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- PDB-3vas: Adenosine kinase from Schistosoma mansoni in complex with adenosi... -

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Basic information

Entry
Database: PDB / ID: 3vas
TitleAdenosine kinase from Schistosoma mansoni in complex with adenosine in occluded loop conformation
ComponentsPutative adenosine kinase
KeywordsTRANSFERASE / ribokinase / enzyme
Function / homology
Function and homology information


adenosine kinase / adenosine kinase activity / purine ribonucleoside salvage / nucleotide binding
Similarity search - Function
Adenosine kinase, small domain - #10 / Adenosine kinase / Adenosine kinase, small domain / pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase ...Adenosine kinase, small domain - #10 / Adenosine kinase / Adenosine kinase, small domain / pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / 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 kinase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsRomanello, L. / Bachega, F.R. / Garatt, R.C. / DeMarco, R. / Brandao-neto, J. / Pereira, H.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Adenosine kinase from Schistosoma mansoni: structural basis for the differential incorporation of nucleoside analogues.
Authors: Romanello, L. / Bachega, J.F. / Cassago, A. / Brandao-Neto, J. / Demarco, R. / Garratt, R.C. / Pereira, H.D.
History
DepositionDec 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Jan 16, 2013Group: Database references
Revision 1.3Sep 13, 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_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_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: Putative adenosine kinase
B: Putative adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2866
Polymers82,6812
Non-polymers6054
Water5,008278
1
A: Putative adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6433
Polymers41,3401
Non-polymers3032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6433
Polymers41,3401
Non-polymers3032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.970, 180.120, 79.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Putative adenosine kinase


Mass: 41340.277 Da / Num. of mol.: 2 / Fragment: Adenosine kinase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: Smp_008360 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: G4V7G8, adenosine kinase
#2: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.55 Å3/Da / Density % sol: 51.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100mM Bis-tris pH 6.1-6.7, 200mM LiSO4, 16-20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
PH range: 6.1-6.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9611 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 25, 2011 / Details: Compound Refractive Lenses
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9611 Å / Relative weight: 1
ReflectionResolution: 2.26→90.06 Å / Num. all: 40098 / Num. obs: 40098 / % possible obs: 97.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 36.926 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 6.43
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.26-2.320.571.63197.4
2.32-2.380.4871.85196.8
2.38-2.450.4072.16197.6
2.45-2.530.3352.58197.7
2.53-2.610.2863.06197.5
2.61-2.70.2313.69197.6
2.7-2.80.1954.33197.8
2.8-2.920.1694.86198.1
2.92-3.050.1445.66198.2
3.05-3.20.1196.72198.3
3.2-3.370.0977.98198.1
3.37-3.570.0759.94197.4
3.57-3.820.06711.06196.6
3.82-4.130.0612.01195.3
4.13-4.520.05413195.1
4.52-5.050.05513.96196.3
5.05-5.840.05313.18196.7
5.84-7.150.05513.05197.9
7.15-10.110.04615.4198.1
10.110.04515.95196.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.1data extraction
DNAdata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3UQ6

3uq6


Resolution: 2.26→90.06 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.25 / σ(F): 1.34 / Phase error: 20.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2216 2011 5.02 %
Rwork0.1771 --
obs0.1792 40098 99.17 %
all-40098 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.0587 Å2
Baniso -1Baniso -2Baniso -3
1--7.6289 Å20 Å2-0 Å2
2--9.2205 Å2-0 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.26→90.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5354 0 40 278 5672
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045501
X-RAY DIFFRACTIONf_angle_d0.8197438
X-RAY DIFFRACTIONf_dihedral_angle_d12.8142010
X-RAY DIFFRACTIONf_chiral_restr0.058830
X-RAY DIFFRACTIONf_plane_restr0.003940
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.31650.27911300.23762650X-RAY DIFFRACTION99
2.3165-2.37920.2891430.22192662X-RAY DIFFRACTION99
2.3792-2.44920.27881460.21232704X-RAY DIFFRACTION99
2.4492-2.52830.24061360.20212683X-RAY DIFFRACTION99
2.5283-2.61860.24041720.18862624X-RAY DIFFRACTION99
2.6186-2.72350.22561490.18332710X-RAY DIFFRACTION99
2.7235-2.84740.24461390.18952691X-RAY DIFFRACTION99
2.8474-2.99760.26751440.19562706X-RAY DIFFRACTION99
2.9976-3.18540.27171270.19492728X-RAY DIFFRACTION99
3.1854-3.43130.24051420.17782736X-RAY DIFFRACTION100
3.4313-3.77660.19211520.15942722X-RAY DIFFRACTION99
3.7766-4.32310.16951410.15182751X-RAY DIFFRACTION99
4.3231-5.44660.18441510.1412787X-RAY DIFFRACTION99
5.4466-90.13150.22071390.18342933X-RAY DIFFRACTION99

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