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- PDB-8v61: UIC-1 mutant - UIC-1-L6I -

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Basic information

Entry
Database: PDB / ID: 8v61
TitleUIC-1 mutant - UIC-1-L6I
ComponentsUIC-1-L6I
KeywordsDE NOVO PROTEIN / synthetic construct
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.13 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-L6I
B: UIC-1-L6I
C: UIC-1-L6I
D: UIC-1-L6I


Theoretical massNumber of molelcules
Total (without water)5,4984
Polymers5,4984
Non-polymers00
Water41423
1
A: UIC-1-L6I


Theoretical massNumber of molelcules
Total (without water)1,3751
Polymers1,3751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UIC-1-L6I


Theoretical massNumber of molelcules
Total (without water)1,3751
Polymers1,3751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: UIC-1-L6I


Theoretical massNumber of molelcules
Total (without water)1,3751
Polymers1,3751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: UIC-1-L6I


Theoretical massNumber of molelcules
Total (without water)1,3751
Polymers1,3751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)10.311, 28.251, 32.535
Angle α, β, γ (deg.)111.070, 90.260, 90.280
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein/peptide
UIC-1-L6I


Mass: 1374.589 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 1.61 Å3/Da / Density % sol: 23.52 %
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: Jun 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.13→15.85 Å / Num. obs: 12284 / % possible obs: 95.2 % / Redundancy: 4.9 % / Biso Wilson estimate: 16.46 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.05303 / Rrim(I) all: 0.05775 / Net I/σ(I): 16.88
Reflection shellResolution: 1.13→1.17 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.8414 / Mean I/σ(I) obs: 1.28 / Num. unique obs: 1104 / CC1/2: 0.817 / CC star: 0.948 / Rrim(I) all: 0.9777 / % possible all: 86.61

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.13→15.85 Å / SU ML: 0.1721 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 37.3486
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: The reported R-work (0.1837) differs from the calculated R-work (0.2011), possibly due to the deposition of detwinned structure factors
RfactorNum. reflection% reflection
Rfree0.2079 1209 9.91 %
Rwork0.1837 10985 -
obs0.1862 12284 95.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.02 Å2
Refinement stepCycle: LAST / Resolution: 1.13→15.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms324 0 76 24 424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0103423
X-RAY DIFFRACTIONf_angle_d1.8138597
X-RAY DIFFRACTIONf_chiral_restr0.065635
X-RAY DIFFRACTIONf_plane_restr0.006269
X-RAY DIFFRACTIONf_dihedral_angle_d37.244480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.13-1.180.4831230.40541087X-RAY DIFFRACTION86.93
1.18-1.230.37541300.35031153X-RAY DIFFRACTION90.99
1.23-1.290.36111410.3291226X-RAY DIFFRACTION92.55
1.29-1.370.33441300.29111167X-RAY DIFFRACTION93.99
1.37-1.480.27221230.23351291X-RAY DIFFRACTION96.72
1.48-1.630.26721410.19121228X-RAY DIFFRACTION98.56
1.63-1.860.25431280.18571276X-RAY DIFFRACTION98.66
1.87-2.350.19151410.17941296X-RAY DIFFRACTION99.24
2.35-15.840.16661520.14871261X-RAY DIFFRACTION99.23

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