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- PDB-4jky: Cobalt between two ADP's in the active site of adenylate kinase -

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Basic information

Entry
Database: PDB / ID: 4jky
TitleCobalt between two ADP's in the active site of adenylate kinase
ComponentsAdenylate kinase
KeywordsTRANSFERASE / phosphoryl transfer reaction / Cobalt binding
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 / cytosol / cytoplasm
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: 2.373 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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)47,7928
Polymers45,9662
Non-polymers1,8276
Water2,594144
1
A: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8964
Polymers22,9831
Non-polymers9133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8964
Polymers22,9831
Non-polymers9133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.550, 73.530, 87.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.36 Å3/Da / Density % sol: 47.95 %
Crystal growTemperature: 298 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, ADP(17.3mM) and CoCl2(41.2mM), pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.6086 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6086 Å / Relative weight: 1
ReflectionResolution: 2.37→56.28 Å / Num. all: 33838 / Num. obs: 18108 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 39.23 Å2 / Net I/σ(I): 25.6
Reflection shellResolution: 2.37→2.5 Å / Rmerge(I) obs: 0.198 / % possible all: 97.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.373→53.463 Å / Occupancy max: 1 / Occupancy min: 0.09 / FOM work R set: 0.7834 / SU ML: 0.78 / σ(F): 1.34 / Phase error: 28.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2666 926 5.09 %random
Rwork0.199 ---
obs0.2025 17150 99.5 %-
all-35559 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.056 Å2 / ksol: 0.296 e/Å3
Displacement parametersBiso max: 120.33 Å2 / Biso mean: 41.5628 Å2 / Biso min: 15.17 Å2
Baniso -1Baniso -2Baniso -3
1--7.4743 Å20 Å2-0 Å2
2--10.821 Å20 Å2
3----3.3467 Å2
Refinement stepCycle: LAST / Resolution: 2.373→53.463 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3236 0 110 144 3490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083424
X-RAY DIFFRACTIONf_angle_d1.2764641
X-RAY DIFFRACTIONf_chiral_restr0.069513
X-RAY DIFFRACTIONf_plane_restr0.006583
X-RAY DIFFRACTIONf_dihedral_angle_d18.7041363
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3731-2.44290.31021300.25472534266495
2.4429-2.52180.45741530.300526632816100
2.5218-2.61190.32621580.251526832841100
2.6119-2.71650.36281280.244727292857100
2.7165-2.84010.32241210.215527152836100
2.8401-2.98980.31491540.222426512805100
2.9898-3.17710.32821380.218127102848100
3.1771-3.42240.26061530.213326932846100
3.4224-3.76670.28281590.203626682827100
3.7667-4.31160.21881430.166826972840100
4.3116-5.43130.19811470.158226802827100
5.4313-53.47680.22491370.17612694283199

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