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- PDB-4jlb: Crystal Structures of Adenylate kinase with 2ADP's -

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Basic information

Entry
Database: PDB / ID: 4jlb
TitleCrystal Structures of Adenylate kinase with 2ADP'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 / adenylate kinase activity / AMP salvage / nucleoside diphosphate kinase activity / phosphorylation / intracellular membrane-bounded organelle / ATP binding / cytosol / cytoplasm
Similarity search - Function
Adenylate kinase, active site lid domain superfamily / 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 / Adenylate kinase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.528 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
Water9,188510
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, 73.730, 87.520
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 / Adenosine 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 / Water


Mass: 18.015 Da / Num. of mol.: 510 / 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: 2.35 Å3/Da / Density % sol: 47.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 0.1M Sodium Acetate trihydrate pH 5.4, 0.2M Ammonium Acetate, 30% w/v Polyethylene Glycol 4000 , VAPOR DIFFUSION, HANGING DROP, temperature 291K

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.53→37.63 Å / Num. all: 926527 / Num. obs: 66347 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 21.95 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 18.8
Reflection shellResolution: 1.53→1.61 Å / Rmerge(I) obs: 1.342 / Mean I/σ(I) obs: 1.9 / % possible all: 99.8

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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: 1.528→36.638 Å / Occupancy max: 1 / Occupancy min: 0.09 / FOM work R set: 0.8499 / SU ML: 0.53 / σ(F): 1.34 / Phase error: 22.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2316 6433 5.08 %random
Rwork0.1726 ---
obs0.1756 62870 99.9 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.589 Å2 / ksol: 0.305 e/Å3
Displacement parametersBiso max: 71.36 Å2 / Biso mean: 29.2877 Å2 / Biso min: 9.86 Å2
Baniso -1Baniso -2Baniso -3
1--2.8557 Å20 Å20 Å2
2--2.7779 Å2-0 Å2
3---0.0778 Å2
Refinement stepCycle: LAST / Resolution: 1.528→36.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3236 0 108 510 3854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053492
X-RAY DIFFRACTIONf_angle_d1.2044742
X-RAY DIFFRACTIONf_chiral_restr0.068520
X-RAY DIFFRACTIONf_plane_restr0.005602
X-RAY DIFFRACTIONf_dihedral_angle_d17.7781399
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.528-1.54540.51081820.48843977415999
1.5454-1.56350.44112030.364240244227100
1.5635-1.58260.3722400.33239924232100
1.5826-1.60260.39132150.328840394254100
1.6026-1.62370.33392390.301239654204100
1.6237-1.6460.32972070.26940284235100
1.646-1.66950.3272010.251939994200100
1.6695-1.69440.30252090.242940334242100
1.6944-1.72090.24892380.199840444282100
1.7209-1.74910.24322190.188739964215100
1.7491-1.77930.27711760.178240294205100
1.7793-1.81160.26382170.171240194236100
1.8116-1.84650.242100.166340454255100
1.8465-1.88410.24152500.160339514201100
1.8841-1.92510.28011770.183540124189100
1.9251-1.96990.2522420.15940074249100
1.9699-2.01920.21232200.154439884208100
2.0192-2.07370.28291820.163740744256100
2.0737-2.13480.22382360.162739844220100
2.1348-2.20370.22492040.157940164220100
2.2037-2.28240.22362180.15823993421199
2.2824-2.37380.20632380.141940004238100
2.3738-2.48180.22481850.147140344219100
2.4818-2.61260.22372160.160439964212100
2.6126-2.77620.23532140.160740314245100
2.7762-2.99050.20932580.168939474205100
2.9905-3.29130.22392210.16740274248100
3.2913-3.76710.25011970.16240364233100
3.7671-4.74450.17562050.149540334238100
4.7445-36.64830.20112140.175340044218100

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