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- PDB-9mdb: Co-MAHF-9 A8V Metal Alpha-Helix Framework -

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Basic information

Entry
Database: PDB / ID: 9mdb
TitleCo-MAHF-9 A8V Metal Alpha-Helix Framework
ComponentsCo-MAHF-9 A8V
KeywordsDE NOVO PROTEIN / synthetic construct
Function / homology:
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.81 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

Downloads & links

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Assembly

Deposited unit
A: Co-MAHF-9 A8V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,0622
Polymers1,0031
Non-polymers591
Water1629
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)10.793, 31.072, 37.915
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-203-

HOH

31A-205-

HOH

41A-207-

HOH

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Components

#1: Protein/peptide Co-MAHF-9 A8V


Mass: 1003.240 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 1.56 Å3/Da / Density % sol: 21.05 %
Crystal growTemperature: 298 K / Method: slow cooling
Details: water, acetonitrile, cobalt acetate, sodium hydroxide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.688801 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.688801 Å / Relative weight: 1
ReflectionResolution: 0.81→15.54 Å / Num. obs: 6821 / % possible obs: 99.59 % / Redundancy: 11.7 % / Biso Wilson estimate: 7.04 Å2 / CC1/2: 0.998 / Net I/σ(I): 18.26
Reflection shellResolution: 0.81→0.8389 Å / Num. unique obs: 657 / CC1/2: 0.864

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.81→15.54 Å / SU ML: 0.0793 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.9619
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1546 1262 10.1 %
Rwork0.1425 11234 -
obs0.1438 6821 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 8.77 Å2
Refinement stepCycle: LAST / Resolution: 0.81→15.54 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms68 0 5 9 82
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111154
X-RAY DIFFRACTIONf_angle_d1.6861212
X-RAY DIFFRACTIONf_chiral_restr0.039523
X-RAY DIFFRACTIONf_plane_restr0.007321
X-RAY DIFFRACTIONf_dihedral_angle_d22.455350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.81-0.840.29551380.25411227X-RAY DIFFRACTION96.81
0.84-0.880.21631390.21981241X-RAY DIFFRACTION99.35
0.88-0.930.20191410.17721250X-RAY DIFFRACTION100
0.93-0.990.17671420.13311268X-RAY DIFFRACTION100
0.99-1.060.1541350.12751241X-RAY DIFFRACTION100
1.06-1.170.13471410.11831256X-RAY DIFFRACTION100
1.17-1.340.13351420.1221250X-RAY DIFFRACTION100
1.34-1.680.19451400.13881245X-RAY DIFFRACTION99.64
1.68-15.540.13491440.14461256X-RAY DIFFRACTION99.86

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