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- PDB-2eck: STRUCTURE OF PHOSPHOTRANSFERASE -

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Basic information

Entry
Database: PDB / ID: 2eck
TitleSTRUCTURE OF PHOSPHOTRANSFERASE
ComponentsADENYLATE KINASE
KeywordsTRANSFERASE / KINASE / ATP-BINDING / PHOSPHOTRANSFERASE
Function / homology
Function and homology information


purine ribonucleotide interconversion / ADP biosynthetic process / nucleoside monophosphate metabolic process / CDP biosynthetic process / (d)CMP kinase activity / UMP kinase activity / nucleoside diphosphate metabolic process / adenylate kinase / adenylate kinase activity / AMP salvage ...purine ribonucleotide interconversion / ADP biosynthetic process / nucleoside monophosphate metabolic process / CDP biosynthetic process / (d)CMP kinase activity / UMP kinase activity / nucleoside diphosphate metabolic process / adenylate kinase / adenylate kinase activity / AMP salvage / UDP biosynthetic process / nucleoside diphosphate kinase activity / AMP binding / phosphorylation / magnesium ion binding / ATP binding / cytosol / cytoplasm
Similarity search - Function
Adenylate kinase, active site lid domain / Adenylate kinase, active site lid / Adenylate kinase subfamily / Adenylate kinase / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold ...Adenylate kinase, active site lid domain / Adenylate kinase, active site lid / Adenylate kinase subfamily / Adenylate kinase / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE MONOPHOSPHATE / Adenylate kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsBerry, M.B. / Bilderback, T. / Glaser, M. / Phillips Jr., G.N.
Citation
Journal: Proteins / Year: 2006
Title: Crystal structure of ADP/AMP complex of Escherichia coli adenylate kinase.
Authors: Berry, M.B. / Bae, E. / Bilderback, T.R. / Glaser, M. / Phillips, G.N.
#1: Journal: Proteins / Year: 1994
Title: The Closed Conformation of a Highly Flexible Protein: The Structure of E. Coli Adenylate Kinase with Bound AMP and Amppnp
Authors: Berry, M.B. / Meador, B. / Bilderback, T. / Liang, P. / Glaser, M. / Phillips Jr., G.N.
History
DepositionDec 16, 1996Processing site: BNL
SupersessionMar 12, 1997ID: 1ECK
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Other / Category: diffrn_source / pdbx_database_status
Item: _diffrn_source.source / _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: ADENYLATE KINASE
B: ADENYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7896
Polymers47,2402
Non-polymers1,5494
Water1,11762
1
A: ADENYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3943
Polymers23,6201
Non-polymers7742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ADENYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3943
Polymers23,6201
Non-polymers7742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.500, 84.800, 80.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99887, 0.025999, 0.039784), (-0.037704, -0.943116, -0.330319), (0.028933, -0.331446, 0.94303)
Vector: 101.7381, 152.5146, -16.5099)

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Components

#1: Protein ADENYLATE KINASE / / ADK


Mass: 23620.029 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ADK+ / Plasmid: PLP101 / Gene (production host): ADK+ / Production host: Escherichia coli (E. coli) / References: UniProt: P69441, adenylate kinase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.6 %
Crystal growpH: 6.7 / Details: pH 6.7

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 1, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→10 Å / Num. obs: 11995 / % possible obs: 99 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.143

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2.8→10 Å / Cross valid method: FREE R / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1243 10 %RANDOM
Rwork0.193 ---
obs0.193 11995 99 %-
Displacement parametersBiso mean: 19.9 Å2
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4068 0 116 186 4370
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.897
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.511
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
Refine LS restraints NCSNCS model details: RESTRAINED / Type: MEDIUM POSITIONAL / Rms dev Biso : 1 Å2 / Rms dev position: 0.105 Å / Weight Biso : 200 / Weight position: 200
LS refinement shellResolution: 2.8→10 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 46 10 %
Rwork0.277 408 -
obs--99 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2

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