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- PDB-9mfk: Mn-MAHF-9 A8S Metal Alpha-Helix Framework -

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Basic information

Entry
Database: PDB / ID: 9mfk
TitleMn-MAHF-9 A8S Metal Alpha-Helix Framework
ComponentsMn-MAHF-9 A8S
KeywordsDE NOVO PROTEIN / synthetic construct
Function / homology:
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.11 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 9, 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: Mn-MAHF-9 A8S
B: Mn-MAHF-9 A8S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,0373
Polymers1,9822
Non-polymers551
Water37821
1
A: Mn-MAHF-9 A8S
hetero molecules


  • defined by author&software
  • 1.05 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,0462
Polymers9911
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Mn-MAHF-9 A8S


Theoretical massNumber of molelcules
Total (without water)9911
Polymers9911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)10.320, 16.270, 20.660
Angle α, β, γ (deg.)81.280, 84.880, 71.620
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 Mn-MAHF-9 A8S


Mass: 991.187 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 1.61 Å3/Da / Density % sol: 23.71 %
Crystal growTemperature: 298 K / Method: slow cooling
Details: acetonitrile, water, manganese acetate, sodium hydroxide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.6888 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 26, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6888 Å / Relative weight: 1
ReflectionResolution: 1.11→15.31 Å / Num. obs: 4925 / % possible obs: 98.46 % / Redundancy: 5.6 % / Biso Wilson estimate: 3.43 Å2 / CC1/2: 0.976 / Net I/σ(I): 15.15
Reflection shellResolution: 1.11→1.15 Å / Rmerge(I) obs: 0.2181 / Num. unique obs: 518 / CC1/2: 0.94

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.11→15.31 Å / SU ML: 0.0681 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 19.4635
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.161 966 10.05 %
Rwork0.13 8648 -
obs0.1333 4925 96.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 4.38 Å2
Refinement stepCycle: LAST / Resolution: 1.11→15.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms134 0 9 21 164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077138
X-RAY DIFFRACTIONf_angle_d1.6294192
X-RAY DIFFRACTIONf_chiral_restr0.057618
X-RAY DIFFRACTIONf_plane_restr0.004620
X-RAY DIFFRACTIONf_dihedral_angle_d24.752922
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.11-1.170.18491380.13551217X-RAY DIFFRACTION92.55
1.17-1.240.13071350.12871198X-RAY DIFFRACTION96.32
1.24-1.340.15971410.11921244X-RAY DIFFRACTION97.26
1.34-1.470.13631380.1251285X-RAY DIFFRACTION96.54
1.47-1.680.17551370.13031227X-RAY DIFFRACTION97.15
1.69-2.120.14271360.12891230X-RAY DIFFRACTION97.29
2.13-15.310.17841410.13511247X-RAY DIFFRACTION97.75

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