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- PDB-8rh3: Nucleoside 2'deoxyribosyltransferase from Chroococcidiopsis therm... -

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Basic information

Entry
Database: PDB / ID: 8rh3
TitleNucleoside 2'deoxyribosyltransferase from Chroococcidiopsis thermalis PCC 7203 WT bound to Gemcitabine
ComponentsNucleoside 2-deoxyribosyltransferase
KeywordsTRANSFERASE / Ribosylated / holoprotein / Gemcitabine
Function / homologydeoxyribonucleoside monophosphate catabolic process / 5-hydroxymethyl-dUMP N-hydrolase activity / : / Nucleoside 2-deoxyribosyltransferase / Nucleoside 2-deoxyribosyltransferase / transferase activity / metal ion binding / : / Nucleoside 2-deoxyribosyltransferase
Function and homology information
Biological speciesChroococcidiopsis thermalis PCC 7203 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsTang, P. / Harding, C.J. / Czekster, C.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other privateIBioIC 2020-2-1 United Kingdom
CitationJournal: Acs Catalysis / Year: 2024
Title: Snapshots of the Reaction Coordinate of a Thermophilic 2'-Deoxyribonucleoside/ribonucleoside Transferase.
Authors: Tang, P. / Harding, C.J. / Dickson, A.L. / da Silva, R.G. / Harrison, D.J. / Czekster, C.M.
History
DepositionDec 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoside 2-deoxyribosyltransferase
B: Nucleoside 2-deoxyribosyltransferase
C: Nucleoside 2-deoxyribosyltransferase
D: Nucleoside 2-deoxyribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1268
Polymers71,5104
Non-polymers6164
Water6,449358
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, The corresponding mass of ~62kDa calculated from a calibration curve of Superdex 75 Increase 10/300 GL
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12640 Å2
ΔGint-89 kcal/mol
Surface area21870 Å2
Unit cell
Length a, b, c (Å)136.092, 136.092, 87.172
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein
Nucleoside 2-deoxyribosyltransferase


Mass: 17877.395 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chroococcidiopsis thermalis PCC 7203 (bacteria)
Strain: PCC 7203 / Gene: Chro_1188 / Production host: Escherichia coli B (bacteria) / References: UniProt: K9TVX3
#2: Chemical
ChemComp-A1H0F / (2~{R},3~{R})-4,4-bis(fluoranyl)-2-(hydroxymethyl)oxolan-3-ol


Mass: 154.112 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H8F2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.31 Å3/Da / Density % sol: 62.86 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30.629% v/v PEG 6000; 0.1 M Tris pH 8; 0.00030367 M Zinc chloride

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.93→70.09 Å / Num. obs: 69176 / % possible obs: 99.98 % / Redundancy: 39 % / CC1/2: 1 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.027 / Rrim(I) all: 0.166 / Net I/σ(I): 12.3
Reflection shellResolution: 1.93→1.96 Å / Mean I/σ(I) obs: 0.5 / Num. unique obs: 3388 / CC1/2: 0.353 / Rpim(I) all: 1.882 / Rrim(I) all: 11.618 / % possible all: 98.89

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
xia23.4.2data reduction
xia23.4.2data scaling
PHENIX1.19.2-4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→48.82 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2552 2946 4.92 %
Rwork0.2085 --
obs0.2108 59881 91.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.96→48.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4958 0 0 418 5376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115104
X-RAY DIFFRACTIONf_angle_d1.326941
X-RAY DIFFRACTIONf_dihedral_angle_d8.746680
X-RAY DIFFRACTIONf_chiral_restr0.061736
X-RAY DIFFRACTIONf_plane_restr0.009897
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-1.990.643410.643458X-RAY DIFFRACTION20
2-2.030.3934530.39341091X-RAY DIFFRACTION37
2.03-2.070.42291110.40062304X-RAY DIFFRACTION77
2.07-2.110.4041500.39232957X-RAY DIFFRACTION100
2.11-2.150.39211460.35942944X-RAY DIFFRACTION100
2.15-2.20.36651550.35192947X-RAY DIFFRACTION100
2.2-2.250.3691610.31452959X-RAY DIFFRACTION100
2.25-2.30.33841650.29172958X-RAY DIFFRACTION100
2.3-2.370.3391530.27482937X-RAY DIFFRACTION100
2.37-2.430.32941710.26022946X-RAY DIFFRACTION100
2.43-2.510.33051320.25322981X-RAY DIFFRACTION100
2.51-2.60.27621520.25812958X-RAY DIFFRACTION100
2.6-2.710.29921610.26162966X-RAY DIFFRACTION100
2.71-2.830.29881370.26852990X-RAY DIFFRACTION100
2.83-2.980.31221620.25542947X-RAY DIFFRACTION100
2.98-3.170.33031580.23432980X-RAY DIFFRACTION100
3.17-3.410.29251540.22092976X-RAY DIFFRACTION100
3.41-3.750.24831680.1992975X-RAY DIFFRACTION100
3.75-4.30.20451530.15132978X-RAY DIFFRACTION100
4.3-5.410.16171640.14673008X-RAY DIFFRACTION100
5.41-48.820.23081390.17983075X-RAY DIFFRACTION100

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