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- PDB-8v5w: UIC-1 mutant UIC-1-B5T -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8v5w
TitleUIC-1 mutant UIC-1-B5T
ComponentsUIC-1-B5T
KeywordsDE NOVO PROTEIN / synthetic construct
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07 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-B5T
B: UIC-1-B5T


Theoretical massNumber of molelcules
Total (without water)2,7812
Polymers2,7812
Non-polymers00
Water19811
1
A: UIC-1-B5T


Theoretical massNumber of molelcules
Total (without water)1,3911
Polymers1,3911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UIC-1-B5T


Theoretical massNumber of molelcules
Total (without water)1,3911
Polymers1,3911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.956, 10.164, 32.761
Angle α, β, γ (deg.)90.000, 99.180, 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

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Components

#1: Protein/peptide UIC-1-B5T


Mass: 1390.588 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 1.59 Å3/Da / Density % sol: 22.85 %
Crystal growTemperature: 298 K / Method: slow cooling / Details: methanol

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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: Oct 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.61992 Å / Relative weight: 1
ReflectionResolution: 1.07→22.39 Å / Num. obs: 7816 / % possible obs: 95.36 % / Redundancy: 5.9 % / Biso Wilson estimate: 48.84 Å2 / CC1/2: 0.925 / CC star: 0.98 / Rpim(I) all: 0.1263 / Rrim(I) all: 0.3103 / Net I/σ(I): 5.23
Reflection shellResolution: 1.07→1.108 Å / Rmerge(I) obs: 0.3845 / Mean I/σ(I) obs: 3.45 / Num. unique obs: 7816 / CC1/2: 0.812 / Rpim(I) all: 0.2094 / Rrim(I) all: 0.44

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.07→22.39 Å / SU ML: 0.0766 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.5955
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1783 1425 9.98 %
Rwork0.1586 12851 -
obs0.1605 7816 94.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 7.68 Å2
Refinement stepCycle: LAST / Resolution: 1.07→22.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms164 0 38 11 213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092222
X-RAY DIFFRACTIONf_angle_d1.7552310
X-RAY DIFFRACTIONf_chiral_restr0.046223
X-RAY DIFFRACTIONf_plane_restr0.011236
X-RAY DIFFRACTIONf_dihedral_angle_d39.406539
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.07-1.110.2121170.19351026X-RAY DIFFRACTION75.25
1.11-1.150.19931370.18131231X-RAY DIFFRACTION89.59
1.15-1.210.1921490.16261317X-RAY DIFFRACTION98.26
1.21-1.270.16741500.15651396X-RAY DIFFRACTION98.53
1.27-1.350.17751440.14941296X-RAY DIFFRACTION97.63
1.35-1.450.17621470.16531335X-RAY DIFFRACTION95.55
1.45-1.60.14621421238X-RAY DIFFRACTION93.69
1.6-1.830.15541491347X-RAY DIFFRACTION97.65
1.83-2.30.18521500.15291346X-RAY DIFFRACTION98.62
2.31-22.390.18731400.15361319X-RAY DIFFRACTION96.43

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