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- PDB-9d5x: Structure of G2L4 RT Apoenzyme -

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Basic information

Entry
Database: PDB / ID: 9d5x
TitleStructure of G2L4 RT Apoenzyme
ComponentsGroup II intron-like 4 reverse transcriptase
KeywordsDNA BINDING PROTEIN / Group II intron reverse transcriptase / Microhomology Mediated End Joining / DNA repair
Function / homologyUREA
Function and homology information
Biological speciesGammaproteobacteria (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.61 Å
AuthorsGuo, M. / Stamos, J.L. / Zhang, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35148356 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Structural basis for the evolution of a domesticated group II intron-like reverse transcriptase to function in host cell DNA repair.
Authors: Park, S.K. / Guo, M. / Stamos, J.L. / Kim, W. / Lee, S. / Zhang, Y.J. / Lambowitz, A.M.
History
DepositionAug 14, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Group II intron-like 4 reverse transcriptase
B: Group II intron-like 4 reverse transcriptase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,1684
Polymers92,0482
Non-polymers1202
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-20 kcal/mol
Surface area33580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.836, 73.227, 82.861
Angle α, β, γ (deg.)90.00, 103.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Group II intron-like 4 reverse transcriptase


Mass: 46024.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: G2L4 RT has no Uniprot entry, only genbank entry as following: ACCESSION WP_071557413 VERSION WP_071557413.1
Source: (gene. exp.) Gammaproteobacteria (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Chemical ChemComp-URE / UREA


Mass: 60.055 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH4N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.53 Å3/Da / Density % sol: 51.45 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M Bis-Tris, 0.2M Ammonium acetate, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.61→48.75 Å / Num. obs: 27113 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.023 / Rrim(I) all: 0.06 / Χ2: 0.99 / Net I/σ(I): 20.8 / Num. measured all: 183499
Reflection shellResolution: 2.61→2.72 Å / % possible obs: 99.4 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.67 / Num. measured all: 21310 / Num. unique obs: 3290 / CC1/2: 0.88 / Rpim(I) all: 0.282 / Rrim(I) all: 0.728 / Χ2: 0.93 / Net I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
AutoSolphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.61→48.75 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.243 1365 5.05 %
Rwork0.2171 --
obs0.2184 27051 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.61→48.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6184 0 8 44 6236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026285
X-RAY DIFFRACTIONf_angle_d0.438465
X-RAY DIFFRACTIONf_dihedral_angle_d12.1892382
X-RAY DIFFRACTIONf_chiral_restr0.037961
X-RAY DIFFRACTIONf_plane_restr0.0031096
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.61-2.70.43831230.3912554X-RAY DIFFRACTION100
2.7-2.810.39711130.32762573X-RAY DIFFRACTION100
2.81-2.930.35421430.28582550X-RAY DIFFRACTION100
2.93-3.090.30391250.28112562X-RAY DIFFRACTION100
3.09-3.280.30031500.282557X-RAY DIFFRACTION100
3.28-3.540.31841310.25992557X-RAY DIFFRACTION100
3.54-3.890.25291350.22772540X-RAY DIFFRACTION99
3.89-4.460.23731380.2012584X-RAY DIFFRACTION100
4.46-5.610.19331540.17762576X-RAY DIFFRACTION100
5.61-48.750.18091530.16062633X-RAY DIFFRACTION100

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