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- PDB-8v56: UIC-1 mutant - UIC-1-B5W -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8v56
TitleUIC-1 mutant - UIC-1-B5W
ComponentsUIC-1-B5W
KeywordsDE NOVO PROTEIN / synthetic construct
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.98 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
DepositionNov 30, 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-B5W
B: UIC-1-B5W


Theoretical massNumber of molelcules
Total (without water)2,9512
Polymers2,9512
Non-polymers00
Water39622
1
A: UIC-1-B5W


Theoretical massNumber of molelcules
Total (without water)1,4761
Polymers1,4761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UIC-1-B5W


Theoretical massNumber of molelcules
Total (without water)1,4761
Polymers1,4761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)16.543, 20.422, 56.557
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein/peptide UIC-1-B5W


Mass: 1475.694 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.: 22 / 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: 1.62 Å3/Da / Density % sol: 24 %
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: 0.6199 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6199 Å / Relative weight: 1
ReflectionResolution: 0.98→16.56 Å / Num. obs: 11436 / % possible obs: 98.55 % / Redundancy: 11.4 % / Biso Wilson estimate: 6.84 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.08324 / Rpim(I) all: 0.02509 / Rrim(I) all: 0.08711 / Net I/σ(I): 17.5
Reflection shellResolution: 0.98→1.015 Å / Rmerge(I) obs: 0.8628 / Mean I/σ(I) obs: 1.43 / Num. unique obs: 1015 / CC1/2: 0.598 / CC star: 0.865 / Rpim(I) all: 0.4011 / Rrim(I) all: 0.9559

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.98→16.56 Å / SU ML: 0.1372 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.8928
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1473 2111 10.07 %
Rwork0.1305 18860 -
obs0.1322 11436 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 10.81 Å2
Refinement stepCycle: LAST / Resolution: 0.98→16.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms178 0 38 22 238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01251
X-RAY DIFFRACTIONf_angle_d1.7368350
X-RAY DIFFRACTIONf_chiral_restr0.044420
X-RAY DIFFRACTIONf_plane_restr0.008539
X-RAY DIFFRACTIONf_dihedral_angle_d38.429142
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.98-10.43771270.42041159X-RAY DIFFRACTION91.92
1-1.030.36051300.34581193X-RAY DIFFRACTION92.26
1.03-1.060.26671420.24861254X-RAY DIFFRACTION98.17
1.06-1.090.21121380.1921259X-RAY DIFFRACTION99.79
1.09-1.120.15381400.14181256X-RAY DIFFRACTION99.93
1.12-1.160.1411460.12861267X-RAY DIFFRACTION99.79
1.16-1.210.15981430.13081286X-RAY DIFFRACTION100
1.21-1.260.15191430.12461291X-RAY DIFFRACTION100
1.26-1.330.1421380.10251247X-RAY DIFFRACTION100
1.33-1.410.12011470.11051266X-RAY DIFFRACTION100
1.41-1.520.13331470.11131298X-RAY DIFFRACTION100
1.52-1.680.12021470.11781271X-RAY DIFFRACTION100
1.68-1.920.11461440.10871249X-RAY DIFFRACTION99.71
1.92-2.410.13391370.1051292X-RAY DIFFRACTION99.86
2.42-16.560.13651420.12441272X-RAY DIFFRACTION99.37

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