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- PDB-3vaq: Adenosine kinase from Schistosoma mansoni in complex with adenosine -

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Basic information

Entry
Database: PDB / ID: 3vaq
TitleAdenosine kinase from Schistosoma mansoni in complex with adenosine
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 / Adenosine kinase, small domain - #10 / 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 / Adenosine kinase, small domain - #10 / 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 / molecular replacement / Resolution: 2.44 Å
AuthorsRomanello, L. / Bachega, F.R. / Garatt, R.C. / DeMarco, R. / 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)83,7516
Polymers83,1452
Non-polymers6054
Water2,738152
1
A: Putative adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8753
Polymers41,5731
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)41,8753
Polymers41,5731
Non-polymers3032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.100, 180.310, 79.430
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: 41572.574 Da / Num. of mol.: 2 / Fragment: Adenosine kinase
Source method: isolated from a genetically manipulated source
Details: 37oC / Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: Adenosine kinase, 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 / Adenosine


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


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


Mass: 18.015 Da / Num. of mol.: 152 / 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: 51.67 %
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: 2.44→79.43 Å / Num. all: 32370 / Num. obs: 32370 / % possible obs: 99.6 % / Observed criterion σ(F): 1.7 / Observed criterion σ(I): 1.7 / Redundancy: 3.8 % / Rsym value: 0.091 / Net I/σ(I): 10.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.44-2.53.70.6741.10.674199.8
2.5-2.573.70.5751.30.575199.9
2.57-2.653.80.4511.70.451199.9
2.65-2.733.80.3821.90.382199.8
2.73-2.823.80.3332.20.333199.9
2.82-2.923.90.2922.60.2921100
2.92-3.033.90.2263.30.226199.8
3.03-3.1540.18740.1871100
3.15-3.2940.1524.90.152199.9
3.29-3.4540.17.40.1199.7
3.45-3.643.90.0819.20.081199.2
3.64-3.863.90.06511.30.065198.6
3.86-4.123.90.05313.60.053198.3
4.12-4.453.80.04615.20.046198.9
4.45-4.883.80.04115.80.041199.7
4.88-5.463.80.04216.70.042199.6
5.46-6.33.90.04416.20.044199.8
6.3-7.723.90.03817.60.038199.9
7.72-10.913.80.02721.50.027199.9
10.91-79.433.40.02721.40.027199.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASERphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.1data extraction
DNAdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3UQ6

3uq6


Resolution: 2.44→59.598 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.23 / σ(F): 1.34 / Phase error: 23.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2301 1639 5.07 %
Rwork0.1873 --
obs0.1895 32318 99.53 %
all-32370 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.3534 Å2
Baniso -1Baniso -2Baniso -3
1--8.2041 Å20 Å2-0 Å2
2--9.9362 Å2-0 Å2
3----1.7256 Å2
Refinement stepCycle: LAST / Resolution: 2.44→59.598 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5376 0 40 152 5568
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025524
X-RAY DIFFRACTIONf_angle_d0.5747472
X-RAY DIFFRACTIONf_dihedral_angle_d10.8552024
X-RAY DIFFRACTIONf_chiral_restr0.044832
X-RAY DIFFRACTIONf_plane_restr0.002948
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.51180.31261400.28232504X-RAY DIFFRACTION100
2.5118-2.59290.33451530.25422525X-RAY DIFFRACTION100
2.5929-2.68560.26821310.24032530X-RAY DIFFRACTION100
2.6856-2.79310.28451190.22912523X-RAY DIFFRACTION100
2.7931-2.92020.28621400.22592537X-RAY DIFFRACTION100
2.9202-3.07420.25761710.2052504X-RAY DIFFRACTION100
3.0742-3.26680.23581370.20982533X-RAY DIFFRACTION100
3.2668-3.5190.21311330.18542547X-RAY DIFFRACTION100
3.519-3.8730.21851270.16292533X-RAY DIFFRACTION98
3.873-4.43330.21151360.15652550X-RAY DIFFRACTION98
4.4333-5.58490.18671270.15222614X-RAY DIFFRACTION100
5.5849-59.61620.19461250.17732779X-RAY DIFFRACTION100

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