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

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Basic information

Entry
Database: PDB / ID: 8pqs
TitleNucleoside 2'deoxyribosyltransferase from Chroococcidiopsis thermalis PCC 7203 E88A Mutant
ComponentsNucleoside 2-deoxyribosyltransferase
KeywordsTRANSFERASE / Mutant
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: 1.95 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
DepositionJul 11, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Database references / Refinement description / Category: citation / software
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _software.classification

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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


Theoretical massNumber of molelcules
Total (without water)71,0494
Polymers71,0494
Non-polymers00
Water7,044391
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 area11300 Å2
ΔGint-80 kcal/mol
Surface area22820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.630, 135.630, 87.560
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: 17762.307 Da / Num. of mol.: 4 / Mutation: E88A
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / Source method: isolated from a natural source / Formula: H2O

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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: 3.33 Å3/Da / Density % sol: 63.03 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 21.43% PEG 6000; 0.1 M Tris; 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: 1.89→70.21 Å / Num. obs: 73355 / % possible obs: 99.96 % / Redundancy: 38.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.294 / Rrim(I) all: 0.0298 / Net I/σ(I): 6.4
Reflection shellResolution: 1.89→1.92 Å / Redundancy: 34.7 % / Rmerge(I) obs: 5.938 / Mean I/σ(I) obs: 0.2 / Num. unique obs: 3617 / CC1/2: 0.343 / Rrim(I) all: 6.026 / % possible all: 98.61

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Processing

Software
NameVersionClassification
PHENIX(1.19.1-4158)refinement
PHENIX1.19.1-4158phasing
xia23.4.2data reduction
xia23.4.2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→44.4 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2237 3239 4.85 %RANDOM
Rwork0.1977 ---
obs0.199 66760 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→44.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4940 0 0 391 5331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065068
X-RAY DIFFRACTIONf_angle_d0.8736890
X-RAY DIFFRACTIONf_dihedral_angle_d6.351675
X-RAY DIFFRACTIONf_chiral_restr0.059731
X-RAY DIFFRACTIONf_plane_restr0.008899
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.980.3581410.35472738X-RAY DIFFRACTION100
1.98-2.010.38291420.3282732X-RAY DIFFRACTION100
2.01-2.040.33271530.30272741X-RAY DIFFRACTION100
2.04-2.080.34841110.29622806X-RAY DIFFRACTION100
2.08-2.120.30861350.27952691X-RAY DIFFRACTION100
2.12-2.160.3061470.26032795X-RAY DIFFRACTION100
2.16-2.20.26891540.26092727X-RAY DIFFRACTION100
2.2-2.250.2821370.252763X-RAY DIFFRACTION100
2.25-2.30.30241460.24072751X-RAY DIFFRACTION100
2.3-2.360.27231510.23532714X-RAY DIFFRACTION100
2.36-2.420.27061520.22682766X-RAY DIFFRACTION100
2.42-2.490.26751260.21612751X-RAY DIFFRACTION100
2.49-2.570.26541210.23052792X-RAY DIFFRACTION100
2.57-2.670.2631090.21222781X-RAY DIFFRACTION100
2.67-2.770.24611520.20382739X-RAY DIFFRACTION100
2.77-2.90.23051370.21082764X-RAY DIFFRACTION100
2.9-3.050.25751350.20652791X-RAY DIFFRACTION100
3.05-3.240.22851640.1932738X-RAY DIFFRACTION100
3.24-3.490.23431380.1982758X-RAY DIFFRACTION100
3.49-3.840.20161420.18072781X-RAY DIFFRACTION100
3.85-4.40.18441170.14612812X-RAY DIFFRACTION100
4.4-5.540.15831580.15892774X-RAY DIFFRACTION100
5.55-44.40.18481710.17932816X-RAY DIFFRACTION100

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