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- PDB-5kb5: Crystal structure of the adenosine kinase from Mus musculus in co... -

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Basic information

Entry
Database: PDB / ID: 5kb5
TitleCrystal structure of the adenosine kinase from Mus musculus in complex with adenosine and adenosine-diphosphate
ComponentsAdenosine kinase
KeywordsTRANSFERASE / adenosine kinase
Function / homology
Function and homology information


dATP biosynthetic process / Purine salvage / Ribavirin ADME / adenosine kinase / adenosine kinase activity / dAMP salvage / deoxyadenosine kinase activity / adenosine metabolic process / GMP salvage / type B pancreatic cell proliferation ...dATP biosynthetic process / Purine salvage / Ribavirin ADME / adenosine kinase / adenosine kinase activity / dAMP salvage / deoxyadenosine kinase activity / adenosine metabolic process / GMP salvage / type B pancreatic cell proliferation / AMP salvage / purine ribonucleoside salvage / positive regulation of cardiac muscle hypertrophy / purine nucleobase metabolic process / positive regulation of T cell proliferation / nucleoplasm / ATP binding / nucleus / metal ion binding / plasma membrane / cytosol
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-5'-DIPHOSPHATE / : / PHOSPHATE ION / Adenosine kinase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsOliveira, R.R. / Neto, R.M. / Polo, C.C. / Tonoli, C.C.C. / Murakami, M.T. / Franchini, K.G.
CitationJournal: To Be Published
Title: Crystal structure of the adenosine kinase from Mus musculus in complex with adenosine and adenosine-diphosphate
Authors: Oliveira, R.R. / Neto, R.M. / Polo, C.C. / Tonoli, C.C.C. / Murakami, M.T. / Franchini, K.G.
History
DepositionJun 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Sep 27, 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
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.ptnr2_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,02911
Polymers40,6331
Non-polymers1,39610
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.264, 73.559, 84.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Adenosine kinase / AK / Adenosine 5'-phosphotransferase


Mass: 40632.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Adk / Production host: Escherichia coli (E. coli) / References: UniProt: P55264, adenosine kinase

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Non-polymers , 8 types, 141 molecules

#2: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.01 Å3/Da / Density % sol: 34.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 40% PEG400 15% PEG1000 0.15M Sodium di-potassium phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 28540 / % possible obs: 97.6 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.093 / Net I/av σ(I): 12.8 / Net I/σ(I): 9.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.8-1.834.20.732198.8
1.83-1.864.30.586198.3
1.86-1.94.30.499198
1.9-1.944.30.424198.3
1.94-1.984.30.366199.2
1.98-2.034.30.305198.5
2.03-2.084.30.269198
2.08-2.134.20.248197.6
2.13-2.24.20.215197
2.2-2.274.10.19196.9
2.27-2.354.10.174196.6
2.35-2.444.10.166196.3
2.44-2.554.10.146195.9
2.55-2.6940.135195.6
2.69-2.863.90.127196
2.86-3.083.80.102196.8
3.08-3.3940.073197.2
3.39-3.884.20.05198.9
3.88-4.884.30.04199.9
4.88-5040.035198

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.15data extraction
SCALEPACKdata scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BX4

1bx4


Resolution: 1.8→24.63 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.081 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.121 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1999 1450 5.1 %RANDOM
Rwork0.1655 ---
obs0.1673 27048 97.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 68.13 Å2 / Biso mean: 24.216 Å2 / Biso min: 12.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0 Å2-0 Å2
2---0.19 Å20 Å2
3---0.29 Å2
Refinement stepCycle: final / Resolution: 1.8→24.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2679 0 86 131 2896
Biso mean--26.91 29.56 -
Num. residues----341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192824
X-RAY DIFFRACTIONr_bond_other_d0.0020.022678
X-RAY DIFFRACTIONr_angle_refined_deg1.8491.983820
X-RAY DIFFRACTIONr_angle_other_deg1.05336171
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7055344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.76824.924132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.66115474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5451513
X-RAY DIFFRACTIONr_chiral_restr0.1190.2421
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023163
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02646
X-RAY DIFFRACTIONr_mcbond_it0.6861.0881367
X-RAY DIFFRACTIONr_mcbond_other0.6861.0871366
X-RAY DIFFRACTIONr_mcangle_it1.0981.6281708
LS refinement shellResolution: 1.797→1.844 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 102 -
Rwork0.237 1947 -
all-2049 -
obs--96.56 %
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)
11.7075-0.3408-0.37931.04470.83853.24440.0080.0194-0.11630.0240.01370.03710.184-0.169-0.02180.1029-0.0204-0.00270.073-0.01570.082149.8613153.9417189.8536
23.12160.08620.8033.69432.28333.5763-0.05310.73540.2812-0.7006-0.0892-0.0363-0.49120.15070.14230.21170.01640.0040.23760.07360.031155.2104162.1326168.1717
31.7332-0.2396-0.09391.1553-0.40261.36590.00120.0872-0.1877-0.02670.03050.13530.1629-0.1474-0.03170.0881-0.0118-0.00480.0624-0.00880.0389145.939150.5915189.1792
415.6767-2.5552-6.8092.4861.28685.44190.20170.65490.5359-0.1258-0.0249-0.0214-0.1001-0.3851-0.17670.1394-0.0154-0.02160.11030.02080.0392148.7371159.8708178.0317
52.5236-0.1146-1.12760.97510.16753.16610.014-0.08980.19090.09850.05580.121-0.0102-0.2859-0.06980.0897-0.00330.00020.0675-0.01210.0707144.0062162.2916195.7566
61.8459-0.1467-0.18031.14890.01931.10120.0273-0.04260.31310.0070.0279-0.1145-0.08350.0491-0.05520.0959-0.0005-0.0080.0618-0.01510.0761161.5654166.6481194.7996
73.5520.1574-1.40894.23410.87085.78960.0455-0.61790.1820.29470.0645-0.29620.10170.3487-0.110.07730.0149-0.06440.1372-0.05010.0693167.2617165.0726204.9981
85.39220.03521.12813.5717-0.142.12930.08230.2013-0.1744-0.04680.0047-0.49150.19480.2347-0.0870.07070.03330.01430.0914-0.00340.0978171.7133151.476187.4178
92.4111-0.07820.13151.23230.17632.00860.0045-0.0462-0.25630.03310.02190.01950.13760.0163-0.02640.11840.01980.00020.06840.00470.0639161.7579145.7409191.3056
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 38
2X-RAY DIFFRACTION2A39 - 75
3X-RAY DIFFRACTION3A76 - 129
4X-RAY DIFFRACTION4A130 - 148
5X-RAY DIFFRACTION5A149 - 179
6X-RAY DIFFRACTION6A180 - 262
7X-RAY DIFFRACTION7A263 - 278
8X-RAY DIFFRACTION8A279 - 313
9X-RAY DIFFRACTION9A314 - 360

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