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- PDB-5g13: Pseudomonas aeruginosa HDAH (H143A) unliganded. -

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Basic information

Entry
Database: PDB / ID: 5g13
TitlePseudomonas aeruginosa HDAH (H143A) unliganded.
ComponentsHDAH
KeywordsHYDROLASE / HDAH / HDAC / HDLP
Function / homology
Function and homology information


Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / histone deacetylase activity / epigenetic regulation of gene expression / hydrolase activity / metal ion binding
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-like amidohydrolase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsKraemer, A. / Meyer-Almes, F.J. / Yildiz, O.
CitationJournal: Biochemistry / Year: 2016
Title: Crystal Structure of a Histone Deacetylase Homologue from Pseudomonas aeruginosa.
Authors: Kramer, A. / Wagner, T. / Yildiz, O. / Meyer-Almes, F.J.
History
DepositionMar 23, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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: HDAH
B: HDAH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,0888
Polymers81,8002
Non-polymers2876
Water8,215456
1
A: HDAH
B: HDAH
hetero molecules

A: HDAH
B: HDAH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,17516
Polymers163,6014
Non-polymers57412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area14860 Å2
ΔGint-237.1 kcal/mol
Surface area44610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.495, 81.495, 205.265
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2015-

HOH

21B-2068-

HOH

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Components

#1: Protein HDAH


Mass: 40900.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PA01 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HXM1
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-K / POTASSIUM ION


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


Mass: 18.015 Da / Num. of mol.: 456 / 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: 2.08 Å3/Da / Density % sol: 40.3 % / Description: NONE
Crystal growpH: 7.5 / Details: pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97902
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97902 Å / Relative weight: 1
ReflectionResolution: 1.99→75.74 Å / Num. obs: 48272 / % possible obs: 99.5 % / Observed criterion σ(I): 4.8 / Redundancy: 15.5 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 11.2
Reflection shellResolution: 1.99→2.05 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 4.8 / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5G0X

5g0x


Resolution: 1.99→75.74 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.919 / SU B: 3.774 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21723 2431 5 %RANDOM
Rwork0.17262 ---
obs0.17484 45724 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.739 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å20 Å20 Å2
2---1.02 Å20 Å2
3---2.03 Å2
Refinement stepCycle: LAST / Resolution: 1.99→75.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5671 0 6 456 6133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195839
X-RAY DIFFRACTIONr_bond_other_d0.0020.025473
X-RAY DIFFRACTIONr_angle_refined_deg1.3231.9547887
X-RAY DIFFRACTIONr_angle_other_deg0.981312519
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8295744
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.56122.643280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78615863
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1651560
X-RAY DIFFRACTIONr_chiral_restr0.080.2842
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216778
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021418
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9531.652982
X-RAY DIFFRACTIONr_mcbond_other0.9511.6492981
X-RAY DIFFRACTIONr_mcangle_it1.6282.4683724
X-RAY DIFFRACTIONr_mcangle_other1.6282.4693725
X-RAY DIFFRACTIONr_scbond_it1.2581.8022857
X-RAY DIFFRACTIONr_scbond_other1.2581.8042856
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1052.6474164
X-RAY DIFFRACTIONr_long_range_B_refined4.47613.7346794
X-RAY DIFFRACTIONr_long_range_B_other4.35613.6036718
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.99→2.042 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 162 -
Rwork0.181 3115 -
obs--93.74 %

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