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- PDB-1kht: Adenylate kinase from Methanococcus voltae -

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Basic information

Entry
Database: PDB / ID: 1kht
TitleAdenylate kinase from Methanococcus voltae
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
ADENOSINE MONOPHOSPHATE / Adenylate kinase
Similarity search - Component
Biological speciesMethanococcus voltae (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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
DepositionNov 30, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 28, 2016Group: Other
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
C: adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6835
Polymers63,9893
Non-polymers6942
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-40 kcal/mol
Surface area24300 Å2
MethodPISA
2
A: adenylate kinase
B: adenylate kinase
C: adenylate kinase
hetero molecules

A: adenylate kinase
B: adenylate kinase
C: adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,36610
Polymers127,9776
Non-polymers1,3894
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+11
Buried area15130 Å2
ΔGint-96 kcal/mol
Surface area46130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)200.500, 200.500, 200.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Cell settingcubic
Space group name H-MI23

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Components

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


Mass: 21329.500 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus voltae (archaea) / Gene: adk / Plasmid: pET11b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P43411, adenylate kinase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 5.25 Å3/Da / Density % sol: 76.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4000, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP at 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
23 mMAMP1drop
33 mMADP1drop
40.1 Msodium acetate/acetic acid1reservoirpH4.6
58 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1.037 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 12, 1999 / Details: bent conical Si-mirror (Rh coating)
RadiationMonochromator: bend cylindrical Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.037 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 46286 / Num. obs: 39038 / % possible obs: 87.4 % / Biso Wilson estimate: 29.9 Å2
Reflection
*PLUS
% possible obs: 84.2 % / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.66 Å / % possible obs: 86.3 % / Rmerge(I) obs: 0.348

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Processing

Software
NameVersionClassification
XDSdata reduction
AMoREphasing
CNS0.9refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1NKS

1nks


Resolution: 2.5→33.42 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 961139.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 3917 10 %RANDOM
Rwork0.22 ---
all0.2201 39038 --
obs0.2201 39001 84.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.0305 Å2 / ksol: 0.33593 e/Å3
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.5→33.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4419 0 46 179 4644
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it2.212
X-RAY DIFFRACTIONc_scbond_it1.422
X-RAY DIFFRACTIONc_scangle_it2.242.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.309 665 10.1 %
Rwork0.289 5915 -
obs--86.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ADENOSINE.PARAMAMP.TOPOLOGY
Refinement
*PLUS
Highest resolution: 2.5 Å / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77

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