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- PDB-8qc0: Nucleoside 2'deoxyribosyltransferase from Chroococcidiopsis therm... -

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Basic information

Entry
Database: PDB / ID: 8qc0
TitleNucleoside 2'deoxyribosyltransferase from Chroococcidiopsis thermalis PCC 7203 WT ribosylated
ComponentsNucleoside 2-deoxyribosyltransferase
KeywordsTRANSFERASE / Ribosylated / holoprotein
Function / homologydeoxyribonucleoside monophosphate catabolic process / 5-hydroxymethyl-dUMP N-hydrolase activity / : / Nucleoside 2-deoxyribosyltransferase / Nucleoside 2-deoxyribosyltransferase / transferase activity / metal ion binding / alpha-D-ribofuranose / Nucleoside 2-deoxyribosyltransferase
Function and homology information
Biological speciesChroococcidiopsis thermalis PCC 7203 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 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
DepositionAug 25, 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 20, 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)71,61912
Polymers70,7574
Non-polymers8628
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
  • 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 area14310 Å2
ΔGint-248 kcal/mol
Surface area21610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.240, 135.240, 87.220
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: 17689.146 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: Sugar
ChemComp-RIB / alpha-D-ribofuranose / alpha-D-ribose / D-ribose / ribose


Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DRibfaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-ribofuranoseCOMMON NAMEGMML 1.0
a-D-RibfIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RibSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 3.23 Å3/Da / Density % sol: 61.92 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 21.43% v/v PEG 6000; 0.1 M Tris pH 8; 0.5 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: 2.02→53.5 Å / Num. obs: 59536 / % possible obs: 100 % / Redundancy: 39.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.031 / Rrim(I) all: 0.194 / Net I/σ(I): 15.6
Reflection shellResolution: 2.02→2.05 Å / Redundancy: 42.1 % / Rmerge(I) obs: 5.534 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 2939 / CC1/2: 0.286 / Rpim(I) all: 0.862 / % possible all: 100

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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: 2.02→44.27 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2408 2958 4.98 %RANDOM
Rwork0.2138 ---
obs0.2152 59456 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.02→44.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4951 0 4 230 5185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095094
X-RAY DIFFRACTIONf_angle_d1.1086918
X-RAY DIFFRACTIONf_dihedral_angle_d6.902695
X-RAY DIFFRACTIONf_chiral_restr0.088745
X-RAY DIFFRACTIONf_plane_restr0.007892
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.050.42551430.42552610X-RAY DIFFRACTION99
2.05-2.090.43271320.4022696X-RAY DIFFRACTION100
2.09-2.130.33731400.3342672X-RAY DIFFRACTION100
2.13-2.170.35051510.32661X-RAY DIFFRACTION100
2.17-2.210.31851240.28942729X-RAY DIFFRACTION100
2.21-2.260.28981470.27362638X-RAY DIFFRACTION100
2.26-2.310.29841360.26372695X-RAY DIFFRACTION100
2.31-2.370.30471540.26372702X-RAY DIFFRACTION100
2.37-2.430.33271460.25912649X-RAY DIFFRACTION100
2.43-2.510.29251420.25882682X-RAY DIFFRACTION100
2.51-2.590.32311500.26552669X-RAY DIFFRACTION100
2.59-2.680.29721440.25812689X-RAY DIFFRACTION100
2.68-2.790.25821100.23392730X-RAY DIFFRACTION100
2.79-2.910.25821170.23392699X-RAY DIFFRACTION100
2.91-3.070.24871450.22462705X-RAY DIFFRACTION100
3.07-3.260.25491310.21712701X-RAY DIFFRACTION100
3.26-3.510.261320.22142710X-RAY DIFFRACTION100
3.51-3.860.21541450.19742699X-RAY DIFFRACTION100
3.86-4.420.19131880.16692670X-RAY DIFFRACTION100
4.42-5.570.20341460.16532715X-RAY DIFFRACTION100
5.57-44.270.2151350.19282777X-RAY DIFFRACTION100

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