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- PDB-1zz3: Crystal structure of a HDAC-like protein with CypX bound -

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Basic information

Entry
Database: PDB / ID: 1zz3
TitleCrystal structure of a HDAC-like protein with CypX bound
ComponentsHistone deacetylase-like amidohydrolase
KeywordsHYDROLASE
Function / homology
Function and homology information


Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / histone deacetylase activity / negative regulation of transcription by RNA polymerase II / metal ion binding / cytoplasm
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
3-CYCLOPENTYL-N-HYDROXYPROPANAMIDE / : / Histone deacetylase-like amidohydrolase
Similarity search - Component
Biological speciesAlcaligenaceae bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 Å
AuthorsNielsen, T.K. / Hildmann, C. / Dickmanns, A. / Schwienhorst, A. / Ficner, R.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal structure of a bacterial class 2 histone deacetylase homologue
Authors: Nielsen, T.K. / Hildmann, C. / Dickmanns, A. / Schwienhorst, A. / Ficner, R.
History
DepositionJun 13, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 29, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Mar 13, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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

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Assembly

Deposited unit
A: Histone deacetylase-like amidohydrolase
B: Histone deacetylase-like amidohydrolase
C: Histone deacetylase-like amidohydrolase
D: Histone deacetylase-like amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,90220
Polymers157,6984
Non-polymers1,20316
Water23,2031288
1
A: Histone deacetylase-like amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7255
Polymers39,4251
Non-polymers3014
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone deacetylase-like amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7255
Polymers39,4251
Non-polymers3014
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Histone deacetylase-like amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7255
Polymers39,4251
Non-polymers3014
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Histone deacetylase-like amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7255
Polymers39,4251
Non-polymers3014
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Histone deacetylase-like amidohydrolase
D: Histone deacetylase-like amidohydrolase
hetero molecules

B: Histone deacetylase-like amidohydrolase
C: Histone deacetylase-like amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,90220
Polymers157,6984
Non-polymers1,20316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,y-1/2,-z1
Buried area15040 Å2
ΔGint-245 kcal/mol
Surface area42140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.098, 94.486, 122.632
Angle α, β, γ (deg.)90.00, 104.27, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 5 / Auth seq-ID: 2 - 368 / Label seq-ID: 2 - 368

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
DetailsProtein is a monomer

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Components

#1: Protein
Histone deacetylase-like amidohydrolase / HDAC-like amidohydrolase / HDAH


Mass: 39424.602 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenaceae bacterium (bacteria) / Strain: FB188 / Plasmid: pQE / Production host: Escherichia coli (E. coli) / Strain (production host): M15
References: UniProt: Q70I53, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Chemical
ChemComp-3YP / 3-CYCLOPENTYL-N-HYDROXYPROPANAMIDE


Mass: 157.210 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO2
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1288 / 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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: NaCl, Na-cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97848 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97848 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å
Reflection shellResolution: 1.75→1.81 Å / % possible all: 72.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.76→44.77 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.122 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19116 7349 5 %RANDOM
Rwork0.15618 ---
obs0.15795 139270 97.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.739 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.76→44.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10988 0 56 1288 12332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02111347
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.94715474
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.22851464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.45223.206496
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.335151648
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0281582
X-RAY DIFFRACTIONr_chiral_restr0.1020.21718
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028844
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2250.26314
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.27806
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.21076
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.20.237
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.2135
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2420.255
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7371.57271
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.251211603
X-RAY DIFFRACTIONr_scbond_it2.47834120
X-RAY DIFFRACTIONr_scangle_it3.6974.53871
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1468medium positional0.160.5
2B1468medium positional0.230.5
3C1468medium positional0.130.5
4D1468medium positional0.150.5
1A1244loose positional0.495
2B1244loose positional0.685
3C1244loose positional0.495
4D1244loose positional0.525
1A1468medium thermal1.582
2B1468medium thermal1.82
3C1468medium thermal1.552
4D1468medium thermal1.442
1A1244loose thermal2.1310
2B1244loose thermal2.4510
3C1244loose thermal2.1810
4D1244loose thermal1.9510
LS refinement shellResolution: 1.757→1.803 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 458 -
Rwork0.224 8614 -
obs--82.25 %

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