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- PDB-2a0k: Crystal structure of Nucleoside 2-deoxyribosyltransferase from Tr... -

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Basic information

Entry
Database: PDB / ID: 2a0k
TitleCrystal structure of Nucleoside 2-deoxyribosyltransferase from Trypanosoma brucei at 1.8 A resolution
ComponentsNucleoside 2-deoxyribosyltransferase
KeywordsTRANSFERASE / SGPP / Structural GENOMICS / PSI / PROTEIN STRUCTURE INITIATIVE / Nucleoside 2-deoxyribosyltransferase / Structural Genomics of Pathogenic Protozoa Consortium
Function / homology
Function and homology information


deoxyribonucleoside monophosphate catabolic process / 5-hydroxymethyl-dUMP N-hydrolase activity / nucleus
Similarity search - Function
: / Nucleoside 2-deoxyribosyltransferase / Nucleoside 2-deoxyribosyltransferase / Rossmann fold - #450 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Nucleoside 2-deoxyribosyltransferase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsBosch, J. / Robien, M.A. / Hol, W.G.J. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
CitationJournal: J.Med.Chem. / Year: 2006
Title: Using fragment cocktail crystallography to assist inhibitor design of Trypanosoma brucei nucleoside 2-deoxyribosyltransferase.
Authors: Bosch, J. / Robien, M.A. / Mehlin, C. / Boni, E. / Riechers, A. / Buckner, F.S. / Van Voorhis, W.C. / Myler, P.J. / Worthey, E.A. / DeTitta, G. / Luft, J.R. / Lauricella, A. / Gulde, S. / ...Authors: Bosch, J. / Robien, M.A. / Mehlin, C. / Boni, E. / Riechers, A. / Buckner, F.S. / Van Voorhis, W.C. / Myler, P.J. / Worthey, E.A. / DeTitta, G. / Luft, J.R. / Lauricella, A. / Gulde, S. / Anderson, L.A. / Kalyuzhniy, O. / Neely, H.M. / Ross, J. / Earnest, T.N. / Soltis, M. / Schoenfeld, L. / Zucker, F. / Merritt, E.A. / Fan, E. / Verlinde, C.L. / Hol, W.G.J.
History
DepositionJun 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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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)37,7046
Polymers37,3282
Non-polymers3764
Water7,494416
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-61 kcal/mol
Surface area14910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.004, 75.156, 87.365
Angle α, β, γ (deg.)90.00, 89.97, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-466-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 2 / Auth seq-ID: 3 - 160 / Label seq-ID: 3 - 160

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Nucleoside 2-deoxyribosyltransferase


Mass: 18664.066 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: Tb05.30H13.400 / Plasmid: PET14B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21STAR(DE3)
References: UniProt: Q57VC7, nucleoside deoxyribosyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O
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: 2.7 Å3/Da / Density % sol: 54.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 30 % PEG MME 2000, 0.2 ammonium sulfate, 0.1 sodium acetate trihydrate pH 4.6 , VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 29, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.8→19.8 Å / Num. obs: 32301 / % possible obs: 94.42 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 14.91 Å2 / Rsym value: 0.109 / Net I/σ(I): 8.6
Reflection shellResolution: 1.8→1.897 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 3676 / Rsym value: 0.458 / % possible all: 74.22

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→19.8 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.65 / SU ML: 0.078 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.123 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20581 1704 5 %RANDOM
Rwork0.17301 ---
all0.17466 ---
obs0.17466 32301 94.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.223 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.08 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2518 0 22 416 2956
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222606
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9531.9553514
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3065314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.91423.939132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.95615440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.221516
X-RAY DIFFRACTIONr_chiral_restr0.0720.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022006
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1870.21282
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21784
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0930.2334
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0980.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1050.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.56741628
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.89762540
X-RAY DIFFRACTIONr_scbond_it2.62961089
X-RAY DIFFRACTIONr_scangle_it3.78210974
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
632tight positional0.010.05
631medium positional0.220.5
632tight thermal0.060.5
631medium thermal0.42
LS refinement shellResolution: 1.8→1.897 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.262 193 -
Rwork0.236 3676 -
obs--74.22 %
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)
15.8911-2.1281-1.89461.33060.87620.7180.24230.14040.078-0.141-0.1833-0.08030.0218-0.0254-0.05910.02380.03670.00180.00930.0236-0.001216.75916.0211.569
21.8027-1.0686-1.19630.73240.10864.44020.028-0.0009-0.37090.05630.0030.05350.62660.0226-0.0310.0968-0.0003-0.0522-0.08340.00410.04935.83512.88113.681
30.2398-0.1045-0.28190.47950.10011.37570.03830.0014-0.05410.0220.02760.00250.09530.0794-0.066-0.00460.00430.0042-0.01420.0109-0.00027.25625.96818.475
42.0455-1.6381-1.68284.06221.16382.33520.07330.1244-0.1044-0.0729-0.03840.3225-0.2238-0.3524-0.0349-0.03860.05070.00780.01480.03750.0061-9.55341.38114.112
50.5266-0.02250.30710.2476-0.15910.82240.04170.0637-0.0287-0.0999-0.01560.04030.02450.0224-0.0260.00520.01280.01270.00070.0095-0.0136.8730.4466.365
63.94951.15721.25861.01890.51640.53290.1753-0.1162-0.03760.1041-0.1342-0.0633-0.0511-0.0329-0.04110.0173-0.03350.0270.00040.01860.002716.79248.3632.111
72.17831.6031.17911.28730.23994.29930.0296-0.01430.4208-0.10530.01720.0853-0.6221-0.0079-0.04670.07320.01360.0613-0.0845-0.00270.04155.86151.48729.991
80.2820.05380.23270.32360.10271.17450.0127-0.00750.01430.0140.0346-0.0038-0.14290.045-0.0473-0.0027-0.00950.0231-0.01490.00630.00277.25638.41625.205
92.13682.17072.14285.3471.77753.00830.081-0.07540.07380.1313-0.00690.28780.2319-0.3211-0.0741-0.0481-0.04710.02130.00930.0322-0.0065-9.57522.95429.601
100.47790.0747-0.35440.2943-0.25310.98860.0838-0.06480.02380.143-0.06310.03170.01270.0168-0.0207-0.0108-0.01160.00930.00450.0097-0.00996.89233.9337.312
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 203 - 20
2X-RAY DIFFRACTION2AA21 - 5221 - 52
3X-RAY DIFFRACTION3AA53 - 10753 - 107
4X-RAY DIFFRACTION4AA108 - 126108 - 126
5X-RAY DIFFRACTION5AA127 - 160127 - 160
6X-RAY DIFFRACTION6BB3 - 203 - 20
7X-RAY DIFFRACTION7BB21 - 5221 - 52
8X-RAY DIFFRACTION8BB53 - 10753 - 107
9X-RAY DIFFRACTION9BB108 - 126108 - 126
10X-RAY DIFFRACTION10BB127 - 160127 - 160

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