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- PDB-8v59: UIC-1 mutant - UIC-1-B5I -

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Basic information

Entry
Database: PDB / ID: 8v59
TitleUIC-1 mutant - UIC-1-B5I
ComponentsUIC-1-B5I
KeywordsDE NOVO PROTEIN / synthetic construct
Function / homologyMETHANOL
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
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-B5I
B: UIC-1-B5I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,8373
Polymers2,8052
Non-polymers321
Water1267
1
A: UIC-1-B5I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,4352
Polymers1,4031
Non-polymers321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UIC-1-B5I


Theoretical massNumber of molelcules
Total (without water)1,4031
Polymers1,4031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.012, 10.316, 32.278
Angle α, β, γ (deg.)90.000, 100.500, 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-B5I


Mass: 1402.642 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4O
#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: 1.58 Å3/Da / Density % sol: 21.95 %
Crystal growTemperature: 298 K / Method: slow cooling / Details: water, 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: 1.12→15.87 Å / Num. obs: 6964 / % possible obs: 97.43 % / Redundancy: 5.8 % / Biso Wilson estimate: 7.41 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.1683 / Rpim(I) all: 0.08011 / Rrim(I) all: 0.1873 / Net I/σ(I): 13.15
Reflection shellResolution: 1.12→1.16 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.3439 / Mean I/σ(I) obs: 6.03 / Num. unique obs: 635 / CC1/2: 0.969 / CC star: 0.992 / Rpim(I) all: 0.1615 / Rrim(I) all: 0.3814 / % possible all: 91.21

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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→15.87 Å / SU ML: 0.0976 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 17.3095
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1535 1264 9.89 %
Rwork0.1311 11514 -
obs0.1333 6964 96.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 9.5 Å2
Refinement stepCycle: LAST / Resolution: 1.12→15.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms166 0 40 7 213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0101254
X-RAY DIFFRACTIONf_angle_d1.7084352
X-RAY DIFFRACTIONf_chiral_restr0.04926
X-RAY DIFFRACTIONf_plane_restr0.010141
X-RAY DIFFRACTIONf_dihedral_angle_d38.944344
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.12-1.160.18911390.14731218X-RAY DIFFRACTION90.89
1.16-1.220.22241380.1311260X-RAY DIFFRACTION99.22
1.22-1.280.15851470.131363X-RAY DIFFRACTION98.69
1.28-1.360.16461440.12891259X-RAY DIFFRACTION98.94
1.36-1.470.17221440.12861333X-RAY DIFFRACTION98.6
1.47-1.610.12721400.14261216X-RAY DIFFRACTION94.43
1.62-1.850.12821450.13051290X-RAY DIFFRACTION98.83
1.85-2.330.13111370.1251306X-RAY DIFFRACTION97.9
2.33-15.870.16331300.13051269X-RAY DIFFRACTION95.17

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