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- PDB-9mnv: Co-MAHF-9 A8Y Metal Alpha-Helix Framework -

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Basic information

Entry
Database: PDB / ID: 9mnv
TitleCo-MAHF-9 A8Y Metal Alpha-Helix Framework
ComponentsCo-MAHF-9 A8Y
KeywordsDE NOVO PROTEIN / synthetic construct
Function / homology: / METHANOL
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 0.8 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 23, 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 A8Y
B: Co-MAHF-9 A8Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,2264
Polymers2,1352
Non-polymers912
Water1267
1
A: Co-MAHF-9 A8Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,1583
Polymers1,0671
Non-polymers912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Co-MAHF-9 A8Y


Theoretical massNumber of molelcules
Total (without water)1,0671
Polymers1,0671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)10.227, 16.303, 20.648
Angle α, β, γ (deg.)92.693, 103.389, 108.099
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 A8Y


Mass: 1067.283 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4O
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 1.46 Å3/Da / Density % sol: 15.51 %
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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-3000 / Detector: PIXEL / Date: Dec 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 0.8→19.92 Å / Num. obs: 12241 / % possible obs: 94.61 % / Redundancy: 4.2 % / Biso Wilson estimate: 4.45 Å2 / CC1/2: 0.995 / Net I/σ(I): 26.67
Reflection shellResolution: 0.8→0.8287 Å / Num. unique obs: 995 / CC1/2: 0.79

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.8→19.92 Å / SU ML: 0.0629 / Cross valid method: FREE R-VALUE / σ(F): 2.05 / Phase error: 12.5706
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1144 1243 10.11 %
Rwork0.1128 11052 -
obs0.113 12241 93.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 5.05 Å2
Refinement stepCycle: LAST / Resolution: 0.8→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms146 0 11 7 164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087183
X-RAY DIFFRACTIONf_angle_d1.5279258
X-RAY DIFFRACTIONf_chiral_restr0.084620
X-RAY DIFFRACTIONf_plane_restr0.006629
X-RAY DIFFRACTIONf_dihedral_angle_d15.341562
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.8-0.830.2629990.2864909X-RAY DIFFRACTION69.57
0.83-0.870.17591350.18561183X-RAY DIFFRACTION89.48
0.87-0.910.16861420.15721240X-RAY DIFFRACTION94.08
0.91-0.970.15131410.13021257X-RAY DIFFRACTION97.76
0.97-1.040.12741410.10631315X-RAY DIFFRACTION99.32
1.04-1.150.10541570.09181315X-RAY DIFFRACTION99.59
1.15-1.310.0941400.08931300X-RAY DIFFRACTION99.86
1.31-1.650.09641500.10291303X-RAY DIFFRACTION99.66
1.65-19.920.09961380.10591230X-RAY DIFFRACTION93.57

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