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- PDB-1c3s: CRYSTAL STRUCTURE OF AN HDAC HOMOLOG COMPLEXED WITH SAHA -

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Basic information

Entry
Database: PDB / ID: 1c3s
TitleCRYSTAL STRUCTURE OF AN HDAC HOMOLOG COMPLEXED WITH SAHA
ComponentsHDLP (HISTONE DEACETYLASE-LIKE PROTEIN)
KeywordsLYASE / ALPHA/BETA FOLD / HYDROXAMIC ACID / PENTA-COORDINATED ZINC / CHARGE-RELAY SYSTEM
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
OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE / : / Acetoin utilization protein AcuC
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.5 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 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)43,0313
Polymers42,7021
Non-polymers3302
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.495, 94.155, 78.977
Angle α, β, γ (deg.)90, 97.024, 90
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 42701.645 Da / Num. of mol.: 1 / Mutation: C75S, C77S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Plasmid: PGEX-4T3 / Production host: Escherichia coli (E. coli) / References: GenBank: AAC07100, UniProt: O67135*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SHH / OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE / SAHA


Mass: 264.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N2O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.22 Å3/Da / Density % sol: 44.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: TERT-BUTANOL, PEG 1500, POTASSIUM CHLORIDE, BIS-TRIS PROPANE-Cl, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
123 %tert-butanol1reservoir
227 %PEG15001reservoir
3600 mM1reservoirKCl
4100 mMBis-Tris propane-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: 2.5→20 Å / Num. all: 11748 / % possible obs: 90.6 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.086
Reflection
*PLUS
Num. obs: 11748 / Num. measured all: 27568

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.5→20 Å / σ(F): 1
RfactorNum. reflection
Rfree0.277 559
Rwork0.2 -
all-111113
obs-111113
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2989 0 20 142 3151
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 20 Å / Num. reflection obs: 11113 / σ(F): 1 / Rfactor obs: 0.2 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.58
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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