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- PDB-9ehn: Co-MAHF-9 A8T Metal Alpha-Helix Framework -

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Basic information

Entry
Database: PDB / ID: 9ehn
TitleCo-MAHF-9 A8T Metal Alpha-Helix Framework
ComponentsCo-MAHF-9 A8T
KeywordsDE NOVO PROTEIN / synthetic construct
Function / homology:
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.98 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 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

Downloads & links

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Assembly

Deposited unit
A: Co-MAHF-9 A8T
B: Co-MAHF-9 A8T
C: Co-MAHF-9 A8T
D: Co-MAHF-9 A8T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,1396
Polymers4,0214
Non-polymers1182
Water73941
1
A: Co-MAHF-9 A8T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,0642
Polymers1,0051
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Co-MAHF-9 A8T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,0642
Polymers1,0051
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Co-MAHF-9 A8T


Theoretical massNumber of molelcules
Total (without water)1,0051
Polymers1,0051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Co-MAHF-9 A8T


Theoretical massNumber of molelcules
Total (without water)1,0051
Polymers1,0051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)16.470, 21.720, 23.650
Angle α, β, γ (deg.)103.640, 109.380, 108.910
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 A8T


Mass: 1005.213 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 1.7 Å3/Da / Density % sol: 27.83 %
Crystal growTemperature: 298 K / Method: slow cooling / Details: water, acetonitrile, cobalt acetate, methanol

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONMAX IV BioMAX10.68879
SYNCHROTRONAPS 21-ID-D20.729405
Detector
TypeIDDetectorDate
DECTRIS EIGER X 16M1PIXELMay 8, 2024
DECTRIS EIGER X 16M2PIXELSep 24, 2022
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.688791
20.7294051
ReflectionResolution: 0.98→18.97 Å / Num. obs: 15329 / % possible obs: 98.75 % / Redundancy: 6.3 % / Biso Wilson estimate: 6.61 Å2 / CC1/2: 0.991 / Net I/σ(I): 5.29
Reflection shellResolution: 0.98→1.015 Å / Num. unique obs: 1463 / CC1/2: 0.939

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.98→18.97 Å / SU ML: 0.0956 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 21.1026
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1839 3035 10.01 %
Rwork0.1649 27285 -
obs0.1668 15329 97.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 8.73 Å2
Refinement stepCycle: LAST / Resolution: 0.98→18.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms272 0 18 41 331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0105520
X-RAY DIFFRACTIONf_angle_d1.9158739
X-RAY DIFFRACTIONf_chiral_restr0.060870
X-RAY DIFFRACTIONf_plane_restr0.012979
X-RAY DIFFRACTIONf_dihedral_angle_d20.4945173
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.98-10.28271340.2671203X-RAY DIFFRACTION92.98
1-1.010.23791240.22171150X-RAY DIFFRACTION93.54
1.01-1.030.25981370.21151265X-RAY DIFFRACTION93.97
1.03-1.050.25351230.22291197X-RAY DIFFRACTION95.24
1.05-1.070.23621380.20351183X-RAY DIFFRACTION95.72
1.07-1.090.22981430.20021240X-RAY DIFFRACTION97.39
1.09-1.110.15971340.18181275X-RAY DIFFRACTION99.51
1.11-1.140.20721450.18541259X-RAY DIFFRACTION99.43
1.14-1.170.20181490.16741223X-RAY DIFFRACTION99.28
1.17-1.20.20441210.16951330X-RAY DIFFRACTION99.25
1.2-1.230.19471320.18051205X-RAY DIFFRACTION99.18
1.23-1.270.20261530.17551305X-RAY DIFFRACTION99.45
1.27-1.320.20821480.17391228X-RAY DIFFRACTION99.14
1.32-1.370.2141170.18071269X-RAY DIFFRACTION98.58
1.37-1.440.20131470.18341221X-RAY DIFFRACTION98.28
1.44-1.510.21391530.14121238X-RAY DIFFRACTION97.55
1.51-1.610.19191250.16061255X-RAY DIFFRACTION99.42
1.61-1.730.18651540.15371245X-RAY DIFFRACTION99.36
1.73-1.90.16811370.16031248X-RAY DIFFRACTION99.35
1.9-2.180.14391360.14791286X-RAY DIFFRACTION99.44
2.18-2.740.15781310.13981244X-RAY DIFFRACTION96.69
2.74-18.970.14841540.14551216X-RAY DIFFRACTION97.44

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