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- PDB-9mkj: Fe-MAHF-9 A8S Metal Alpha-Helix Framework -

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Basic information

Entry
Database: PDB / ID: 9mkj
TitleFe-MAHF-9 A8S Metal Alpha-Helix Framework
ComponentsFe-MAHF-9 A8S
KeywordsDE NOVO PROTEIN / synthetic construct
Function / homologyACETONITRILE / :
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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 17, 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: Fe-MAHF-9 A8S
B: Fe-MAHF-9 A8S
C: Fe-MAHF-9 A8S
D: Fe-MAHF-9 A8S
E: Fe-MAHF-9 A8S
F: Fe-MAHF-9 A8S
G: Fe-MAHF-9 A8S
H: Fe-MAHF-9 A8S
I: Fe-MAHF-9 A8S
J: Fe-MAHF-9 A8S
K: Fe-MAHF-9 A8S
L: Fe-MAHF-9 A8S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,31120
Polymers11,89412
Non-polymers4178
Water2,324129
1
A: Fe-MAHF-9 A8S


Theoretical massNumber of molelcules
Total (without water)9911
Polymers9911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fe-MAHF-9 A8S
hetero molecules


  • defined by author
  • 1.05 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,0472
Polymers9911
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Fe-MAHF-9 A8S
hetero molecules


  • defined by author
  • 1.09 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,0883
Polymers9911
Non-polymers972
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Fe-MAHF-9 A8S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,0883
Polymers9911
Non-polymers972
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Fe-MAHF-9 A8S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,0472
Polymers9911
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Fe-MAHF-9 A8S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,0472
Polymers9911
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Fe-MAHF-9 A8S


Theoretical massNumber of molelcules
Total (without water)9911
Polymers9911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Fe-MAHF-9 A8S


Theoretical massNumber of molelcules
Total (without water)9911
Polymers9911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Fe-MAHF-9 A8S


Theoretical massNumber of molelcules
Total (without water)9911
Polymers9911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Fe-MAHF-9 A8S


Theoretical massNumber of molelcules
Total (without water)9911
Polymers9911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: Fe-MAHF-9 A8S
hetero molecules


  • defined by author
  • 1.05 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,0472
Polymers9911
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: Fe-MAHF-9 A8S


Theoretical massNumber of molelcules
Total (without water)9911
Polymers9911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)16.206, 84.925, 30.610
Angle α, β, γ (deg.)90.000, 103.730, 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
Fe-MAHF-9 A8S


Mass: 991.187 Da / Num. of mol.: 12 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: Fe
#3: Chemical ChemComp-CCN / ACETONITRILE


Mass: 41.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3N
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 1.69 Å3/Da / Density % sol: 27.4 %
Crystal growTemperature: 298 K / Method: slow cooling / Details: water, acetonitrile, iron acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.61984 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.61984 Å / Relative weight: 1
ReflectionResolution: 1.1→15.53 Å / Num. obs: 31966 / % possible obs: 88.31 % / Redundancy: 6.9 % / Biso Wilson estimate: 7.75 Å2 / CC1/2: 0.99 / Net I/σ(I): 7.86
Reflection shellResolution: 1.1→1.139 Å / Num. unique obs: 2909 / CC1/2: 0.896

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→15.53 Å / SU ML: 0.1059 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.9218
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2108 3612 5.79 %
Rwork0.2051 58734 -
obs0.2054 31966 96.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.65 Å2
Refinement stepCycle: LAST / Resolution: 1.1→15.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms804 0 60 129 993
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00871209
X-RAY DIFFRACTIONf_angle_d1.76911690
X-RAY DIFFRACTIONf_chiral_restr0.0764157
X-RAY DIFFRACTIONf_plane_restr0.0072182
X-RAY DIFFRACTIONf_dihedral_angle_d19.1797408
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.110.28911490.28532293X-RAY DIFFRACTION97.6
1.11-1.130.33961270.29542284X-RAY DIFFRACTION98.01
1.13-1.150.26921490.27172317X-RAY DIFFRACTION97.32
1.15-1.160.23851520.27852280X-RAY DIFFRACTION97.67
1.16-1.180.28481190.2792236X-RAY DIFFRACTION96.95
1.18-1.20.23731280.26842247X-RAY DIFFRACTION97.5
1.2-1.220.25531500.26362331X-RAY DIFFRACTION97.87
1.22-1.240.27471340.25182342X-RAY DIFFRACTION97.94
1.24-1.270.25191430.2622184X-RAY DIFFRACTION96.92
1.27-1.290.21631440.24292270X-RAY DIFFRACTION97.73
1.29-1.320.24941570.23752224X-RAY DIFFRACTION97.66
1.32-1.350.22791380.22322408X-RAY DIFFRACTION97.62
1.35-1.390.25721230.24532125X-RAY DIFFRACTION95.21
1.39-1.420.20491550.21742256X-RAY DIFFRACTION97.85
1.42-1.470.22951380.2162364X-RAY DIFFRACTION97.01
1.47-1.510.19861270.20832156X-RAY DIFFRACTION95.72
1.51-1.570.21891300.20372042X-RAY DIFFRACTION87.86
1.57-1.630.16531240.18822091X-RAY DIFFRACTION86.93
1.63-1.70.20691350.1822269X-RAY DIFFRACTION98.56
1.7-1.790.16441550.18242317X-RAY DIFFRACTION98.41
1.79-1.90.17081350.18842254X-RAY DIFFRACTION98.8
1.9-2.050.21361460.16842346X-RAY DIFFRACTION98.5
2.05-2.260.161390.17832236X-RAY DIFFRACTION97.54
2.26-2.580.15671430.17052305X-RAY DIFFRACTION98.75
2.58-3.250.21311340.18732308X-RAY DIFFRACTION98.03
3.25-15.530.21621380.17182249X-RAY DIFFRACTION96.8

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