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- PDB-8sw2: Porous framework formed by assembly of a bipyridyl-conjugated hel... -

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Basic information

Entry
Database: PDB / ID: 8sw2
TitlePorous framework formed by assembly of a bipyridyl-conjugated helical peptide
ComponentsLEU-AIB-ALA-SER-LEU-ALA-CYS-AIB-LEU
KeywordsDE NOVO PROTEIN
Function / homologyACETATE ION / : / Chem-I77 / NICOTINIC ACID
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsHess, S.S. / Nguyen, A.I.
Funding support1items
OrganizationGrant numberCountry
Other private
Citation
Journal: J.Am.Chem.Soc. / Year: 2023
Title: Noncovalent Peptide Assembly Enables Crystalline, Permutable, and Reactive Thiol Frameworks.
Authors: Hess, S.S. / Coppola, F. / Dang, V.T. / Tran, P.N. / Mickel, P.J. / Oktawiec, J. / Ren, Z. / Kral, P. / Nguyen, A.I.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V.
History
DepositionMay 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LEU-AIB-ALA-SER-LEU-ALA-CYS-AIB-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,9017
Polymers8601
Non-polymers1,0416
Water905
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)8.527, 16.603, 60.908
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein/peptide , 1 types, 1 molecules A

#1: Protein/peptide LEU-AIB-ALA-SER-LEU-ALA-CYS-AIB-LEU


Mass: 860.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 11 molecules

#2: Chemical ChemComp-NIO / NICOTINIC ACID / Niacin


Mass: 123.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO2
#3: Chemical ChemComp-I77 / 5'-(hydrazinecarbonyl)[2,2'-bipyridine]-5-carboxamide


Mass: 257.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H11N5O2
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Hg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.51 Å3/Da / Density % sol: 50.93 %
Crystal growTemperature: 298 K / Method: slow cooling / Details: Water/Acetonitrile

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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: May 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.2→12.85 Å / Num. obs: 3040 / % possible obs: 99.77 % / Redundancy: 11.4 % / Biso Wilson estimate: 6.65 Å2 / Rmerge(I) obs: 0.1379 / Net I/σ(I): 58.17
Reflection shellResolution: 1.2→1.243 Å / Rmerge(I) obs: 0.2268 / Num. unique obs: 290

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→12.85 Å / SU ML: 0.115 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 18.5477
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1945 305 10.03 %
Rwork0.1843 2735 -
obs0.1855 3040 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 9.73 Å2
Refinement stepCycle: LAST / Resolution: 1.2→12.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms58 0 34 5 97
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008396
X-RAY DIFFRACTIONf_angle_d1.9128128
X-RAY DIFFRACTIONf_chiral_restr0.067610
X-RAY DIFFRACTIONf_plane_restr0.010915
X-RAY DIFFRACTIONf_dihedral_angle_d23.375123
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.510.23831470.21511315X-RAY DIFFRACTION99.86
1.51-12.850.17931580.1721420X-RAY DIFFRACTION100

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