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- PDB-9vyv: Crystal structure of UPF0235 protein PF1765 from Pyrococcus furio... -

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Basic information

Entry
Database: PDB / ID: 9vyv
TitleCrystal structure of UPF0235 protein PF1765 from Pyrococcus furiosus at pH 4
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: 1.19 Å
AuthorsYadav, B. / Gaikwad, S.S. / Shubhangi, S. / Kumar, A. / Chandravanshi, K. / Makde, R.D.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India) India
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2025
Title: Crystal structures of PF1765 from Pyrococcus furiosus from several different crystallization conditions with varied pH, salt and precipitant.
Authors: Gaikwad, S.S. / Yadav, B. / Sharma, S. / Kumar, A. / 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
DepositionJul 21, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 10, 2025Group: 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: UPF0235 protein PF1765
B: UPF0235 protein PF1765
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9504
Polymers27,9042
Non-polymers462
Water4,486249
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)44.453, 59.347, 79.505
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 17 or resid 19...
d_2ens_1(chain "B" and (resid -4 through 17 or resid 19...

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_11LEULEUPROPROAA-4 - 1732 - 53
d_12ALAALAGLYGLYAA19 - 2655 - 62
d_13ARGARGASNASNAA33 - 4869 - 84
d_14GLUGLUVALVALAA50 - 6686 - 102
d_15GLYGLYLEULEUAA68 - 77104 - 113
d_16LYSLYSLYSLYSAA79 - 84115 - 120
d_17VALVALVALVALAA86122
d_18GLUGLULEULEUAA88 - 92124 - 128
d_21LEULEUPROPROBB-4 - 1732 - 53
d_22ALAALAGLYGLYBB19 - 2655 - 62
d_23ARGARGASNASNBB33 - 4869 - 84
d_24GLUGLUVALVALBB50 - 6686 - 102
d_25GLYGLYLEULEUBB68 - 77104 - 113
d_26LYSLYSLYSLYSBB79 - 84115 - 120
d_27VALVALVALVALBB86122
d_28GLUGLULEULEUBB88 - 92124 - 128

NCS oper: (Code: givenMatrix: (-0.644431111809, -0.594720987216, -0.480640707283), (-0.698142234728, 0.201189287488, 0.687110100849), (-0.311939036067, 0.778350703709, -0.544852475274)Vector: 20. ...NCS oper: (Code: given
Matrix: (-0.644431111809, -0.594720987216, -0.480640707283), (-0.698142234728, 0.201189287488, 0.687110100849), (-0.311939036067, 0.778350703709, -0.544852475274)
Vector: 20.1258365596, -16.6284665864, 43.8869577071)

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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
Details: Contains 38 amino acid long Streptavidin Histidine Tev tag at the N-terminal of the protein PF1765 in the construct. Contains 2 polypeptides in the asymmetric unit but exists as a monomer in the solution.
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 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.88 Å3/Da / Density % sol: 34.55 %
Crystal growTemperature: 294 K / Method: batch mode / pH: 4 / Details: 0.1 M PCB buffer pH 4, 25% PEG 1500 / 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: Apr 1, 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: 1.19→44.45 Å / Num. obs: 64647 / % possible obs: 95.1 % / Redundancy: 12.4 % / Biso Wilson estimate: 11.482 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.014 / Rrim(I) all: 0.048 / Net I/σ(I): 36
Reflection shellResolution: 1.19→1.21 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 5.8 / Num. unique obs: 2126 / CC1/2: 0.971 / Rpim(I) all: 0.086 / Rrim(I) all: 0.212 / % possible all: 64.1

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.21.2_5419refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9UNT

9unt


Resolution: 1.19→32.48 Å / SU ML: 0.0938 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.3148
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2032 3187 4.94 %
Rwork0.1828 61380 -
obs0.1838 64567 95.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.68 Å2
Refinement stepCycle: LAST / Resolution: 1.19→32.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1506 0 2 249 1757
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151616
X-RAY DIFFRACTIONf_angle_d1.40272175
X-RAY DIFFRACTIONf_chiral_restr0.115260
X-RAY DIFFRACTIONf_plane_restr0.0188275
X-RAY DIFFRACTIONf_dihedral_angle_d17.2123651
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.56884116904 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.19-1.210.2432900.23871745X-RAY DIFFRACTION62.8
1.21-1.230.21021080.20552031X-RAY DIFFRACTION73.61
1.23-1.250.19671240.20162178X-RAY DIFFRACTION78.62
1.25-1.270.17961020.19532384X-RAY DIFFRACTION85.28
1.27-1.290.22441310.19962521X-RAY DIFFRACTION91.35
1.29-1.320.22211440.21122691X-RAY DIFFRACTION97.02
1.32-1.340.21151560.20052765X-RAY DIFFRACTION99.66
1.34-1.370.20081600.20422769X-RAY DIFFRACTION99.97
1.37-1.410.24481450.20432755X-RAY DIFFRACTION99.93
1.41-1.440.21881410.20162789X-RAY DIFFRACTION100
1.44-1.480.20511610.18712780X-RAY DIFFRACTION100
1.48-1.520.19441400.18062770X-RAY DIFFRACTION99.97
1.52-1.570.19741610.17712802X-RAY DIFFRACTION99.97
1.57-1.630.20941450.17492775X-RAY DIFFRACTION100
1.63-1.690.19141120.17842839X-RAY DIFFRACTION99.97
1.69-1.770.20361220.18422840X-RAY DIFFRACTION100
1.77-1.860.20331470.18282793X-RAY DIFFRACTION99.93
1.86-1.980.18591400.17882830X-RAY DIFFRACTION100
1.98-2.130.19711330.17362844X-RAY DIFFRACTION100
2.13-2.350.18851520.16922822X-RAY DIFFRACTION100
2.35-2.690.21331500.18432838X-RAY DIFFRACTION99.87
2.69-3.390.21161610.18842824X-RAY DIFFRACTION97.87
3.39-32.480.20011620.1762995X-RAY DIFFRACTION99.28
Refinement TLS params.Method: refined / Origin x: 7.70929467169 Å / Origin y: -6.61608255842 Å / Origin z: 23.0938475417 Å
111213212223313233
T0.0804189798359 Å2-0.00465320980665 Å20.0111944996178 Å2-0.0696255730022 Å2-0.000456742246012 Å2--0.0728416489262 Å2
L1.14445959006 °2-0.0924427926347 °20.72788641272 °2-0.60001880536 °2-0.0949753229838 °2--1.01896732127 °2
S-0.0152725529158 Å °0.0449141864821 Å °-0.0126901338186 Å °0.028050366584 Å °0.0170733594236 Å °-0.0161182191705 Å °-0.00252160058148 Å °0.0645565524062 Å °-0.00435950740765 Å °
Refinement TLS groupSelection details: all

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