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- PDB-8v5z: UIC-1 mutant - UIC-1-L6M -

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Basic information

Entry
Database: PDB / ID: 8v5z
TitleUIC-1 mutant - UIC-1-L6M
ComponentsUIC-1-L6M
KeywordsDE NOVO PROTEIN / synthetic construct
Function / homologyACETONITRILE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.84 Å
AuthorsHeinz-Kunert, S.L.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: Biomacromolecules / Year: 2024
Title: Pore Restructuring of Peptide Frameworks by Mutations at Distal Packing Residues.
Authors: Heinz-Kunert, S.L. / Pandya, A. / Dang, V.T. / Oktawiec, J. / Nguyen, A.I.
History
DepositionDec 1, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UIC-1-L6M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,4342
Polymers1,3931
Non-polymers411
Water1267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)8.554, 16.942, 57.368
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

#1: Protein/peptide UIC-1-L6M


Mass: 1392.627 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-CCN / ACETONITRILE


Mass: 41.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3N / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.49 Å3/Da / Density % sol: 17.59 %
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: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.6888 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6888 Å / Relative weight: 1
ReflectionResolution: 0.84→16.25 Å / Num. obs: 6645 / % possible obs: 80.28 % / Redundancy: 5.8 % / Biso Wilson estimate: 4.36 Å2 / CC1/2: 0.985 / CC star: 0.996 / Rmerge(I) obs: 0.1341 / Rrim(I) all: 0.1469 / Net I/σ(I): 8.72
Reflection shellResolution: 0.84→0.87 Å / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.83 / Num. unique obs: 614 / CC1/2: 0.841 / CC star: 0.956 / Rrim(I) all: 0.4893

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.84→16.25 Å / SU ML: 0.0911 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 16.7473
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1391 1132 9.98 %
Rwork0.118 10216 -
obs0.1201 6645 77.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 6.58 Å2
Refinement stepCycle: LAST / Resolution: 0.84→16.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms81 0 22 7 110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0102105
X-RAY DIFFRACTIONf_angle_d1.9217143
X-RAY DIFFRACTIONf_chiral_restr0.03917
X-RAY DIFFRACTIONf_plane_restr0.008616
X-RAY DIFFRACTIONf_dihedral_angle_d35.703319
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.84-0.880.22871280.1941238X-RAY DIFFRACTION74.81
0.88-0.920.20611190.16671046X-RAY DIFFRACTION63.63
0.92-0.980.15541390.14581241X-RAY DIFFRACTION75.41
0.98-1.060.1561510.12121368X-RAY DIFFRACTION80.33
1.06-1.160.1131440.1021317X-RAY DIFFRACTION82.03
1.16-1.330.14161400.10881311X-RAY DIFFRACTION78.26
1.33-1.680.13891500.11521340X-RAY DIFFRACTION80.72
1.68-16.250.12171610.1061355X-RAY DIFFRACTION83.21

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