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- PDB-9unt: Crystal structure of UPF0235 protein PF1765 from Pyrococcus furiosus -

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Basic information

Entry
Database: PDB / ID: 9unt
TitleCrystal structure of UPF0235 protein PF1765 from Pyrococcus furiosus
ComponentsUPF0235 protein PF1765
KeywordsUNKNOWN FUNCTION / PF02594 / evolutionary conserved
Function / homologyProtein of unknown function DUF167 / YggU-like superfamily / Uncharacterised ACR, YggU family COG1872 / DUF167 / cytoplasm / UPF0235 protein PF1765
Function and homology information
Biological speciesPyrococcus furiosus DSM 3638 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsYadav, B. / Gaikwad, S.S. / Kumar, A. / Chandravanshi, K. / Makde, R.D.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India) India
Citation
Journal: Biochem.Biophys.Res.Commun. / Year: 2025
Title: Crystal structure and nucleic acid binding activity of the conserved UPF0235 family protein PF1765 from Pyrococcus furiosus.
Authors: Yadav, B. / Gaikwad, S.S. / Kumar, A. / Gupta, G.D. / Kumar, A. / Makde, R.D.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionApr 24, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2025Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UPF0235 protein PF1765
B: UPF0235 protein PF1765
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9504
Polymers27,9042
Non-polymers462
Water4,378243
1
A: UPF0235 protein PF1765
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9752
Polymers13,9521
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UPF0235 protein PF1765
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9752
Polymers13,9521
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.479, 59.358, 79.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid -4 through -2 or resid 0...
d_2ens_1(chain "B" and (resid -4 through -2 or resid 0...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11LEULEUPHEPHEAA-4 - -232 - 34
d_12GLYGLYILEILEAA0 - 1436 - 50
d_13ALAALAILEILEAA16 - 2452 - 60
d_14GLYGLYPROPROAA26 - 4262 - 78
d_15LYSLYSGLYGLYAA44 - 4580 - 81
d_16ALAALAASNASNAA47 - 4883 - 84
d_17GLUGLUVALVALAA50 - 6686 - 102
d_18GLYGLYTHRTHRAA68 - 70104 - 106
d_19ARGARGLEULEUAA72 - 77108 - 113
d_110LYSLYSGLYGLYAA79 - 80115 - 116
d_111THRTHRLYSLYSAA82 - 84118 - 120
d_112VALVALVALVALAA86122
d_113GLUGLULEULEUAA88 - 92124 - 128
d_21LEULEUPHEPHEBB-4 - -232 - 34
d_22GLYGLYILEILEBB0 - 1436 - 50
d_23ALAALAILEILEBB16 - 2452 - 60
d_24GLYGLYPROPROBB26 - 4262 - 78
d_25LYSLYSGLYGLYBB44 - 4580 - 81
d_26ALAALAASNASNBB47 - 4883 - 84
d_27GLUGLUVALVALBB50 - 6686 - 102
d_28GLYGLYTHRTHRBB68 - 70104 - 106
d_29ARGARGLEULEUBB72 - 77108 - 113
d_210LYSLYSGLYGLYBB79 - 80115 - 116
d_211THRTHRLYSLYSBB82 - 84118 - 120
d_212VALVALVALVALBB86122
d_213GLUGLULEULEUBB88 - 92124 - 128

NCS oper: (Code: givenMatrix: (-0.641356771587, 0.60105623173, -0.476857313919), (0.687429501322, 0.174149254702, -0.70506220846), (-0.340737688335, -0.780002207295, -0.524875589415)Vector: -20. ...NCS oper: (Code: given
Matrix: (-0.641356771587, 0.60105623173, -0.476857313919), (0.687429501322, 0.174149254702, -0.70506220846), (-0.340737688335, -0.780002207295, -0.524875589415)
Vector: -20.2471440304, -16.974248245, -43.4787775485)

