+Open data
-Basic information
Entry | Database: PDB / ID: 4h0o | ||||||
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Title | Crystal Structure of Acetate Kinase from Entamoeba histolytica | ||||||
Components | Acetate kinase | ||||||
Keywords | TRANSFERASE / pyrophosphate-dependent acetate kinase / ASKHA (acetate and sugar kinase / hsc70 / actin) superfamily / Ribonuclease H-like fold | ||||||
Function / homology | Function and homology information acetate kinase / organic acid metabolic process / acetate kinase activity / acetyl-CoA biosynthetic process / magnesium ion binding / ATP binding Similarity search - Function | ||||||
Biological species | Entamoeba histolytica (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Thaker, T.M. / Tanabe, M. / Iverson, T.M. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4h0o.cif.gz | 160.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4h0o.ent.gz | 127.4 KB | Display | PDB format |
PDBx/mmJSON format | 4h0o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4h0o_validation.pdf.gz | 434.4 KB | Display | wwPDB validaton report |
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Full document | 4h0o_full_validation.pdf.gz | 440.7 KB | Display | |
Data in XML | 4h0o_validation.xml.gz | 28.8 KB | Display | |
Data in CIF | 4h0o_validation.cif.gz | 40 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h0/4h0o ftp://data.pdbj.org/pub/pdb/validation_reports/h0/4h0o | HTTPS FTP |
-Related structure data
Related structure data | 4h0pC 1g99S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | 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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.82 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 17, 2008 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 2.4→2.44 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 3 / Rsym value: 0.44 / % possible all: 93.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1G99 Resolution: 2.4→45.319 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 21.56 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→45.319 Å
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Refine LS restraints |
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LS refinement shell |
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