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- PDB-4jld: Crystal Structures of adenylate kinase with 2 ADP's -

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Basic information

Entry
Database: PDB / ID: 4jld
TitleCrystal Structures of adenylate kinase with 2 ADP's
ComponentsAdenylate kinase
KeywordsTRANSFERASE / ADP binding / phosphoryl transfer reaction
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 / Adenylate kinase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.552 Å
AuthorsCho, Y.-J. / Kern, D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: The energy landscape of adenylate kinase during catalysis.
Authors: Kerns, S.J. / Agafonov, R.V. / Cho, Y.J. / Pontiggia, F. / Otten, R. / Pachov, D.V. / Kutter, S. / Phung, L.A. / Murphy, P.N. / Thai, V. / Alber, T. / Hagan, M.F. / Kern, D.
History
DepositionMar 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2015Group: Database references
Revision 1.2Feb 18, 2015Group: Database references
Revision 1.3Feb 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)47,6746
Polymers45,9662
Non-polymers1,7094
Water8,467470
1
A: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8373
Polymers22,9831
Non-polymers8542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8373
Polymers22,9831
Non-polymers8542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.640, 70.540, 85.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 22982.814 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: adk, aq_078 / Production host: Escherichia coli (E. coli) / References: UniProt: O66490, adenylate kinase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 470 / 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: 2.2 Å3/Da / Density % sol: 43.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 0.1M Sodium Acetate trihydrate, 0.2M Ammonium Acetate, 30% w/v Polyethylene Glycol 4000, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.55→42.94 Å / Num. all: 665952 / Num. obs: 57677 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 22.48 Å2 / Net I/σ(I): 8.1
Reflection shell
Resolution (Å)Mean I/σ(I) obsDiffraction-ID% possible all
1.55-1.641.4193.5
4.91-42.9418.6197.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_865refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.552→36.096 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8433 / SU ML: 0.48 / σ(F): 1.34 / Phase error: 22.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2294 2906 5.08 %random
Rwork0.1849 ---
obs0.1871 57161 96.57 %-
all-60067 --
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.174 Å2 / ksol: 0.366 e/Å3
Displacement parametersBiso max: 69.82 Å2 / Biso mean: 26.1307 Å2 / Biso min: 11.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.9659 Å2-0 Å20 Å2
2--3.9862 Å2-0 Å2
3----3.0202 Å2
Refinement stepCycle: LAST / Resolution: 1.552→36.096 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3236 0 108 470 3814
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063556
X-RAY DIFFRACTIONf_angle_d1.2154839
X-RAY DIFFRACTIONf_chiral_restr0.071531
X-RAY DIFFRACTIONf_plane_restr0.005614
X-RAY DIFFRACTIONf_dihedral_angle_d18.9231452
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.552-1.57750.48031310.42472426255792
1.5775-1.60470.34431140.32452461257593
1.6047-1.63380.34441180.28792467258593
1.6338-1.66530.31951480.25912427257593
1.6653-1.69930.28521310.24482481261293
1.6993-1.73620.29971420.22642480262294
1.7362-1.77660.29781450.20562488263395
1.7766-1.8210.24391320.17012551268396
1.821-1.87020.26731300.18032549267996
1.8702-1.92530.38161180.27422481259993
1.9253-1.98740.21631360.19362568270496
1.9874-2.05840.22261660.20512614278099
2.0584-2.14080.2861470.22322624277199
2.1408-2.23830.19631200.18192647276799
2.2383-2.35630.2441540.18612653280799
2.3563-2.50380.22551520.165426382790100
2.5038-2.69710.23671320.177627222854100
2.6971-2.96840.20231440.180326812825100
2.9684-3.39770.18271460.16127152861100
3.3977-4.27960.1911410.145127532894100
4.2796-36.10530.21141590.17422829298898

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