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- PDB-3otx: Crystal Structure of Trypanosoma brucei rhodesiense Adenosine Kin... -

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Basic information

Entry
Database: PDB / ID: 3otx
TitleCrystal Structure of Trypanosoma brucei rhodesiense Adenosine Kinase Complexed with Inhibitor AP5A
ComponentsAdenosine kinase, putative
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Adenosine Kinase / AP5A / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


purine ribonucleotide biosynthetic process / adenosine kinase / adenosine kinase activity / AMP salvage / glycosome / ciliary plasm / purine ribonucleoside salvage / purine nucleobase metabolic process / phosphorylation / nucleoplasm ...purine ribonucleotide biosynthetic process / adenosine kinase / adenosine kinase activity / AMP salvage / glycosome / ciliary plasm / purine ribonucleoside salvage / purine nucleobase metabolic process / phosphorylation / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Adenosine kinase / Adenosine kinase, small domain - #10 / Adenosine kinase, small domain / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BIS(ADENOSINE)-5'-PENTAPHOSPHATE / Adenosine kinase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsKuettel, S. / Greenwald, J. / Kostrewa, D. / Ahmed, S. / Scapozza, L. / Perozzo, R.
CitationJournal: Plos Negl Trop Dis / Year: 2011
Title: Crystal Structures of T. b. rhodesiense Adenosine Kinase Complexed with Inhibitor and Activator: Implications for Catalysis and Hyperactivation
Authors: Kuettel, S. / Greenwald, J. / Kostrewa, D. / Ahmed, S. / Scapozza, L. / Perozzo, R.
History
DepositionSep 14, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenosine kinase, putative
B: Adenosine kinase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1426
Polymers76,2632
Non-polymers1,8794
Water11,277626
1
A: Adenosine kinase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0713
Polymers38,1311
Non-polymers9392
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Adenosine kinase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0713
Polymers38,1311
Non-polymers9392
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.893, 70.549, 72.410
Angle α, β, γ (deg.)90.00, 90.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Adenosine kinase, putative /


Mass: 38131.480 Da / Num. of mol.: 2 / Mutation: S2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Strain: rhodesiense / Gene: Tb927.6.2360 / Plasmid: pET30b / Production host: Escherichia coli (E. coli) / References: UniProt: Q584S0, adenosine kinase
#2: Chemical ChemComp-AP5 / BIS(ADENOSINE)-5'-PENTAPHOSPHATE


Mass: 916.367 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H29N10O22P5
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 626 / 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: 2.31 Å3/Da / Density % sol: 46.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M sodium citrate, 20% iso-propanol, 20% PEG 4000, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 24, 2007 / Details: Mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→80 Å / Num. all: 97047 / Num. obs: 97047 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 26.4 Å2 / Rsym value: 0.054 / Net I/σ(I): 14.6
Reflection shellResolution: 1.55→1.6 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 8658 / Rsym value: 0.434 / % possible all: 95.1

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Processing

Software
NameVersionClassification
PHASERphasing
MOLREPphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BX4

1bx4


Resolution: 1.55→72.36 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.863 / SU ML: 0.062 / Isotropic thermal model: TLS and isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.088 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21417 4858 5 %RANDOM
Rwork0.18093 ---
obs0.1826 92189 96.49 %-
all-97047 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.354 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å20.57 Å2
2---0.15 Å20 Å2
3----0.2 Å2
Refine analyzeLuzzati coordinate error free: 0.088 Å
Refinement stepCycle: LAST / Resolution: 1.55→72.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5253 0 116 626 5995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225558
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.987570
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5245703
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.61423.695249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.08415926
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8781542
X-RAY DIFFRACTIONr_chiral_restr0.0980.2844
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214187
X-RAY DIFFRACTIONr_mcbond_it1.74723414
X-RAY DIFFRACTIONr_mcangle_it3.14815514
X-RAY DIFFRACTIONr_scbond_it4.6424.52144
X-RAY DIFFRACTIONr_scangle_it7.1612042
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 324 -
Rwork0.266 6689 -
obs-7013 95.19 %
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)
11.4449-0.1717-0.3571.08990.1431.20720.00080.06490.0363-0.0855-0.0435-0.0531-0.03210.07710.04260.01950.0019-0.01160.01260.00690.022816.4990.24129.535
21.31640.08220.11281.11570.24371.1599-0.00910.21160.0159-0.1045-0.0204-0.0273-0.0469-0.08620.02950.05230.0070.01520.0810.0090.020951.3447.3967.532
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 345
2X-RAY DIFFRACTION1A346
3X-RAY DIFFRACTION2B4 - 345
4X-RAY DIFFRACTION2B346

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