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- PDB-9mfi: Cu-MAHF-9 A8S Metal Alpha-Helix Framework -

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Basic information

Entry
Database: PDB / ID: 9mfi
TitleCu-MAHF-9 A8S Metal Alpha-Helix Framework
ComponentsCu-MAHF-9 A8S
KeywordsDE NOVO PROTEIN / synthetic construct
Function / homologyCOPPER (II) ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.89 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

Downloads & links

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Assembly

Deposited unit
A: Cu-MAHF-9 A8S
B: Cu-MAHF-9 A8S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,0463
Polymers1,9822
Non-polymers641
Water30617
1
A: Cu-MAHF-9 A8S


  • defined by author
  • 991 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)9911
Polymers9911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cu-MAHF-9 A8S
hetero molecules


  • defined by author
  • 1.05 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,0552
Polymers9911
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)10.395, 16.286, 20.196
Angle α, β, γ (deg.)80.280, 87.880, 71.660
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 Cu-MAHF-9 A8S


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


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 1.59 Å3/Da / Density % sol: 22.46 %
Crystal growTemperature: 298 K / Method: slow cooling / Details: water, acetonitrile, copper acetate, methanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.688797 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.688797 Å / Relative weight: 1
ReflectionResolution: 0.89→15.25 Å / Num. obs: 21942 / % possible obs: 86.39 % / Redundancy: 2 % / Biso Wilson estimate: 3.44 Å2 / CC1/2: 0.994 / Net I/σ(I): 7.12
Reflection shellResolution: 0.89→0.9 Å / Num. unique obs: 12 / CC1/2: 0.533

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.89→9.95 Å / SU ML: 0.0339 / Cross valid method: FREE R-VALUE / σ(F): 2.06 / Phase error: 6.9254
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.0813 1671 10.16 %
Rwork0.081 14772 -
obs0.081 16443 86.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 4.59 Å2
Refinement stepCycle: LAST / Resolution: 0.89→9.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms134 0 9 17 160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058146
X-RAY DIFFRACTIONf_angle_d1.9261203
X-RAY DIFFRACTIONf_chiral_restr0.046920
X-RAY DIFFRACTIONf_plane_restr0.002821
X-RAY DIFFRACTIONf_dihedral_angle_d20.560549
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.89-0.920.13961550.14821225X-RAY DIFFRACTION84.87
0.92-0.950.12121320.13251246X-RAY DIFFRACTION86.67
0.95-0.980.13431350.12311205X-RAY DIFFRACTION86.68
0.98-1.020.09221360.10551261X-RAY DIFFRACTION86.56
1.02-1.060.08771400.09841219X-RAY DIFFRACTION87.12
1.07-1.120.08661480.08711253X-RAY DIFFRACTION89.69
1.12-1.190.0731400.07891238X-RAY DIFFRACTION86.45
1.19-1.280.08381350.07671231X-RAY DIFFRACTION85.48
1.28-1.410.07941450.07191225X-RAY DIFFRACTION86.71
1.41-1.620.06311470.06841218X-RAY DIFFRACTION86.61
1.62-2.030.07661370.06491258X-RAY DIFFRACTION86.86
2.03-9.950.06121210.06291193X-RAY DIFFRACTION83.69

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