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- PDB-4jl8: A various kinds of ADP conformations in the Adenylate kinase acti... -

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Basic information

Entry
Database: PDB / ID: 4jl8
TitleA various kinds of ADP conformations in the Adenylate kinase active site
ComponentsAdenylate kinase
KeywordsTRANSFERASE / 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: 1.79 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
Water11,602644
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)67.000, 74.720, 88.150
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 / Fragment: transferase
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.: 644 / 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: 2.4 Å3/Da / Density % sol: 48.75 %
Crystal growTemperature: 291 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 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→37.96 Å / Num. all: 511723 / Num. obs: 42592 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 19.56 Å2 / Net I/σ(I): 14.5
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.79-1.880.5663.21100
5.65-37.960.06927.8199.8

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_860refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→37.96 Å / Occupancy max: 1 / Occupancy min: 0.29 / FOM work R set: 0.8416 / SU ML: 0.49 / σ(F): 1.33 / Phase error: 22.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.232 2140 5.04 %random
Rwork0.1801 ---
obs0.1827 42421 99.74 %-
all-44561 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.648 Å2 / ksol: 0.322 e/Å3
Displacement parametersBiso max: 84.64 Å2 / Biso mean: 23.0515 Å2 / Biso min: 6.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.4678 Å20 Å2-0 Å2
2--2.2635 Å2-0 Å2
3----2.7313 Å2
Refinement stepCycle: LAST / Resolution: 1.79→37.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3236 0 108 644 3988
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073579
X-RAY DIFFRACTIONf_angle_d1.2344863
X-RAY DIFFRACTIONf_chiral_restr0.072529
X-RAY DIFFRACTIONf_plane_restr0.006620
X-RAY DIFFRACTIONf_dihedral_angle_d16.271445
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.788-1.82960.28711320.246226652797100
1.8296-1.87540.29051410.251426432784100
1.8754-1.92610.39171320.263326492781100
1.9261-1.98270.2651660.222626312797100
1.9827-2.04670.25261370.178426722809100
2.0467-2.11990.24371670.18826252792100
2.1199-2.20470.27571410.198226582799100
2.2047-2.30510.29921450.22332609275497
2.3051-2.42660.26511280.187526652793100
2.4266-2.57860.23281420.177427222864100
2.5786-2.77760.20841390.174426922831100
2.7776-3.0570.23351370.178426982835100
3.057-3.49910.2261420.166427262868100
3.4991-4.40750.17151500.14327382888100
4.4075-37.97110.1881410.160528883029100

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