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- PDB-4jlp: Crystal structure of R150K aquifex adenylate kinase mutant -

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Basic information

Entry
Database: PDB / ID: 4jlp
TitleCrystal structure of R150K aquifex adenylate kinase mutant
ComponentsAdenylate kinase
KeywordsTRANSFERASE / 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 / intracellular membrane-bounded organelle / 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: 1.433 Å
AuthorsCho, Y.-J. / Phung, L. / 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)47,6186
Polymers45,9102
Non-polymers1,7094
Water12,647702
1
A: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8093
Polymers22,9551
Non-polymers8542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8093
Polymers22,9551
Non-polymers8542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.010, 70.460, 85.580
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: 22954.801 Da / Num. of mol.: 2 / Fragment: transferase / Mutation: R150K
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.: 702 / 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: 44.1 %
Crystal growTemperature: 295 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 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: 1.43→36.57 Å / Num. all: 499971 / Num. obs: 75039 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 15.75 Å2 / Net I/σ(I): 17.5
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.43-1.510.2684.3199.8
4.53-36.570.03732.1199

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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: 1.433→36.064 Å / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.8833 / SU ML: 0.4 / σ(F): 1.35 / Phase error: 18.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1949 3791 5.06 %random
Rwork0.1529 ---
obs0.155 74937 99.9 %-
all-78728 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.393 Å2 / ksol: 0.344 e/Å3
Displacement parametersBiso max: 63.56 Å2 / Biso mean: 22.2692 Å2 / Biso min: 7.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.5846 Å20 Å2-0 Å2
2--1.551 Å20 Å2
3----0.9664 Å2
Refinement stepCycle: LAST / Resolution: 1.433→36.064 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3232 0 108 702 4042
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053557
X-RAY DIFFRACTIONf_angle_d1.2534837
X-RAY DIFFRACTIONf_chiral_restr0.07530
X-RAY DIFFRACTIONf_plane_restr0.006616
X-RAY DIFFRACTIONf_dihedral_angle_d14.9921432
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.433-1.45120.40181480.31032587273599
1.4512-1.47030.30781280.261126362764100
1.4703-1.49040.26821230.224425822705100
1.4904-1.51170.2621410.199226012742100
1.5117-1.53430.2491430.188126032746100
1.5343-1.55820.24781300.18226272757100
1.5582-1.58380.26591220.167726102732100
1.5838-1.61110.22461510.163625932744100
1.6111-1.64040.22041580.150526122770100
1.6404-1.67190.20681390.142625972736100
1.6719-1.70610.23521520.135826132765100
1.7061-1.74320.19131440.125225892733100
1.7432-1.78370.17631600.121226092769100
1.7837-1.82830.17711510.120826012752100
1.8283-1.87770.20731400.130426352775100
1.8777-1.9330.2071260.137326422768100
1.933-1.99540.20421400.148126002740100
1.9954-2.06670.19151380.15126542792100
2.0667-2.14940.19311400.157726342774100
2.1494-2.24720.19441330.143126392772100
2.2472-2.36570.19171300.140826692799100
2.3657-2.51390.16651250.149426672792100
2.5139-2.70790.20271330.157526742807100
2.7079-2.98030.18971370.162726582795100
2.9803-3.41130.17531500.147726912841100
3.4113-4.29670.17351570.139227032860100
4.2967-36.07570.18051520.16252820297299

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