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Components

#1: Protein UPF0235 protein PF1765


Mass: 13952.041 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Strain: ATCC 43587 / DSM 3638 / Gene: PF1765 / Plasmid: pST50Trc2STRHISN / Details (production host): Tan Lab USA / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q8U052
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 1.89 Å3/Da / Density % sol: 34.78 %
Crystal growTemperature: 294 K / Method: batch mode / pH: 6.5
Details: 0.2 M sodium sulfate, 0.1 M Bis-Tris-propane, pH6.5, 20% PEG3350
Temp details: constant

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: constant / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97893 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 15, 2025 / Details: Mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97893 Å / Relative weight: 1
ReflectionResolution: 1.3→47.61 Å / Num. obs: 52465 / % possible obs: 99.6 % / Redundancy: 6.5 % / Biso Wilson estimate: 17.96 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.025 / Net I/σ(I): 15.1
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2434 / CC1/2: 0.672 / Rpim(I) all: 0.353 / Rrim(I) all: 0.669 / % possible all: 94.5

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXmodel building
PHENIX1.21.2_5419refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AF-Q8U052-F1

Resolution: 1.3→39.87 Å / SU ML: 0.178 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.3456
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.195 2605 4.97 %
Rwork0.1808 49799 -
obs0.1816 52404 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24 Å2
Refinement stepCycle: LAST / Resolution: 1.3→39.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1506 0 2 243 1751
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01511610
X-RAY DIFFRACTIONf_angle_d1.43352176
X-RAY DIFFRACTIONf_chiral_restr0.1119263
X-RAY DIFFRACTIONf_plane_restr0.0183274
X-RAY DIFFRACTIONf_dihedral_angle_d15.5809658
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.927116457158 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.320.37961510.31892424X-RAY DIFFRACTION93.77
1.32-1.350.34051340.31892536X-RAY DIFFRACTION97.2
1.35-1.380.2931490.26652570X-RAY DIFFRACTION99.78
1.38-1.410.28321300.25012583X-RAY DIFFRACTION99.96
1.41-1.440.25131360.21172611X-RAY DIFFRACTION100
1.44-1.480.19441560.19832580X-RAY DIFFRACTION100
1.48-1.520.22051290.18992604X-RAY DIFFRACTION99.96
1.52-1.560.22421360.19352598X-RAY DIFFRACTION100
1.56-1.610.23071490.19212617X-RAY DIFFRACTION100
1.61-1.670.2341150.20322635X-RAY DIFFRACTION99.96
1.67-1.730.23791040.21142645X-RAY DIFFRACTION100
1.73-1.810.22511450.20812611X-RAY DIFFRACTION99.93
1.81-1.910.18041240.1842653X-RAY DIFFRACTION99.96
1.91-2.030.20681310.18352648X-RAY DIFFRACTION100
2.03-2.190.19051290.18012639X-RAY DIFFRACTION100
2.19-2.40.20781440.17482653X-RAY DIFFRACTION100
2.41-2.750.19181410.17852677X-RAY DIFFRACTION100
2.75-3.470.18331550.17052689X-RAY DIFFRACTION99.96
3.47-39.870.15661470.15552826X-RAY DIFFRACTION99.73
Refinement TLS params.Method: refined / Origin x: -7.88253559677 Å / Origin y: -6.30766820791 Å / Origin z: -23.2238654538 Å
111213212223313233
T0.124296462428 Å20.00680651252549 Å20.0180588361931 Å2-0.0843984152925 Å20.00356355539536 Å2--0.108319110947 Å2
L1.43959493633 °2-0.0703021723748 °20.923871338506 °2-0.929346749616 °20.0348037892393 °2--1.43808399066 °2
S-0.0187643325808 Å °-0.0603409908604 Å °-0.0115076537483 Å °-0.0435851332527 Å °0.0322732974201 Å °0.0212442616105 Å °0.00402060290706 Å °-0.0674140403247 Å °-0.0169192173275 Å °
Refinement TLS groupSelection details: all

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