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- PDB-3slc: Crystal structure of apo form of acetate kinase (AckA) from Salmo... -

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Basic information

Entry
Database: PDB / ID: 3slc
TitleCrystal structure of apo form of acetate kinase (AckA) from Salmonella typhimurium
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 / phosphorylation / 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
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 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 24, 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

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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
C: Acetate kinase
D: Acetate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,4738
Polymers180,2254
Non-polymers2484
Water3,675204
1
A: Acetate kinase
B: Acetate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2995
Polymers90,1122
Non-polymers1863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint-44 kcal/mol
Surface area29660 Å2
MethodPISA
2
C: Acetate kinase
D: Acetate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1753
Polymers90,1122
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-47 kcal/mol
Surface area29520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)283.159, 62.168, 91.695
Angle α, β, γ (deg.)90.00, 93.57, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Acetate kinase / / Acetokinase


Mass: 45056.242 Da / Num. of mol.: 4
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.23 Å3/Da / Density % sol: 44.96 %
Crystal growTemperature: 298 K / Method: under-oil microbatch / pH: 7.5
Details: 0.1M HEPES, 30%(w/v) PEG 4000, 0.2M Calcium Chloride, pH 7.5, UNDER-OIL MICROBATCH, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 5, 2009 / Details: Mirror
RadiationMonochromator: Osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 43980 / Num. obs: 42614 / % possible obs: 96.9 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.138
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.558 / Mean I/σ(I) obs: 2.06 / Num. unique all: 4322 / % possible all: 84.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IIR

2iir


Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.868 / SU B: 36.705 / SU ML: 0.334 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.429 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28324 2151 5.1 %RANDOM
Rwork0.22082 ---
obs0.224 40430 96.54 %-
all-44122 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.703 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å2-0.19 Å2
2--1.03 Å20 Å2
3----0.67 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11736 0 16 204 11956
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02111972
X-RAY DIFFRACTIONr_angle_refined_deg0.9771.9616223
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.02451577
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.15724.367490
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.382151936
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4181557
X-RAY DIFFRACTIONr_chiral_restr0.0660.21868
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0219017
X-RAY DIFFRACTIONr_mcbond_it0.1621.57797
X-RAY DIFFRACTIONr_mcangle_it0.309212409
X-RAY DIFFRACTIONr_scbond_it0.4334175
X-RAY DIFFRACTIONr_scangle_it0.7564.53812
LS refinement shellResolution: 2.702→2.772 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 133 -
Rwork0.346 2379 -
obs--78.72 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.853-0.85440.36571.0145-0.22241.49540.07320.2317-0.0049-0.0883-0.0414-0.08120.12450.4411-0.03180.06690.0297-0.00050.1496-0.01440.0882-40.2311-4.243932.5785
21.5405-0.6798-0.15041.63-0.22640.86330.0490.3250.1334-0.1779-0.03840.235-0.1083-0.0989-0.01060.0812-0.0017-0.02750.08070.0440.1696-68.875621.239725.4179
31.82480.35770.49881.0382-0.01332.3364-0.117-0.1710.3181-0.02530.0760.2965-0.6218-0.99170.0410.25760.26020.02790.6610.03730.16784.93950.263524.3481
40.765-0.17760.03330.27840.13653.33450.01540.186-0.0211-0.08380.0645-0.09530.3663-0.048-0.07990.1359-0.05390.0050.0981-0.04430.104733.7362-20.598512.8934
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 400
2X-RAY DIFFRACTION2B3 - 400
3X-RAY DIFFRACTION3C3 - 400
4X-RAY DIFFRACTION4D3 - 400

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