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- PDB-3uq6: Adenosine kinase from Schistosoma mansoni in complex with adenosi... -

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Basic information

Entry
Database: PDB / ID: 3uq6
TitleAdenosine kinase from Schistosoma mansoni in complex with adenosine and AMP
ComponentsAdenosine kinase, putative
KeywordsTRANSFERASE / Ribokinase
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 MONOPHOSPHATE / : / Adenosine kinase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsRomanello, L. / Cassago, A. / 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
DepositionNov 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 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

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)84,5198
Polymers83,2192
Non-polymers1,3006
Water3,315184
1
A: Adenosine kinase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2604
Polymers41,6101
Non-polymers6503
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Adenosine kinase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2604
Polymers41,6101
Non-polymers6503
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.983, 180.530, 78.329
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 Adenosine kinase, putative


Mass: 41609.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 37oC / Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: AK2, Smp_008360 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: C4PZB4, UniProt: G4V7G8*PLUS, adenosine kinase
#2: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 184 / 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: 51.73 %
Crystal growTemperature: 293 K
Details: 100mM Bis-tris, 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: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 26, 2008
RadiationMonochromator: DCM SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45 Å / Relative weight: 1
ReflectionResolution: 2.3→180.53 Å / Num. obs: 35871 / % possible obs: 93.3 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 10.7
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.552 / Mean I/σ(I) obs: 1.4 / Rsym value: 0.552 / % possible all: 88.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHASERphasing
DMphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BX4

1bx4


Resolution: 2.3→49.958 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.25 / σ(F): 1.35 / Phase error: 25.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2302 1788 4.99 %
Rwork0.208 --
obs0.2092 35822 92.64 %
all-38633 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.24 Å2
Baniso -1Baniso -2Baniso -3
1-19.2487 Å2-0 Å2-0 Å2
2---13.0254 Å2-0 Å2
3----6.0073 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5244 0 86 184 5514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025439
X-RAY DIFFRACTIONf_angle_d0.5737371
X-RAY DIFFRACTIONf_dihedral_angle_d11.531924
X-RAY DIFFRACTIONf_chiral_restr0.042834
X-RAY DIFFRACTIONf_plane_restr0.002925
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.36220.28641270.26822422X-RAY DIFFRACTION88
2.3622-2.43170.33011220.2582478X-RAY DIFFRACTION88
2.4317-2.51020.29951300.25812467X-RAY DIFFRACTION89
2.5102-2.59990.27491240.2462503X-RAY DIFFRACTION89
2.5999-2.7040.25461430.23742485X-RAY DIFFRACTION90
2.704-2.82710.30221360.2472537X-RAY DIFFRACTION91
2.8271-2.97610.26031240.24142587X-RAY DIFFRACTION92
2.9761-3.16250.24531480.23432601X-RAY DIFFRACTION93
3.1625-3.40670.25731510.22012660X-RAY DIFFRACTION95
3.4067-3.74940.19321600.19772748X-RAY DIFFRACTION98
3.7494-4.29170.1841490.17772827X-RAY DIFFRACTION99
4.2917-5.4060.20191450.15922837X-RAY DIFFRACTION98
5.406-49.97020.20921290.19672882X-RAY DIFFRACTION94

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