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- PDB-4h0o: Crystal Structure of Acetate Kinase from Entamoeba histolytica -

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Basic information

Entry
Database: PDB / ID: 4h0o
TitleCrystal Structure of Acetate Kinase from Entamoeba histolytica
ComponentsAcetate kinase
KeywordsTRANSFERASE / pyrophosphate-dependent acetate kinase / ASKHA (acetate and sugar kinase / hsc70 / actin) superfamily / Ribonuclease H-like fold
Function / homology
Function and homology information


acetate kinase / acetate kinase activity / acetate metabolic process / acetyl-CoA biosynthetic process / magnesium ion binding / ATP binding
Similarity search - Function
Acetate/propionate kinase / 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
Probable acetate kinase
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsThaker, T.M. / Tanabe, M. / Iverson, T.M.
CitationJournal: J.Struct.Biol. / Year: 2013
Title: Crystal structures of acetate kinases from the eukaryotic pathogens Entamoeba histolytica and Cryptococcus neoformans.
Authors: Thaker, T.M. / Tanabe, M. / Fowler, M.L. / Preininger, A.M. / Ingram-Smith, C. / Smith, K.S. / Iverson, T.M.
History
DepositionSep 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetate kinase
B: Acetate kinase


Theoretical massNumber of molelcules
Total (without water)89,4072
Polymers89,4072
Non-polymers00
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-49 kcal/mol
Surface area32280 Å2
MethodPISA
2
A: Acetate kinase
B: Acetate kinase

A: Acetate kinase
B: Acetate kinase

A: Acetate kinase
B: Acetate kinase

A: Acetate kinase
B: Acetate kinase


Theoretical massNumber of molelcules
Total (without water)357,6298
Polymers357,6298
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area33730 Å2
ΔGint-246 kcal/mol
Surface area116750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.885, 126.874, 145.559
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Acetate kinase


Mass: 44703.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Strain: HM-1:IMSS / Gene: ACKA, EHI_170010 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): YBS121 / References: UniProt: C4M1C3, EC: 2.7.2.12
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.55 Å3/Da / Density % sol: 51.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 0.6 M potassium/sodium tartrate, 10 mM iron(III) chloride, 50 mM ADA, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 17, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.4→45.319 Å / Num. all: 44735 / Num. obs: 44735 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.7 % / Rsym value: 0.138 / Net I/σ(I): 15.6
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 3 / Rsym value: 0.44 / % possible all: 93.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G99

1g99


Resolution: 2.4→45.319 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 21.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2243 1601 4.47 %
Rwork0.1788 --
obs0.1809 35836 99.16 %
all-44735 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→45.319 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5986 0 0 163 6149
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046093
X-RAY DIFFRACTIONf_angle_d0.8328221
X-RAY DIFFRACTIONf_dihedral_angle_d13.162267
X-RAY DIFFRACTIONf_chiral_restr0.055959
X-RAY DIFFRACTIONf_plane_restr0.0031040
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.47750.24321350.22192899X-RAY DIFFRACTION94
2.4775-2.5660.26881420.22323036X-RAY DIFFRACTION98
2.566-2.66870.27841440.22143081X-RAY DIFFRACTION99
2.6687-2.79020.28141470.20543116X-RAY DIFFRACTION100
2.7902-2.93730.26211450.20023109X-RAY DIFFRACTION100
2.9373-3.12120.26031450.19813109X-RAY DIFFRACTION100
3.1212-3.36220.24381470.18743122X-RAY DIFFRACTION100
3.3622-3.70040.20671460.16573132X-RAY DIFFRACTION100
3.7004-4.23550.18621470.15583154X-RAY DIFFRACTION100
4.2355-5.33490.17131500.15013182X-RAY DIFFRACTION100
5.3349-45.32690.23541530.17283295X-RAY DIFFRACTION100

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