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- PDB-4n09: Structure of Trypanosoma brucei brucei adenosine kinase in comple... -

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Basic information

Entry
Database: PDB / ID: 4n09
TitleStructure of Trypanosoma brucei brucei adenosine kinase in complex with adenosine and AMPPNP
ComponentsAdenosine kinase
KeywordsTRANSFERASE / anion hole / adenosine kinase / adenosine / AMPPNP
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 / nucleoplasm / ATP binding ...purine ribonucleotide biosynthetic process / adenosine kinase / adenosine kinase activity / AMP salvage / glycosome / ciliary plasm / purine ribonucleoside salvage / purine nucleobase metabolic process / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Adenosine kinase, small domain - #10 / Adenosine kinase / 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
ADENOSINE / ADENOSINE-5'-DIPHOSPHATE / Adenosine kinase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsTimm, J. / Gonzalez-Pacanowska, D. / Wilson, K.S.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2014
Title: Structures of adenosine kinase from Trypanosoma brucei brucei.
Authors: Timm, J. / Gonzalez-Pacanowska, D. / Wilson, K.S.
History
DepositionOct 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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

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Assembly

Deposited unit
A: Adenosine kinase
B: Adenosine kinase
C: Adenosine kinase
D: Adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,81614
Polymers152,9144
Non-polymers2,90210
Water2,666148
1
A: Adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9854
Polymers38,2291
Non-polymers7573
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9854
Polymers38,2291
Non-polymers7573
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9233
Polymers38,2291
Non-polymers6942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9233
Polymers38,2291
Non-polymers6942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)184.530, 90.220, 98.040
Angle α, β, γ (deg.)90.00, 103.78, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETPROPROAA1 - 3454 - 348
21METMETPROPROBB1 - 3454 - 348
12METMETPROPROAA1 - 3454 - 348
22METMETPROPROCC1 - 3454 - 348
13SERSERPHEPHEAA3 - 3436 - 346
23SERSERPHEPHEDD3 - 3436 - 346
14METMETPROPROBB1 - 3454 - 348
24METMETPROPROCC1 - 3454 - 348
15SERSERPHEPHEBB3 - 3436 - 346
25SERSERPHEPHEDD3 - 3436 - 346
16SERSERPHEPHECC3 - 3436 - 346
26SERSERPHEPHEDD3 - 3436 - 346

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Adenosine kinase


Mass: 38228.598 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / Gene: Tb927.6.2360 / Production host: Escherichia coli (E. coli) / References: UniProt: Q584S0, adenosine kinase
#2: Chemical
ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.59 Å3/Da / Density % sol: 52.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Bis Tris propane, pH 8.5, 0.2 M sodium citrate, 24 % (w/v) polyethylene glycol 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.6→65.04 Å / Num. obs: 45507

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
REFMAC5.8.0033refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→65.04 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.926 / SU B: 11.697 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R: 0.922 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22144 2428 5.1 %RANDOM
Rwork0.1862 ---
obs0.18802 45507 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.964 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å20.84 Å2
2--0.42 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.6→65.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10261 0 192 148 10601
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01910687
X-RAY DIFFRACTIONr_bond_other_d0.0060.029802
X-RAY DIFFRACTIONr_angle_refined_deg1.5311.96714561
X-RAY DIFFRACTIONr_angle_other_deg1.264322397
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.46451377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.74423.541449
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.814151584
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2661571
X-RAY DIFFRACTIONr_chiral_restr0.0790.21666
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212283
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022492
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9294.3775505
X-RAY DIFFRACTIONr_mcbond_other2.9274.3775504
X-RAY DIFFRACTIONr_mcangle_it4.4856.5666874
X-RAY DIFFRACTIONr_mcangle_other2.1963.4346875
X-RAY DIFFRACTIONr_scbond_it3.7544.6735182
X-RAY DIFFRACTIONr_scbond_other2.0962.4765181
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2453.6347685
X-RAY DIFFRACTIONr_long_range_B_refined4.83918.52811922
X-RAY DIFFRACTIONr_long_range_B_other4.83918.53111923
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A187510.1
12B187510.1
21A188340.1
22C188340.1
31A173720.1
32D173720.1
41B191480.1
42C191480.1
51B177220.11
52D177220.11
61C178180.1
62D178180.1
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 173 -
Rwork0.283 3343 -
obs--99.1 %

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