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- PDB-3c0y: Crystal structure of catalytic domain of human histone deacetylas... -

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Basic information

Entry
Database: PDB / ID: 3c0y
TitleCrystal structure of catalytic domain of human histone deacetylase HDAC7
ComponentsHistone deacetylase 7a
KeywordsHYDROLASE / HISTONE DEACETYLASE / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC / Alternative splicing / Chromatin regulator / Cytoplasm / Nucleus / Phosphoprotein / Polymorphism / Repressor / Transcription / Transcription regulation
Function / homology
Function and homology information


regulation of mRNA processing / histone deacetylase activity, hydrolytic mechanism / histone deacetylase / protein deacetylation / cell-cell junction assembly / SUMO transferase activity / negative regulation of non-canonical NF-kappaB signal transduction / positive regulation of cell migration involved in sprouting angiogenesis / protein lysine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides ...regulation of mRNA processing / histone deacetylase activity, hydrolytic mechanism / histone deacetylase / protein deacetylation / cell-cell junction assembly / SUMO transferase activity / negative regulation of non-canonical NF-kappaB signal transduction / positive regulation of cell migration involved in sprouting angiogenesis / protein lysine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / negative regulation of interleukin-2 production / histone deacetylase activity / Notch-HLH transcription pathway / histone deacetylase complex / protein sumoylation / negative regulation of osteoblast differentiation / vasculogenesis / SUMOylation of DNA damage response and repair proteins / 14-3-3 protein binding / protein kinase C binding / epigenetic regulation of gene expression / Regulation of PTEN gene transcription / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / transcription corepressor activity / DNA-binding transcription factor binding / chromatin binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / 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
: / Histone deacetylase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMin, J.R. / Schuetz, A. / Allali-Hassani, A. / Loppnau, P. / Kwiatkowski, N.P. / Mazitschek, R. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. ...Min, J.R. / Schuetz, A. / Allali-Hassani, A. / Loppnau, P. / Kwiatkowski, N.P. / Mazitschek, R. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Vedadi, M. / Bochkarev, A. / Plotnikov, A.N. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Human HDAC7 harbors a class IIa histone deacetylase-specific zinc binding motif and cryptic deacetylase activity.
Authors: Schuetz, A. / Min, J. / Allali-Hassani, A. / Schapira, M. / Shuen, M. / Loppnau, P. / Mazitschek, R. / Kwiatkowski, N.P. / Lewis, T.A. / Maglathin, R.L. / McLean, T.H. / Bochkarev, A. / ...Authors: Schuetz, A. / Min, J. / Allali-Hassani, A. / Schapira, M. / Shuen, M. / Loppnau, P. / Mazitschek, R. / Kwiatkowski, N.P. / Lewis, T.A. / Maglathin, R.L. / McLean, T.H. / Bochkarev, A. / Plotnikov, A.N. / Vedadi, M. / Arrowsmith, C.H.
History
DepositionJan 21, 2008Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 19, 2008ID: 2NVR
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 / 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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone deacetylase 7a
B: Histone deacetylase 7a
C: Histone deacetylase 7a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,18215
Polymers136,5553
Non-polymers62712
Water6,305350
1
A: Histone deacetylase 7a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7275
Polymers45,5181
Non-polymers2094
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Histone deacetylase 7a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7275
Polymers45,5181
Non-polymers2094
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Histone deacetylase 7a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7275
Polymers45,5181
Non-polymers2094
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.750, 81.750, 148.895
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Histone deacetylase 7a / HD7a / HDAC7


Mass: 45518.340 Da / Num. of mol.: 3 / Fragment: Catalytic domain: Residues 482-903
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC7A, HDAC7 / Plasmid: p28a-LIC / Production host: Escherichia coli (E. coli)
Strain (production host): BL21(DE3)Codon Plus RIL (Stratagen)
References: UniProt: Q8WUI4
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.1 Å3/Da / Density % sol: 41.53 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 13 % PEG 3350, 0.1 M HEPES pH 7.5, 10 % Isopropanol, 1 mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 29, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 65508 / Num. obs: 64241 / % possible obs: 98.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 33
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 2.6 / Num. unique all: 5579 / % possible all: 85.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2NVR

2nvr
PDB Unreleased entry


Resolution: 2.1→34.44 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.928 / SU B: 6.425 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.256 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26404 3222 5.1 %RANDOM
Rwork0.20174 ---
obs0.20499 60432 98.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.494 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.1→34.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8429 0 12 350 8791
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0218632
X-RAY DIFFRACTIONr_angle_refined_deg1.7871.93311709
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.94851106
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.48823.703397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.131151330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4971556
X-RAY DIFFRACTIONr_chiral_restr0.1280.21257
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026710
X-RAY DIFFRACTIONr_nbd_refined0.2370.24196
X-RAY DIFFRACTIONr_nbtor_refined0.3080.25753
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2463
X-RAY DIFFRACTIONr_metal_ion_refined0.2860.232
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.275
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.215
X-RAY DIFFRACTIONr_mcbond_it1.0111.55483
X-RAY DIFFRACTIONr_mcangle_it1.79328717
X-RAY DIFFRACTIONr_scbond_it2.68533173
X-RAY DIFFRACTIONr_scangle_it4.0554.52992
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 180 -
Rwork0.272 3826 -
obs--83.74 %

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