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- PDB-1g99: AN ANCIENT ENZYME: ACETATE KINASE FROM METHANOSARCINA THERMOPHILA -

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Basic information

Entry
Database: PDB / ID: 1g99
TitleAN ANCIENT ENZYME: ACETATE KINASE FROM METHANOSARCINA THERMOPHILA
ComponentsACETATE KINASE
KeywordsTRANSFERASE / ALPHA/BETA / ASKHA (ACETATE AND SUGAR KINASES / HSC70 / ACTIN) SUPERFAMILY / CONSERVED EPSILON CONFORMATION / TWO SIMILAR DOMAINS
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
ADENOSINE-5'-DIPHOSPHATE / Acetate kinase
Similarity search - Component
Biological speciesMethanosarcina thermophila (archaea)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.5 Å
AuthorsBuss, K.A. / Cooper, D.R. / Ingram-Smith, C. / Ferry, J.G. / Sanders, D.A. / Hasson, M.S.
CitationJournal: J.Bacteriol. / Year: 2001
Title: Urkinase: structure of acetate kinase, a member of the ASKHA superfamily of phosphotransferases.
Authors: Buss, K.A. / Cooper, D.R. / Ingram-Smith, C. / Ferry, J.G. / Sanders, D.A. / Hasson, M.S.
History
DepositionNov 22, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Advisory / Experimental preparation / Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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)89,8356
Polymers88,7882
Non-polymers1,0474
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7930 Å2
ΔGint-88 kcal/mol
Surface area30210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.3, 67.4, 82.6
Angle α, β, γ (deg.)90.0, 102.9, 90.0
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ACETATE KINASE /


Mass: 44393.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina thermophila (archaea) / Gene: ACK / Plasmid: PML703 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P38502, acetate kinase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.77 Å3/Da / Density % sol: 55.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Ammonium sulfate, sodium HEPES, adenosine triphosphate, magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Crystal grow
*PLUS
Details: Buss, K.A., (1997) Protein Sci., 6, 2659.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
20.75 mMATP1drop
30.75 mM1dropMgCl2
4315 mMammonium sulfate1drop
50.8 mMdithiothreitol1drop
625 mMsodium HEPES1drop
71.7 Mammonium sulfate1reservoir
1acetate1drop0.0049mg

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 9, 1996 / Details: mirrors
RadiationMonochromator: 0.001 mm Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. all: 33872 / Num. obs: 32857 / % possible obs: 97 % / Redundancy: 5.6 % / Rsym value: 13
Reflection shellResolution: 2.5→2.7 Å / Rsym value: 13 / % possible all: 95
Reflection
*PLUS
Lowest resolution: 40 Å

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.5→36 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 1.5
RfactorNum. reflection% reflectionSelection details
Rfree0.1877 3266 -RANDOM
Rwork0.1466 ---
all-33872 --
obs-32857 97 %-
Displacement parametersBiso mean: 28.9227 Å2
Refinement stepCycle: LAST / Resolution: 2.5→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6056 0 64 158 6278
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011602
X-RAY DIFFRACTIONc_angle_deg1.55144
X-RAY DIFFRACTIONc_dihedral_angle_d23.17244
X-RAY DIFFRACTIONc_improper_angle_d0.9526
LS refinement shellResolution: 2.5→2.59 Å
RfactorNum. reflection% reflection
Rfree0.2179 316 -
Rwork0.1623 --
obs-2879 94.8 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 36 Å / σ(F): 1.5
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.17244
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9526

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