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- PDB-1tuy: Acetate Kinase complexed with ADP, AlF3 and acetate -

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Basic information

Entry
Database: PDB / ID: 1tuy
TitleAcetate Kinase complexed with ADP, AlF3 and acetate
ComponentsAcetate kinase
KeywordsTRANSFERASE / alpha/beta / ASKHA (acetate and sugar kinases / hsc70 / actin) superfamily / AlF3 and acetate
Function / homology
Function and homology information


acetate kinase / organic acid metabolic process / acetate kinase activity / acetyl-CoA biosynthetic process / phosphorylation / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Acetate and butyrate kinases family signature 2. / Acetate/propionate kinase / Aliphatic acid kinase, short-chain, conserved site / Acetate and butyrate kinases family signature 1. / Aliphatic acid kinase, short-chain / Acetokinase family / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / ADENOSINE-5'-DIPHOSPHATE / ALUMINUM FLUORIDE / Acetate kinase
Similarity search - Component
Biological speciesMethanosarcina thermophila (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGorrell, A. / Lawrence, S.H. / Ferry, J.G.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structural and Kinetic Analyses of Arginine Residues in the Active Site of the Acetate Kinase from Methanosarcina thermophila.
Authors: Gorrell, A. / Lawrence, S.H. / Ferry, J.G.
History
DepositionJun 25, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 10, 2014Group: Database references
Revision 1.4Feb 14, 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: Acetate kinase
B: Acetate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9187
Polymers86,8242
Non-polymers1,0945
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7800 Å2
ΔGint-71 kcal/mol
Surface area30230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.043, 67.196, 82.142
Angle α, β, γ (deg.)90.00, 103.13, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Acetate kinase / / Acetokinase


Mass: 43411.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina thermophila (archaea) / Gene: ACKA, ACK / Plasmid: pET-AK / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P38502, acetate kinase

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Non-polymers , 5 types, 54 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE / Aluminium fluoride


Mass: 83.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF3
#5: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.79 Å3/Da / Density % sol: 55.86 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: Tris, lithium chloride, aluminum chloride, sodium flouride, acetate, ammonium sulfate, ADP, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 310K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1.073 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.073 Å / Relative weight: 1
ReflectionResolution: 3→28.43 Å / Num. all: 30164 / Num. obs: 18882 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.106
Reflection shellResolution: 3→3.19 Å / Num. unique all: 2530 / % possible all: 85.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→28.43 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1756850.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1295 6.9 %RANDOM
Rwork0.201 ---
all0.206 ---
obs0.201 18882 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 25.5732 Å2 / ksol: 0.396248 e/Å3
Displacement parametersBiso mean: 14.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.75 Å20 Å24.35 Å2
2--2.96 Å20 Å2
3----0.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 3→28.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6066 0 67 49 6182
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.071.5
X-RAY DIFFRACTIONc_mcangle_it1.792
X-RAY DIFFRACTIONc_scbond_it1.672
X-RAY DIFFRACTIONc_scangle_it2.532.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.327 203 7.4 %
Rwork0.262 2530 -
obs--85.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2MERGE2_XPLOR_PAR.TXTMERGE2_XPLOR_TOP.TXT
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP

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