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- PDB-1bx4: STRUCTURE OF HUMAN ADENOSINE KINASE AT 1.50 ANGSTROMS -

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Basic information

Entry
Database: PDB / ID: 1bx4
TitleSTRUCTURE OF HUMAN ADENOSINE KINASE AT 1.50 ANGSTROMS
ComponentsPROTEIN (ADENOSINE KINASE)
KeywordsTRANSFERASE / HUMAN ADENOSINE KINASE
Function / homology
Function and homology information


dATP biosynthetic process / adenosine kinase / adenosine kinase activity / ribonucleoside monophosphate biosynthetic process / dAMP salvage / deoxyadenosine kinase activity / Ribavirin ADME / Purine salvage / GMP salvage / AMP salvage ...dATP biosynthetic process / adenosine kinase / adenosine kinase activity / ribonucleoside monophosphate biosynthetic process / dAMP salvage / deoxyadenosine kinase activity / Ribavirin ADME / Purine salvage / GMP salvage / AMP salvage / purine ribonucleoside salvage / purine nucleobase metabolic process / RNA binding / nucleoplasm / ATP binding / metal ion binding / nucleus / plasma membrane / cytosol
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsMathews, I.I. / Erion, M.D. / Ealick, S.E.
CitationJournal: Biochemistry / Year: 1998
Title: Structure of human adenosine kinase at 1.5 A resolution.
Authors: Mathews, I.I. / Erion, M.D. / Ealick, S.E.
History
DepositionOct 13, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 13, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: PROTEIN (ADENOSINE KINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4348
Polymers38,7551
Non-polymers6787
Water6,377354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.300, 111.080, 49.690
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 PROTEIN (ADENOSINE KINASE)


Mass: 38755.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: NATIVE PROTEIN WAS EXPRESSED IN BL21[DE3] CELLS SELENO METHIONINE PROTEIN IN B834[DE3] CELLS
Production host: Escherichia coli (E. coli) / Strain (production host): BL21[DE3], B834[DE3] / References: UniProt: P55263, adenosine kinase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 2.3 Å3/Da / Density % sol: 47 % / Description: MLPHARE WAS USED FOR THE REFINEMENT
Crystal growpH: 7.5 / Details: 20%PEG 4K, 0.16M MGCL2, 0.1M TRIS, PH 7.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
220 %PEG40001reservoir
30.16 M1reservoirMgCl2
40.1 MTris1reservoircan be replaced by HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.929
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.929 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 57595 / % possible obs: 98.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 6.3
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 3.7 / Rsym value: 0.185 / % possible all: 91.4
Reflection
*PLUS
Num. measured all: 259153
Reflection shell
*PLUS
% possible obs: 91.4 %

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Processing

Software
NameVersionClassification
SnBphasing
SOLVEphasing
X-PLOR3.8refinement
MOSFLMdata reduction
CCP4data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.5→20 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / σ(F): 2
Details: TOPOLOGY AND PARAMETER FILES FOR ADENOSINE WERE GENERATED.
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2438 5 %RANDOM
Rwork0.192 ---
obs0.192 55983 95.4 %-
Displacement parametersBiso mean: 16.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.197 Å0.17 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2696 0 57 340 3093
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.36
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.5→1.57 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.267 281 5 %
Rwork0.247 5289 -
obs--81.5 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 16.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4
LS refinement shell
*PLUS
Rfactor Rfree: 0.267 / % reflection Rfree: 5 % / Rfactor Rwork: 0.247

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