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- PDB-9kza: Crystal structure of TapT-Sinefungin complex from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 9kza
TitleCrystal structure of TapT-Sinefungin complex from Escherichia coli
ComponentstRNA-uridine aminocarboxypropyltransferase
KeywordsTRANSFERASE / tRNA-uridine aminocarboxypropyltransferase
Function / homologySINEFUNGIN / :
Function and homology information
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsWang, W. / Sun, A.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32000846, 32201209 and 22137009 China
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Molecular basis of tRNA aminocarboxypropyl-transferase TapT for substrate recognition.
Authors: Wang, W.Y. / Liang, H.R. / Wu, Y.C. / Liu, P.W. / Wang, Z. / Jiang, Y.Y. / Pan, H.X. / Tang, G.L. / Pu, J.Y. / Sun, A.A.
History
DepositionDec 10, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA-uridine aminocarboxypropyltransferase
B: tRNA-uridine aminocarboxypropyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9777
Polymers42,9882
Non-polymers9905
Water2,252125
1
B: tRNA-uridine aminocarboxypropyltransferase
hetero molecules

A: tRNA-uridine aminocarboxypropyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9777
Polymers42,9882
Non-polymers9905
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area920 Å2
ΔGint-23 kcal/mol
Surface area17430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.660, 41.980, 74.640
Angle α, β, γ (deg.)90.00, 97.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein tRNA-uridine aminocarboxypropyltransferase


Mass: 21493.799 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Gene: ECBD_1097 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A140N7F9, EC: 2.5.1.25
#2: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N7O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.12 Å3/Da / Density % sol: 41.98 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Magnesium acetate tetrahydrate, 0.1 M Ammonium sulfate, 0.1 M Sodium citrate pH 6.5, 29% w/v PEG 4000

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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 PILATUS3 6M / Detector: PIXEL / Date: Dec 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.94→23.91 Å / Num. obs: 26871 / % possible obs: 99.4 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.1
Reflection shellResolution: 1.94→1.99 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.153 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1954 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIXV1.21.2-5419refinement
PDB_EXTRACTdata extraction
xia2data scaling
PHENIXV1.21.2-5419phasing
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→23.91 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2558 1301 4.85 %
Rwork0.2169 --
obs0.2187 26847 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.94→23.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2827 0 7 125 2959
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072903
X-RAY DIFFRACTIONf_angle_d0.8613963
X-RAY DIFFRACTIONf_dihedral_angle_d14.1591069
X-RAY DIFFRACTIONf_chiral_restr0.053461
X-RAY DIFFRACTIONf_plane_restr0.008499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-2.020.33311360.29792810X-RAY DIFFRACTION99
2.02-2.110.32251370.27642791X-RAY DIFFRACTION99
2.11-2.220.28081570.24132788X-RAY DIFFRACTION99
2.22-2.360.27771390.23062808X-RAY DIFFRACTION99
2.36-2.540.26611490.22952831X-RAY DIFFRACTION100
2.54-2.80.28121470.24022850X-RAY DIFFRACTION99
2.8-3.20.28861440.23622842X-RAY DIFFRACTION100
3.2-4.030.25171470.20272878X-RAY DIFFRACTION100
4.03-23.910.21281450.1892948X-RAY DIFFRACTION100

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