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- PDB-4ike: Crystal Structure of a partly open ATP-lid of liganded Adenylate ... -

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Basic information

Entry
Database: PDB / ID: 4ike
TitleCrystal Structure of a partly open ATP-lid of liganded Adenylate kinase
ComponentsAdenylate kinase
KeywordsTRANSFERASE / tansferase (phosphotransferase) / phosphoryl transfer / nucleotide binding / phosphoryl transfer of nucleotides
Function / homology
Function and homology information


nucleoside monophosphate metabolic process / nucleoside diphosphate metabolic process / adenylate kinase / AMP kinase activity / AMP salvage / nucleoside diphosphate kinase activity / ATP binding / cytoplasm / cytosol
Similarity search - Function
Adenylate kinase, active site lid domain superfamily / Adenylate kinase subfamily / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / Adenylate kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE MONOPHOSPHATE / Adenylate kinase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsCho, Y.-J. / Kern, D.
CitationJournal: To be Published
Title: The ATP-Lid Opened Adenylate Kinase with Fully Occupied Substrates
Authors: Cho, Y.-J. / Kern, D.
History
DepositionDec 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 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

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Assembly

Deposited unit
A: Adenylate kinase
B: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0876
Polymers46,5382
Non-polymers1,5494
Water9,224512
1
A: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0433
Polymers23,2691
Non-polymers7742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0433
Polymers23,2691
Non-polymers7742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.370, 61.570, 58.890
Angle α, β, γ (deg.)90.00, 94.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Adenylate kinase / AK / ATP-AMP transphosphorylase


Mass: 23269.057 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: adk, Aquifex, aq_078 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O66490, adenylate kinase
#2: Chemical ChemComp-AMP / 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


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


Mass: 18.015 Da / Num. of mol.: 512 / 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: 2.19 Å3/Da / Density % sol: 43.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9998 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 20, 2009
RadiationMonochromator: KOHZU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.48→34.82 Å / Num. all: 66860 / Num. obs: 66831 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.076

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
AutoBuildmodel building
PHENIX(phenix.refine: dev_1039)refinement
MOSFLMdata reduction
SCALAdata scaling
AutoBuildphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→33.04 Å / SU ML: 0.17 / σ(F): 0 / Phase error: 20.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.198 3384 5.07 %RANDOM
Rwork0.1609 ---
all0.1629 66844 --
obs0.1629 66830 100 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.48→33.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3276 0 100 512 3888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063638
X-RAY DIFFRACTIONf_angle_d1.1414953
X-RAY DIFFRACTIONf_dihedral_angle_d15.651461
X-RAY DIFFRACTIONf_chiral_restr0.068540
X-RAY DIFFRACTIONf_plane_restr0.005641
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.50110.31191690.24832582X-RAY DIFFRACTION100
1.5011-1.52360.32221210.24812668X-RAY DIFFRACTION100
1.5236-1.54740.3451210.22952655X-RAY DIFFRACTION100
1.5474-1.57270.26771340.20322625X-RAY DIFFRACTION100
1.5727-1.59980.23771400.17712639X-RAY DIFFRACTION100
1.5998-1.62890.25221270.16372629X-RAY DIFFRACTION100
1.6289-1.66030.19921540.16522657X-RAY DIFFRACTION100
1.6603-1.69420.20981370.16832598X-RAY DIFFRACTION100
1.6942-1.7310.24131490.17262630X-RAY DIFFRACTION100
1.731-1.77130.2191540.16482622X-RAY DIFFRACTION100
1.7713-1.81550.26151150.16052672X-RAY DIFFRACTION100
1.8155-1.86460.23881500.15792589X-RAY DIFFRACTION100
1.8646-1.91950.20261410.15542658X-RAY DIFFRACTION100
1.9195-1.98140.20941390.16012641X-RAY DIFFRACTION100
1.9814-2.05230.2251350.15442634X-RAY DIFFRACTION100
2.0523-2.13440.22131750.15442620X-RAY DIFFRACTION100
2.1344-2.23150.18361430.14422628X-RAY DIFFRACTION100
2.2315-2.34920.16321500.14132646X-RAY DIFFRACTION100
2.3492-2.49630.19721350.15512641X-RAY DIFFRACTION100
2.4963-2.68890.20041400.16712687X-RAY DIFFRACTION100
2.6889-2.95940.18311220.17272666X-RAY DIFFRACTION100
2.9594-3.38730.18251450.16592650X-RAY DIFFRACTION100
3.3873-4.26610.18551590.14892676X-RAY DIFFRACTION100
4.2661-33.04820.1611330.15442743X-RAY DIFFRACTION100

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