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- PDB-9kop: Crystal structure of the Trove domain -

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Basic information

Entry
Database: PDB / ID: 9kop
TitleCrystal structure of the Trove domain
ComponentsTROVE domain-containing protein
KeywordsRNA BINDING PROTEIN / trove / ro60 / phage
Function / homologyTROVE domain / TROVE domain superfamily / RNA-binding protein RO60 / TROVE domain profile. / von Willebrand factor A-like domain superfamily / ribonucleoprotein complex / RNA binding / metal ion binding / TROVE domain-containing protein
Function and homology information
Biological speciesThermus phage phiLo (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsHu, Z. / Huang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171186 China
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Structural and molecular mechanisms of an Ro60 homolog from a Thermus bacteriophage.
Authors: Hu, Z. / Jin, Z. / Guo, L. / Zeng, L. / Dong, X. / Jiang, L. / Dai, W. / Ma, J. / Huang, Y.
History
DepositionNov 21, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TROVE domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2102
Polymers57,1701
Non-polymers401
Water5,423301
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.877, 60.124, 65.590
Angle α, β, γ (deg.)90.000, 100.610, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein TROVE domain-containing protein


Mass: 57169.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus phage phiLo (virus) / Gene: phiLo_26 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3S7URH6
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.17 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 25% PEG 4000, 0.1 M MES,pH 6.0, 6% Tacsimate,pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 18, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.99→64.47 Å / Num. obs: 33397 / % possible obs: 99.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 25.72 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 14
Reflection shellResolution: 1.99→2.1 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4818

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIX1.20.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→49.79 Å / SU ML: 0.1952 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.7762
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1999 1993 5.97 %
Rwork0.1737 31369 -
obs0.1753 33362 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.04 Å2
Refinement stepCycle: LAST / Resolution: 1.99→49.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3696 0 1 301 3998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00923777
X-RAY DIFFRACTIONf_angle_d1.07915117
X-RAY DIFFRACTIONf_chiral_restr0.0605569
X-RAY DIFFRACTIONf_plane_restr0.011650
X-RAY DIFFRACTIONf_dihedral_angle_d5.389513
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.040.24341410.21752210X-RAY DIFFRACTION99.92
2.04-2.10.251450.20332207X-RAY DIFFRACTION99.87
2.1-2.160.26251440.19422230X-RAY DIFFRACTION99.96
2.16-2.230.19641380.18132271X-RAY DIFFRACTION99.79
2.23-2.310.23531440.17532220X-RAY DIFFRACTION99.96
2.31-2.40.22261410.18032233X-RAY DIFFRACTION99.87
2.4-2.510.24071420.1752247X-RAY DIFFRACTION99.92
2.51-2.650.2511440.17812229X-RAY DIFFRACTION99.96
2.65-2.810.21021450.17522222X-RAY DIFFRACTION99.87
2.81-3.030.20231410.17872264X-RAY DIFFRACTION99.92
3.03-3.330.18381410.17382236X-RAY DIFFRACTION99.71
3.33-3.820.1841420.162249X-RAY DIFFRACTION99.17
3.82-4.810.15931410.14872240X-RAY DIFFRACTION99.04
4.81-49.790.17871440.18362311X-RAY DIFFRACTION98.87
Refinement TLS params.Method: refined / Origin x: -3.01934840221 Å / Origin y: 11.4987476931 Å / Origin z: 17.3277668202 Å
111213212223313233
T0.0688851742219 Å2-0.0139142901505 Å2-0.00482253349103 Å2-0.0808478659619 Å20.00992028107034 Å2--0.0658976964623 Å2
L-0.0375771274747 °2-0.0935541841705 °2-0.0612287036822 °2-0.509868015075 °2-0.00598751483485 °2--0.150189116279 °2
S0.0163391972728 Å °0.00896612157062 Å °-0.00476126519729 Å °-0.0713080059232 Å °-0.024766978319 Å °-0.00529269620598 Å °-0.00173005817181 Å °-0.014495394722 Å °1.08448286472E-10 Å °
Refinement TLS groupSelection details: all

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