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- PDB-8v5x: UIC-1 mutant - UIC-1-L6A -

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Basic information

Entry
Database: PDB / ID: 8v5x
TitleUIC-1 mutant - UIC-1-L6A
ComponentsUIC-1-L6A
KeywordsDE NOVO PROTEIN / synthetic construct
Function / homologyACETONITRILE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 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-L6A
B: UIC-1-L6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,7474
Polymers2,6652
Non-polymers822
Water1086
1
A: UIC-1-L6A
hetero molecules


  • defined by author
  • 1.37 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,3742
Polymers1,3331
Non-polymers411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UIC-1-L6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,3742
Polymers1,3331
Non-polymers411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.801, 16.792, 20.200
Angle α, β, γ (deg.)90.000, 103.990, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-202-

HOH

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Components

#1: Protein/peptide UIC-1-L6A


Mass: 1332.509 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-CCN / ACETONITRILE


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


Mass: 18.015 Da / Num. of mol.: 6 / 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: 1.57 Å3/Da / Density % sol: 21.58 %
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: 0.61992 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.61992 Å / Relative weight: 1
ReflectionResolution: 1.12→17.55 Å / Num. obs: 6420 / % possible obs: 98.09 % / Redundancy: 6.3 % / Biso Wilson estimate: 9.06 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.1191 / Rrim(I) all: 0.1304 / Net I/σ(I): 8.69
Reflection shellResolution: 1.12→1.16 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.7525 / Mean I/σ(I) obs: 2.55 / Num. unique obs: 593 / CC1/2: 0.734 / Rrim(I) all: 0.8301 / % possible all: 94.59

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.12→17.55 Å / SU ML: 0.1591 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 29.9154
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.217 1192 9.98 %
Rwork0.1668 10752 -
obs0.1718 6420 95.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 10.67 Å2
Refinement stepCycle: LAST / Resolution: 1.12→17.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms156 0 44 6 206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0102254
X-RAY DIFFRACTIONf_angle_d1.8136349
X-RAY DIFFRACTIONf_chiral_restr0.07315
X-RAY DIFFRACTIONf_plane_restr0.009843
X-RAY DIFFRACTIONf_dihedral_angle_d40.617746
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.12-1.160.35581200.29121109X-RAY DIFFRACTION91.1
1.16-1.220.2831340.26371198X-RAY DIFFRACTION95.9
1.22-1.280.29261400.2461230X-RAY DIFFRACTION97.51
1.28-1.360.29071340.22941191X-RAY DIFFRACTION97.43
1.36-1.470.24711330.19461212X-RAY DIFFRACTION96.48
1.47-1.620.24531230.19531171X-RAY DIFFRACTION93.23
1.62-1.850.22581390.15111220X-RAY DIFFRACTION98.12
1.85-2.330.16991360.13431218X-RAY DIFFRACTION98.54
2.33-17.550.1781330.1271203X-RAY DIFFRACTION95.7

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