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

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Basic information

Entry
Database: PDB / ID: 8pqp
TitleNucleoside 2'deoxyribosyltransferase from Chroococcidiopsis thermalis PCC 7203 D62N Mutant bound to ImmH-Forodesine
ComponentsNucleoside 2-deoxyribosyltransferase
KeywordsPROTEIN BINDING / Complex / Transferase / ImmH-Forodesine / Mutant
Function / homologydeoxyribonucleoside 5'-monophosphate N-glycosidase activity / deoxyribonucleoside monophosphate catabolic process / Nucleoside 2-deoxyribosyltransferase / Nucleoside 2-deoxyribosyltransferase / transferase activity / Chem-IMH / Nucleoside 2-deoxyribosyltransferase
Function and homology information
Biological speciesChroococcidiopsis thermalis PCC 7203 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.709 Å
AuthorsTang, P. / Harding, C.J. / Czekster, M.C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other privateSBS0-YGS014 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 / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9053
Polymers35,6392
Non-polymers2661
Water1,67593
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 area2440 Å2
ΔGint-5 kcal/mol
Surface area15610 Å2
Unit cell
Length a, b, c (Å)93.573, 93.573, 63.124
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-351-

HOH

21B-229-

HOH

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Components

#1: Protein Nucleoside 2-deoxyribosyltransferase


Mass: 17819.359 Da / Num. of mol.: 2 / Mutation: D62N
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-IMH / 1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHYPOXANTHIN-9-YL)-D-RIBITOL / Forodesine / Immucillin H


Mass: 266.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14N4O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 45.05 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 28% v/v PEG Smear Broad; 0.1 M Sodium Phosphate pH 6.2; 0.2 M Sodium Chloride

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 31, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.709→49.8 Å / Num. obs: 34700 / % possible obs: 99.6 % / Redundancy: 16.7 % / CC1/2: 1 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.05 / Net I/σ(I): 21.8
Reflection shellResolution: 1.71→1.74 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.094 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 1649 / CC1/2: 0.4 / Rrim(I) all: 2.464 / % possible all: 95.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
PHASER2.8.3phasing
autoPROC1.0.5data processing
autoPROC1.0.5data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.709→49.799 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2122 1665 4.88 %
Rwork0.1866 --
obs0.1879 34134 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.709→49.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2485 0 19 93 2597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072570
X-RAY DIFFRACTIONf_angle_d0.8383497
X-RAY DIFFRACTIONf_dihedral_angle_d6.2471527
X-RAY DIFFRACTIONf_chiral_restr0.055372
X-RAY DIFFRACTIONf_plane_restr0.006454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.709-1.75930.43421410.4252142X-RAY DIFFRACTION79
1.7593-1.81610.41811350.38462622X-RAY DIFFRACTION97
1.8161-1.8810.34031430.32042732X-RAY DIFFRACTION100
1.881-1.95630.25841220.2362755X-RAY DIFFRACTION100
1.9563-2.04540.27881230.22022750X-RAY DIFFRACTION100
2.0454-2.15320.26151270.21932741X-RAY DIFFRACTION100
2.1532-2.28810.25081520.2142729X-RAY DIFFRACTION100
2.2881-2.46480.26531490.22782757X-RAY DIFFRACTION100
2.4648-2.71280.2811330.22822767X-RAY DIFFRACTION100
2.7128-3.10530.24831500.21792760X-RAY DIFFRACTION100
3.1053-3.91210.20931510.18692804X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.16890.52510.68552.38810.32122.3145-0.04320.0362-0.0476-0.1142-0.1143-0.06390.34220.15270.14280.45660.02680.11070.38880.07440.54941.6031-22.883-3.6816
22.64920.26490.07471.8470.02840.64150.5125-0.655-0.8330.0532-0.2966-0.50860.6092-0.153-0.20780.7891-0.2194-0.1070.56450.17220.5623-8.3509-48.26338.0511
33.6126-1.76220.34723.99311.25820.8940.07781.2744-0.91580.9046-0.2234-1.24830.88650.2486-0.23441.29620.0487-0.21251.1835-0.27160.9532-5.8854-46.042-7.8511
42.7843-0.1259-0.06185.6209-2.66648.17160.34450.0514-0.5922-1.3052-0.1169-0.35750.66250.1683-0.1931.1522-0.0673-0.15090.416-0.01280.6533-15.496-52.1944-7.2762
53.88950.46180.72922.6208-0.51452.27340.3323-1.0603-0.31850.0285-0.17660.12150.1311-0.3269-0.18990.6997-0.3367-0.0660.77960.13550.3671-21.2167-41.872213.186
63.61680.55791.32225.0447-0.47883.63210.2174-0.3741-0.06650.4272-0.3187-0.43440.5166-0.02770.11420.483-0.02880.00930.40190.06230.44382.6506-26.646210.7557
73.247-2.0581-4.88723.71541.5028.3327-0.9482-1.776-0.26710.80240.42450.10360.89490.21790.38320.59090.0515-0.04740.78580.04640.6328-1.9237-18.084518.1435
82.81442.3281-3.45815.9087-2.1394.4440.0198-0.74720.29970.252-0.1808-0.3938-0.16230.16960.02420.4895-0.0318-0.06920.5174-0.06270.5583-7.3334-11.023614.4918
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 69 through 155 )
2X-RAY DIFFRACTION2chain 'B' and (resid 2 through 43 )
3X-RAY DIFFRACTION3chain 'B' and (resid 44 through 51 )
4X-RAY DIFFRACTION4chain 'B' and (resid 52 through 68 )
5X-RAY DIFFRACTION5chain 'B' and (resid 69 through 155 )
6X-RAY DIFFRACTION6chain 'A' and (resid 2 through 33 )
7X-RAY DIFFRACTION7chain 'A' and (resid 34 through 51 )
8X-RAY DIFFRACTION8chain 'A' and (resid 52 through 68 )

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