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- PDB-9ml0: Co-MAHF-9 A8Q Hydrated Metal Alpha-Helix Framework -

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Basic information

Entry
Database: PDB / ID: 9ml0
TitleCo-MAHF-9 A8Q Hydrated Metal Alpha-Helix Framework
ComponentsCo-MAHF-9 A8Q Hydrated
KeywordsDE NOVO PROTEIN / synthetic construct
Function / homology:
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 0.92 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 18, 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 A8Q Hydrated
B: Co-MAHF-9 A8Q Hydrated
C: Co-MAHF-9 A8Q Hydrated
D: Co-MAHF-9 A8Q Hydrated
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,2476
Polymers4,1294
Non-polymers1182
Water93752
1
A: Co-MAHF-9 A8Q Hydrated
hetero molecules


  • defined by author
  • 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
2
B: Co-MAHF-9 A8Q Hydrated


Theoretical massNumber of molelcules
Total (without water)1,0321
Polymers1,0321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Co-MAHF-9 A8Q Hydrated
hetero molecules


  • defined by author
  • 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
4
D: Co-MAHF-9 A8Q Hydrated


Theoretical massNumber of molelcules
Total (without water)1,0321
Polymers1,0321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)16.206, 46.634, 19.845
Angle α, β, γ (deg.)90.000, 106.200, 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 Hydrated


Mass: 1032.238 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.: 52 / 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: 1.72 Å3/Da / Density % sol: 28.31 %
Crystal growTemperature: 298 K / Method: slow cooling / Details: water

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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 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 0.92→15.56 Å / Num. obs: 19497 / % possible obs: 99.08 % / Redundancy: 9.3 % / Biso Wilson estimate: 6.24 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.86
Reflection shellResolution: 0.92→0.9529 Å / Num. unique obs: 1817 / CC1/2: 0.795

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.92→15.56 Å / SU ML: 0.1021 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.6077
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.167 1955 10 %
Rwork0.1394 17593 -
obs0.1422 19497 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 9.02 Å2
Refinement stepCycle: LAST / Resolution: 0.92→15.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms280 0 18 52 350
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093375
X-RAY DIFFRACTIONf_angle_d1.9723530
X-RAY DIFFRACTIONf_chiral_restr0.055547
X-RAY DIFFRACTIONf_plane_restr0.003668
X-RAY DIFFRACTIONf_dihedral_angle_d19.6856142
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.92-0.940.29691030.3057933X-RAY DIFFRACTION73.11
0.94-0.960.27741400.25151252X-RAY DIFFRACTION98.93
0.96-0.990.2741440.21291297X-RAY DIFFRACTION100
0.99-1.020.24881400.19371259X-RAY DIFFRACTION99.71
1.02-1.060.19561410.17451269X-RAY DIFFRACTION99.93
1.06-1.10.20381450.16481299X-RAY DIFFRACTION100
1.1-1.150.18081430.14531286X-RAY DIFFRACTION100
1.15-1.210.19331410.13791266X-RAY DIFFRACTION99.93
1.21-1.290.19211400.14381265X-RAY DIFFRACTION100
1.29-1.390.17311430.12871292X-RAY DIFFRACTION100
1.39-1.530.16061440.12561285X-RAY DIFFRACTION99.93
1.53-1.750.1351430.12471285X-RAY DIFFRACTION100
1.75-2.20.14241440.10951302X-RAY DIFFRACTION99.93
2.2-15.560.12651440.11671303X-RAY DIFFRACTION99.79

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