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- PDB-9kyt: Crystal structure of TapT-SAM complex from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 9kyt
TitleCrystal structure of TapT-SAM complex from Escherichia coli
ComponentstRNA-uridine aminocarboxypropyltransferase
KeywordsTRANSFERASE / tRNA-uridine aminocarboxypropyltransferase
Function / homologyS-ADENOSYLMETHIONINE / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 9, 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)44,0117
Polymers42,9882
Non-polymers1,0245
Water1,69394
1
A: tRNA-uridine aminocarboxypropyltransferase
hetero molecules

B: tRNA-uridine aminocarboxypropyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0117
Polymers42,9882
Non-polymers1,0245
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_656x+1,y,z+11
Buried area860 Å2
ΔGint-24 kcal/mol
Surface area18110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.848, 42.251, 75.492
Angle α, β, γ (deg.)90.00, 97.18, 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 (strain B / BL21-DE3) (bacteria)
Gene: ECBD_1097 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A140N7F9, EC: 2.5.1.25
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S / 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.: 94 / 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: 43.22 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium sulfate monohydrate, 0.1 M Tris hydrochloride pH 8.5, 30 % w/v polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97911 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.05→58.39 Å / Num. obs: 23123 / % possible obs: 97.9 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 7.3
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3436 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIXV1.21.2-5419refinement
PDB_EXTRACTdata extraction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→37.45 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2385 2026 4.85 %
Rwork0.1985 --
obs0.2005 23099 91.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→37.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2793 0 61 94 2948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072924
X-RAY DIFFRACTIONf_angle_d0.9223990
X-RAY DIFFRACTIONf_dihedral_angle_d16.2011065
X-RAY DIFFRACTIONf_chiral_restr0.05460
X-RAY DIFFRACTIONf_plane_restr0.008501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10.33261350.28253081X-RAY DIFFRACTION96
2.1-2.150.36981320.27912967X-RAY DIFFRACTION95
2.15-2.220.29911500.26342893X-RAY DIFFRACTION95
2.22-2.290.33611100.25772423X-RAY DIFFRACTION77
2.29-2.370.29821530.22862948X-RAY DIFFRACTION95
2.37-2.460.3091730.24222978X-RAY DIFFRACTION96
2.46-2.580.29071580.23662887X-RAY DIFFRACTION94
2.58-2.710.25161270.24022908X-RAY DIFFRACTION93
2.71-2.880.27781690.23422827X-RAY DIFFRACTION92
2.88-3.10.2451280.2232849X-RAY DIFFRACTION91
3.11-3.420.25781400.20852782X-RAY DIFFRACTION90
3.42-3.910.1841350.16462739X-RAY DIFFRACTION88
3.91-4.930.18591450.15072716X-RAY DIFFRACTION88
4.93-37.450.21451710.16952772X-RAY DIFFRACTION90
Refinement TLS params.Method: refined / Origin x: -7.669 Å / Origin y: 0.7869 Å / Origin z: 12.8098 Å
111213212223313233
T0.2708 Å20.0191 Å20.0345 Å2-0.2664 Å20.0062 Å2--0.2899 Å2
L1.2986 °20.2106 °21.868 °2-0.0938 °20.2748 °2--2.9471 °2
S0.0153 Å °0.1986 Å °-0.0188 Å °-0.0371 Å °0.0145 Å °-0.0305 Å °-0.0063 Å °0.3065 Å °-0.0351 Å °
Refinement TLS groupSelection details: all

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