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- PDB-2f67: Crystal structure of Nucleoside 2-deoxyribosyltransferase from Tr... -

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Basic information

Entry
Database: PDB / ID: 2f67
TitleCrystal structure of Nucleoside 2-deoxyribosyltransferase from Trypanosoma brucei at 1.6 A resolution with BENZO[CD]INDOL-2(1H)-ONE bound
ComponentsNucleoside 2-deoxyribosyltransferase
KeywordsTRANSFERASE / SGPP / Structural GENOMICS / PSI / PROTEIN STRUCTURE INITIATIVE NDRT / Nucleoside 2-deoxyribosyltransferase / Trypanosoma brucei / Structural Genomics of Pathogenic Protozoa Consortium
Function / homology
Function and homology information


deoxyribonucleoside 5'-monophosphate N-glycosidase activity / deoxyribonucleoside monophosphate catabolic process / 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
BENZO[CD]INDOL-2(1H)-ONE / Nucleoside 2-deoxyribosyltransferase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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
DepositionNov 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Remark 999SEQUENCE Authors state that there are two independent sequence confirmations of two different ...SEQUENCE Authors state that there are two independent sequence confirmations of two different clones which clearly show the sequence as given. Authors also have expressed multiple clones at different times and all of these batches show the same electron density for these residues.

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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)38,1399
Polymers37,3282
Non-polymers8117
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-85 kcal/mol
Surface area14680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.928, 75.513, 86.336
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-494-

HOH

21B-480-

HOH

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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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-12B / BENZO[CD]INDOL-2(1H)-ONE


Mass: 169.179 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H7NO
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.57 Å3/Da / Density % sol: 52.17 %
Crystal growTemperature: 277 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 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 6, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 42601 / % possible obs: 89.94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 20.35 Å2 / Rsym value: 0.094 / Net I/σ(I): 7.8
Reflection shellResolution: 1.6→1.686 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 3828 / Rsym value: 0.282 / % possible all: 55.95

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2A0K

2a0k


Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.525 / SU ML: 0.047 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.092 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20777 2251 5 %RANDOM
Rwork0.17779 ---
all0.17926 ---
obs0.17926 42601 89.94 %-
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: 20.065 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20.02 Å2
2---0.01 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2518 0 53 302 2873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222682
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0261.9693631
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9375330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.05323.75136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.05915449
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3531518
X-RAY DIFFRACTIONr_chiral_restr0.0680.2372
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022092
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1920.21262
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21817
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.310.2260
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1260.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0870.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.71741652
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.94962576
X-RAY DIFFRACTIONr_scbond_it2.65261173
X-RAY DIFFRACTIONr_scangle_it3.763101047
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.686 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.243 207 -
Rwork0.218 3828 -
obs--55.95 %
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)
110.4678-5.8716-0.911410.0258-1.20371.06890.29490.4633-0.6401-0.4804-0.06870.4704-0.04750.1612-0.22620.00170.0406-0.0077-0.0556-0.0462-0.07570.376913.6286.6554
23.4249-0.5181.71150.6259-0.35782.14810.03230.04470.279-0.0431-0.0903-0.1289-0.31190.03690.0580.0030.01920.0168-0.04820.0029-0.014323.48269.912112.4927
31.2730.27621.17770.73510.66531.3382-0.02160.00070.08280.00460.01160.0867-0.1943-0.0690.00990.01130.0150.0090.0257-0.0010.001817.0375.88525.1315
40.5056-0.16480.13620.8336-0.07980.70760.05010.0386-0.0099-0.0644-0.0279-0.03310.01120.0087-0.0222-0.03550.0120.0067-0.0046-0.0053-0.029727.1736-7.353411.2667
518.22996.6838-0.580623.6976-5.228511.7820.2163-0.49120.670.85610.09380.6763-0.1077-0.0733-0.3101-0.0541-0.01960.0212-0.0884-0.0672-0.1056-2.1032-29.904137.358
63.39950.6251-1.44210.6976-0.20751.10440.0197-0.0153-0.30760.016-0.0916-0.06710.23520.00920.07190.0035-0.014-0.014-0.03090.0047-0.006122.5805-24.861830.8659
72.0531-1.30680.03975.7171-1.57093.96410.05390.0243-0.1797-0.0911-0.06060.17510.1461-0.13420.0067-0.0507-0.029-0.0076-0.0265-0.0156-0.040719.5857-22.576914.5736
80.50650.1639-0.06370.78210.03250.65460.0369-0.0380.00230.0564-0.0182-0.03260.0022-0.005-0.0187-0.032-0.012-0.005-0.001-0.0008-0.030425.9663-8.434331.254
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 93 - 9
2X-RAY DIFFRACTION2AA10 - 4710 - 47
3X-RAY DIFFRACTION3AA48 - 6948 - 69
4X-RAY DIFFRACTION4AA70 - 16070 - 160
5X-RAY DIFFRACTION5BB3 - 73 - 7
6X-RAY DIFFRACTION6BB8 - 478 - 47
7X-RAY DIFFRACTION7BB48 - 6148 - 61
8X-RAY DIFFRACTION8BB62 - 16062 - 160

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