slow cooling / Details: water, acetonitrile, cobalt acetate, methanol

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS-II 17-ID-110.68879
SYNCHROTRONMAX IV BioMAX20.68879
Detector
TypeIDDetectorDate
DECTRIS EIGER X 9M1PIXELJun 12, 2024
DECTRIS EIGER X 16M2PIXELMay 8, 2024
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.688791
21
ReflectionResolution: 1.67→15.45 Å / Num. obs: 1336 / % possible obs: 98.09 % / Redundancy: 3.5 % / Biso Wilson estimate: 15.83 Å2 / CC1/2: 0.992 / Net I/σ(I): 7.38
Reflection shellResolution: 1.67→1.73 Å / Num. unique obs: 119 / CC1/2: 0.854

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→15.45 Å / SU ML: 0.1476 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 21.689
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2491 264 10.1 %
Rwork0.2 2351 -
obs0.205 1336 96.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.65 Å2
Refinement stepCycle: LAST / Resolution: 1.67→15.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms134 0 9 6 149
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088138
X-RAY DIFFRACTIONf_angle_d1.5685192
X-RAY DIFFRACTIONf_chiral_restr0.039918
X-RAY DIFFRACTIONf_plane_restr0.011520
X-RAY DIFFRACTIONf_dihedral_angle_d24.773622
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-2.10.29831320.26211167X-RAY DIFFRACTION96.36
2.11-15.450.23241320.17911184X-RAY DIFFRACTION95.78

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