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- PDB-9efy: Co-MAHF-9 A8G Metal Alpha-Helix Framework -

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Basic information

Entry
Database: PDB / ID: 9efy
TitleCo-MAHF-9 A8G Metal Alpha-Helix Framework
ComponentsCo-MAHF-9 A8G
KeywordsDE NOVO PROTEIN / synthetic construct
Function / homology:
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.91 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 A8G
B: Co-MAHF-9 A8G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,9813
Polymers1,9222
Non-polymers591
Water905
1
A: Co-MAHF-9 A8G


Theoretical massNumber of molelcules
Total (without water)9611
Polymers9611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Co-MAHF-9 A8G
hetero molecules


  • defined by author&software
  • 1.02 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,0202
Polymers9611
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)10.320, 16.240, 21.570
Angle α, β, γ (deg.)67.920, 89.370, 71.850
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 A8G


Mass: 961.161 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.: 5 / 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: 1.62 Å3/Da / Density % sol: 23.85 %
Crystal growTemperature: 298 K / Method: slow cooling / Details: water, acetonitrile, cobalt acetate

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONMAX IV BioMAX10.6888
SYNCHROTRONAPS 21-ID-D20.72925
Detector
TypeIDDetectorDate
DECTRIS EIGER X 16M1PIXELMay 8, 2024
DECTRIS EIGER X 16M2PIXELFeb 15, 2023
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.68881
20.729251
ReflectionResolution: 0.91→14.56 Å / Num. obs: 24651 / % possible obs: 92.63 % / Redundancy: 2.6 % / Biso Wilson estimate: 8.73 Å2 / CC1/2: 0.993 / Net I/σ(I): 3.95
Reflection shellResolution: 0.91→0.94 Å / Num. unique obs: 172 / CC1/2: 0.0247

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.91→14.56 Å / SU ML: 0.0852 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 27.7689
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2069 1632 10.03 %
Rwork0.1798 14640 -
obs0.1824 24651 92.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 9.43 Å2
Refinement stepCycle: LAST / Resolution: 0.91→14.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms130 0 9 5 144
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081134
X-RAY DIFFRACTIONf_angle_d1.5425186
X-RAY DIFFRACTIONf_chiral_restr0.043716
X-RAY DIFFRACTIONf_plane_restr0.005920
X-RAY DIFFRACTIONf_dihedral_angle_d25.022722
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.91-0.940.32291360.27131237X-RAY DIFFRACTION90.81
0.94-0.970.25921280.23491184X-RAY DIFFRACTION93.45
0.97-10.2961380.2141215X-RAY DIFFRACTION92.93
1-1.040.25441320.23471253X-RAY DIFFRACTION93.33
1.04-1.090.23891160.19511002X-RAY DIFFRACTION75.64
1.09-1.150.19281450.17211281X-RAY DIFFRACTION95.7
1.15-1.220.23271360.18781208X-RAY DIFFRACTION96
1.22-1.310.19261460.20291252X-RAY DIFFRACTION94.2
1.31-1.440.21531320.2021264X-RAY DIFFRACTION94.07
1.44-1.650.21971450.17051270X-RAY DIFFRACTION97.45
1.65-2.080.1971400.181237X-RAY DIFFRACTION94.97
2.08-14.560.18421380.1561237X-RAY DIFFRACTION93.79

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