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- PDB-1ki9: Adenylate kinase from Methanococcus thermolithotrophicus -

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Basic information

Entry
Database: PDB / ID: 1ki9
TitleAdenylate kinase from Methanococcus thermolithotrophicus
Componentsadenylate kinase
KeywordsSIGNALING PROTEIN / TRANSFERASE / kinase / phosphotransferase
Function / homology
Function and homology information


adenylate kinase / AMP kinase activity / ATP binding / cytoplasm
Similarity search - Function
Adenylate kinase AdkA / AAA domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMethanothermococcus thermolithotrophicus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsCriswell, A.R. / Konisky, J. / Phillips Jr., G.N.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Structures of thermophilic and mesophilic adenylate kinases from the genus Methanococcus
Authors: Criswell, A.R. / Bae, E. / Stec, B. / Konisky, J. / Phillips Jr., G.N.
History
DepositionDec 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1May 5, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: adenylate kinase


Theoretical massNumber of molelcules
Total (without water)64,4603
Polymers64,4603
Non-polymers00
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-36 kcal/mol
Surface area26790 Å2
MethodPISA
2
A: adenylate kinase
B: adenylate kinase
C: adenylate kinase

A: adenylate kinase
B: adenylate kinase
C: adenylate kinase


Theoretical massNumber of molelcules
Total (without water)128,9216
Polymers128,9216
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_557y,x,-z+21
Buried area12030 Å2
ΔGint-96 kcal/mol
Surface area50390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.500, 128.500, 88.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Cell settingtetragonal
Space group name H-MP4212

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Components

#1: Protein adenylate kinase / E.C.2.7.4.3 / ATP-AMP TRANSPHOSPHORYLASE


Mass: 21486.764 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermococcus thermolithotrophicus (archaea)
Gene: adk / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P43410, adenylate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.8 Å3/Da / Density % sol: 55.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 6000, MPD, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP at 298K
Crystal grow
*PLUS
pH: 4.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
23 mMAMP1drop
33 mMADP1drop
40.1 MHEPES1reservoirpH4.6
510 %(w/v)PEG60001reservoir
65 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 14, 1999 / Details: confocal
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 27043 / Num. obs: 25623 / % possible obs: 94.7 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.068
Reflection
*PLUS
Highest resolution: 2.76 Å / % possible obs: 95.1 % / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
Highest resolution: 2.76 Å / Lowest resolution: 2.95 Å / % possible obs: 94.4 % / Rmerge(I) obs: 0.175

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Processing

Software
NameVersionClassification
CrystalCleardata collection
d*TREKdata reduction
AMoREphasing
CNS0.9refinement
CrystalClear(MSC/RIGAKU)data reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1NKS

1nks


Resolution: 2.76→30.78 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 157151.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1812 9.9 %RANDOM
Rwork0.204 ---
all0.2041 18370 --
obs0.2041 18370 94 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.3445 Å2 / ksol: 0.33371 e/Å3
Displacement parametersBiso mean: 43 Å2
Baniso -1Baniso -2Baniso -3
1-2.83 Å20 Å20 Å2
2--2.83 Å20 Å2
3----5.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.76→30.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4498 0 0 160 4658
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d20.7
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it2.351.5
X-RAY DIFFRACTIONc_mcangle_it3.792
X-RAY DIFFRACTIONc_scbond_it3.422
X-RAY DIFFRACTIONc_scangle_it4.882.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76

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