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- PDB-9mdg: Co-MAHF-9 A8L Metal Alpha-Helix Framework -

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Basic information

Entry
Database: PDB / ID: 9mdg
TitleCo-MAHF-9 A8L Metal Alpha-Helix Framework
ComponentsCo-MAHF-9 A8L
KeywordsDE NOVO PROTEIN / synthetic construct
Function / homology: / METHANOL
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 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
DepositionDec 5, 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 A8L
B: Co-MAHF-9 A8L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,1845
Polymers2,0352
Non-polymers1503
Water25214
1
A: Co-MAHF-9 A8L
hetero molecules


  • defined by author
  • 1.14 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,1353
Polymers1,0171
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Co-MAHF-9 A8L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,0492
Polymers1,0171
Non-polymers321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.315, 16.450, 17.586
Angle α, β, γ (deg.)90.000, 101.080, 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

21A-102-

CO

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Components

#1: Protein/peptide Co-MAHF-9 A8L


Mass: 1017.267 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.: 2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 1.66 Å3/Da / Density % sol: 25.8 %
Crystal growTemperature: 298 K / Method: slow cooling
Details: water, acetonitrile, cobalt acetate, sodium hydroxide, 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: 1.41→17.26 Å / Num. obs: 2652 / % possible obs: 97.21 % / Redundancy: 6.3 % / Biso Wilson estimate: 13.36 Å2 / CC1/2: 0.992 / Net I/σ(I): 7.58
Reflection shellResolution: 1.41→1.46 Å / Num. unique obs: 250 / CC1/2: 0.753

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.41→17.26 Å / SU ML: 0.1556 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5773
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1971 499 10.14 %
Rwork0.1445 4421 -
obs0.1501 2652 96.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.85 Å2
Refinement stepCycle: LAST / Resolution: 1.41→17.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms138 0 12 14 164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0106152
X-RAY DIFFRACTIONf_angle_d1.65212
X-RAY DIFFRACTIONf_chiral_restr0.073522
X-RAY DIFFRACTIONf_plane_restr0.011922
X-RAY DIFFRACTIONf_dihedral_angle_d20.040152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.550.29671160.23951042X-RAY DIFFRACTION92.12
1.55-1.770.2521250.15921098X-RAY DIFFRACTION94.29
1.78-2.240.20251290.16581130X-RAY DIFFRACTION99.37
2.24-17.260.16751290.11611151X-RAY DIFFRACTION99.07

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