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- PDB-9mep: Co-MAHF-9 A8W Metal Alpha-Helix Framework -

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Basic information

Entry
Database: PDB / ID: 9mep
TitleCo-MAHF-9 A8W Metal Alpha-Helix Framework
ComponentsCo-MAHF-9 A8W
KeywordsDE NOVO PROTEIN / synthetic construct
Function / homology: / METHANOL
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.99 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 7, 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 A8W
B: Co-MAHF-9 A8W
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,3045
Polymers2,1812
Non-polymers1233
Water19811
1
A: Co-MAHF-9 A8W
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,1492
Polymers1,0901
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Co-MAHF-9 A8W
hetero molecules


  • defined by author&software
  • 1.15 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,1543
Polymers1,0901
Non-polymers642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)9.958, 16.313, 21.437
Angle α, β, γ (deg.)89.760, 87.000, 72.400
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 A8W


Mass: 1090.319 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.: 1 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH4O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 1.5 Å3/Da / Density % sol: 17.82 %
Crystal growTemperature: 298 K / Method: slow cooling / Details: water, acetonitrile, cobalt acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 0.99→15.55 Å / Num. obs: 6172 / % possible obs: 86.31 % / Redundancy: 3.4 % / Biso Wilson estimate: 5.99 Å2 / CC1/2: 0.954 / Net I/σ(I): 11.78
Reflection shellResolution: 0.99→1.025 Å / Num. unique obs: 464 / CC1/2: 0.913

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.99→15.55 Å / SU ML: 0.0975 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 14.0996
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1163 1067 9.93 %
Rwork0.0939 9680 -
obs0.096 6172 75.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 7.5 Å2
Refinement stepCycle: LAST / Resolution: 0.99→15.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms150 0 13 11 174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088238
X-RAY DIFFRACTIONf_angle_d1.5159334
X-RAY DIFFRACTIONf_chiral_restr0.058927
X-RAY DIFFRACTIONf_plane_restr0.006534
X-RAY DIFFRACTIONf_dihedral_angle_d19.326231
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.99-1.040.26171150.25967X-RAY DIFFRACTION61.48
1.04-1.090.21341390.16271235X-RAY DIFFRACTION74.35
1.09-1.160.16681330.12141147X-RAY DIFFRACTION73.48
1.16-1.250.12951440.10281251X-RAY DIFFRACTION76.73
1.25-1.370.11651320.10341213X-RAY DIFFRACTION77.12
1.37-1.570.12931230.08071281X-RAY DIFFRACTION79.05
1.57-1.980.09961380.07741353X-RAY DIFFRACTION81.74
1.98-15.550.08161430.07551233X-RAY DIFFRACTION77.65

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