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- PDB-9ke2: Crystal structure of SxRhaGT in complex with TDP -

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Basic information

Entry
Database: PDB / ID: 9ke2
TitleCrystal structure of SxRhaGT in complex with TDP
ComponentsRhamnosyltransferase
KeywordsTRANSFERASE / rhamosyltransferase
Function / homologyTHYMIDINE-5'-DIPHOSPHATE
Function and homology information
Biological speciesStreptomyces xanthophaeus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsTingting, Y. / Tingting, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22378230 China
CitationJournal: To Be Published
Title: Crystal structure of SxRhaGT in complex with TDP
Authors: Tingting, Y.
History
DepositionNov 4, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 27, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rhamnosyltransferase
B: Rhamnosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0944
Polymers77,2892
Non-polymers8042
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-37 kcal/mol
Surface area27810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.390, 91.980, 102.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Rhamnosyltransferase


Mass: 38644.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces xanthophaeus (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE


Mass: 402.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O11P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.28 Å3/Da / Density % sol: 46.15 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 2% v/v Polyethylene glycol 400, 0.1 M Imidazole pH7.0, 24% w/v PEG monomethyl ether 5,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.61→68.53 Å / Num. obs: 104690 / % possible obs: 99.8 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.182 / Rpim(I) all: 0.067 / Rrim(I) all: 0.195 / Net I/σ(I): 7.2
Reflection shellResolution: 1.61→1.62 Å / Rmerge(I) obs: 1.47 / Num. unique obs: 4559

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata scaling
HKL-3000data reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→39.29 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.193 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24547 4586 4.9 %RANDOM
Rwork0.21616 ---
obs0.21762 88527 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.714 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å2-0 Å20 Å2
2---0.01 Å2-0 Å2
3----1.41 Å2
Refinement stepCycle: 1 / Resolution: 1.61→39.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5413 0 50 303 5766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195606
X-RAY DIFFRACTIONr_bond_other_d0.0010.025371
X-RAY DIFFRACTIONr_angle_refined_deg1.5311.987680
X-RAY DIFFRACTIONr_angle_other_deg0.825312303
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3265751
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.71623.44218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.83615794
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0261544
X-RAY DIFFRACTIONr_chiral_restr0.0830.2916
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216475
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021185
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5962.4333001
X-RAY DIFFRACTIONr_mcbond_other1.5952.4323000
X-RAY DIFFRACTIONr_mcangle_it2.373.6473753
X-RAY DIFFRACTIONr_mcangle_other2.373.6483754
X-RAY DIFFRACTIONr_scbond_it2.1362.7082605
X-RAY DIFFRACTIONr_scbond_other2.1312.7092597
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2843.9433915
X-RAY DIFFRACTIONr_long_range_B_refined4.57330.8976247
X-RAY DIFFRACTIONr_long_range_B_other4.52430.6656139
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.61→1.649 Å
RfactorNum. reflection% reflection
Rfree0.359 347 -
Rwork0.327 6450 -
obs--99.91 %

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