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- PDB-9eh3: Co-MAHF-9 A8Q Metal Alpha-Helix Frameworks -

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Basic information

Entry
Database: PDB / ID: 9eh3
TitleCo-MAHF-9 A8Q Metal Alpha-Helix Frameworks
ComponentsCo-MAHF-9 A8Q
KeywordsDE NOVO PROTEIN / synthetic construct
Function / homology:
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 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
DepositionNov 21, 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 A8Q
B: Co-MAHF-9 A8Q
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,1233
Polymers2,0642
Non-polymers591
Water30617
1
A: Co-MAHF-9 A8Q
hetero molecules


  • defined by author&software
  • 1.09 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,0912
Polymers1,0321
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Co-MAHF-9 A8Q


Theoretical massNumber of molelcules
Total (without water)1,0321
Polymers1,0321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)9.973, 41.838, 16.105
Angle α, β, γ (deg.)90.000, 106.170, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein/peptide Co-MAHF-9 A8Q


Mass: 1032.238 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: 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: 1.54 Å3/Da / Density % sol: 20.01 %
Crystal growTemperature: 298 K / Method: slow cooling
Details: water, acetonitrile, sodium hydroxide, cobalt acetate, methanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.68879 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.68879 Å / Relative weight: 1
ReflectionResolution: 0.8→15.47 Å / Num. obs: 25857 / % possible obs: 97.63 % / Redundancy: 3.3 % / Biso Wilson estimate: 7.69 Å2 / CC1/2: 0.993 / Net I/σ(I): 6.24
Reflection shellResolution: 0.8→0.82 Å / Mean I/σ(I) obs: 0.69 / Num. unique obs: 1394 / CC1/2: 0.391 / % possible all: 90.13

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.8→15.47 Å / SU ML: 0.0896 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.7117
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1527 2579 9.99 %
Rwork0.1314 23246 -
obs0.1333 25857 97.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 9.38 Å2
Refinement stepCycle: LAST / Resolution: 0.8→15.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms140 0 9 17 166
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096154
X-RAY DIFFRACTIONf_angle_d1.6973215
X-RAY DIFFRACTIONf_chiral_restr0.067219
X-RAY DIFFRACTIONf_plane_restr0.008425
X-RAY DIFFRACTIONf_dihedral_angle_d22.93424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.8-0.820.36981170.32251274X-RAY DIFFRACTION90.44
0.82-0.830.30921530.29041171X-RAY DIFFRACTION91.44
0.83-0.850.31611340.28191309X-RAY DIFFRACTION98.77
0.85-0.870.29721470.29181267X-RAY DIFFRACTION98.95
0.87-0.890.24531480.25871349X-RAY DIFFRACTION99.4
0.89-0.920.26251440.23441321X-RAY DIFFRACTION98.52
0.92-0.940.25211350.21571272X-RAY DIFFRACTION99.86
0.94-0.970.20061510.18461334X-RAY DIFFRACTION99.8
0.97-1.010.16691480.15521340X-RAY DIFFRACTION99.4
1.01-1.050.19451400.13941287X-RAY DIFFRACTION99.72
1.05-1.10.1841510.13481360X-RAY DIFFRACTION99.74
1.1-1.150.13711450.11241288X-RAY DIFFRACTION99.44
1.15-1.230.12521500.11851302X-RAY DIFFRACTION99.25
1.23-1.320.14521220.1231153X-RAY DIFFRACTION88.24
1.32-1.450.12511520.12311347X-RAY DIFFRACTION99.8
1.45-1.660.15591420.11551332X-RAY DIFFRACTION99.53
1.66-2.090.12641500.10831281X-RAY DIFFRACTION99.79
2.1-15.470.11961500.09331259X-RAY DIFFRACTION95.59

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