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- PDB-1c3p: CRYSTAL STRUCTURE OF AN HDAC HOMOLOG FROM AQUIFEX AEOLICUS -

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Basic information

Entry
Database: PDB / ID: 1c3p
TitleCRYSTAL STRUCTURE OF AN HDAC HOMOLOG FROM AQUIFEX AEOLICUS
ComponentsPROTEIN (HDLP (HISTONE DEACETYLASE-LIKE PROTEIN))
KeywordsLYASE / ALPHA/BETA FOLD
Function / homology
Function and homology information


acetoin catabolic process / histone deacetylase activity / epigenetic regulation of gene expression / metal ion binding
Similarity search - Function
Acetoin utilization protein AcuC / Histone deacetylase domain / Arginase; Chain A / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Acetoin utilization protein AcuC
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsFinnin, M.S. / Donigian, J.R. / Pavletich, N.P.
CitationJournal: Nature / Year: 1999
Title: Structures of a histone deacetylase homologue bound to the TSA and SAHA inhibitors.
Authors: Finnin, M.S. / Donigian, J.R. / Cohen, A. / Richon, V.M. / Rifkind, R.A. / Marks, P.A. / Breslow, R. / Pavletich, N.P.
History
DepositionJul 28, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (HDLP (HISTONE DEACETYLASE-LIKE PROTEIN))


Theoretical massNumber of molelcules
Total (without water)42,7341
Polymers42,7341
Non-polymers00
Water4,107228
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.400, 93.800, 78.700
Angle α, β, γ (deg.)90.00, 96.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PROTEIN (HDLP (HISTONE DEACETYLASE-LIKE PROTEIN))


Mass: 42733.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Plasmid: PGEX-4T3 / Production host: Escherichia coli (E. coli) / References: UniProt: O67135
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.2 Å3/Da / Density % sol: 44.16 %
Crystal growpH: 7
Details: PEG 1500, SODIUM CHLORIDE, ISOPROPANOL, TRIS-HCL, pH 7.00
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17.5 %isopropanol1reservoir
228 %PEG15001reservoir
3425 mM1reservoirNaCl
4100 mMTris-Cl1reservoir

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 134952 / Redundancy: 4 % / Rmerge(I) obs: 0.029
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 20 Å / Num. obs: 32143 / % possible obs: 92.3 % / Redundancy: 4 % / Num. measured all: 134952

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.8→20 Å / σ(F): 1
RfactorNum. reflection
Rfree0.24 1606
Rwork0.198 -
obs0.198 31550
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2985 0 0 228 3213
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.63

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