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- PDB-3sk3: Crystal structure of Salmonella typhimurium acetate kinase (AckA)... -

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Basic information

Entry
Database: PDB / ID: 3sk3
TitleCrystal structure of Salmonella typhimurium acetate kinase (AckA) with citrate bound at the dimeric interface
ComponentsAcetate kinase
KeywordsTRANSFERASE / Actin-like ATPase domain / ASKHA superfamily of phosphotransferase / Acetokinase / ATP binding / Phosphotransferase
Function / homology
Function and homology information


formate kinase activity / acetate kinase / propionate kinase activity / acetate kinase activity / acetate metabolic process / acetyl-CoA biosynthetic process / magnesium ion binding / ATP binding / cytosol
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
CITRIC ACID / Acetate kinase AckA
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsChittori, S. / Savithri, H.S. / Murthy, M.R.N.
CitationJournal: Bmc Struct.Biol. / Year: 2012
Title: Structural and mechanistic investigations on Salmonella typhimurium acetate kinase (AckA): identification of a putative ligand binding pocket at the dimeric interface
Authors: Chittori, S. / Savithri, H.S. / Murthy, M.R.N.
History
DepositionJun 22, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Nov 1, 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_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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)90,5537
Polymers90,1122
Non-polymers4405
Water7,963442
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-10 kcal/mol
Surface area30230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.012, 78.500, 97.480
Angle α, β, γ (deg.)90.00, 116.37, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-621-

HOH

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Components

#1: Protein Acetate kinase / Acetokinase


Mass: 45056.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: 12529 / Gene: ackA / Plasmid: pRSET C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P63411, acetate kinase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.87 Å3/Da / Density % sol: 57.18 %
Crystal growTemperature: 298 K / Method: under-oil microbatch / pH: 7.5
Details: 0.1M HEPES, 1.4M Sodium citrate, pH 7.5, UNDER-OIL MICROBATCH, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 28, 2009 / Details: Bent collimating mirror and toroid
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 80227 / % possible obs: 98.6 % / Redundancy: 4.3 % / Biso Wilson estimate: 41.9 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 15.9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.786 / Mean I/σ(I) obs: 2.18 / % possible all: 90.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IIR

2iir


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.31 / SU ML: 0.096 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22459 3977 5 %RANDOM
Rwork0.18992 ---
obs0.1917 75099 98.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.551 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å2-0.99 Å2
2--1.49 Å20 Å2
3----1.54 Å2
Refine analyzeLuzzati coordinate error obs: 0.237 Å
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5804 0 29 442 6275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0215976
X-RAY DIFFRACTIONr_angle_refined_deg1.4141.9618098
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9085781
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.84124.427253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.8515983
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7011529
X-RAY DIFFRACTIONr_chiral_restr0.0980.2925
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214503
X-RAY DIFFRACTIONr_mcbond_it0.8581.53831
X-RAY DIFFRACTIONr_mcangle_it1.54926121
X-RAY DIFFRACTIONr_scbond_it2.38832145
X-RAY DIFFRACTIONr_scangle_it3.9044.51970
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.425 300 -
Rwork0.344 4885 -
obs--87.67 %

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