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- PDB-5g10: Pseudomonas aeruginosa HDAH bound to 9,9,9 trifluoro-8,8-dihydroy... -

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Basic information

Entry
Database: PDB / ID: 5g10
TitlePseudomonas aeruginosa HDAH bound to 9,9,9 trifluoro-8,8-dihydroy-N-phenylnonanamide
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 / hydrolase 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
Chem-6DK / : / Histone deacetylase-like amidohydrolase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 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 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

Downloads & links

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Assembly

Deposited unit
A: HDAH
B: HDAH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,86010
Polymers81,9342
Non-polymers9268
Water11,277626
1
A: HDAH
B: HDAH
hetero molecules

A: HDAH
B: HDAH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,72120
Polymers163,8694
Non-polymers1,85216
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area13770 Å2
ΔGint-94.2 kcal/mol
Surface area44400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.740, 81.740, 205.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein HDAH


Mass: 40967.242 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: Chemical ChemComp-6DK / 9,9,9-tris(fluoranyl)-8,8-bis(oxidanyl)-~{N}-phenyl-nonanamide


Mass: 319.319 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H20F3NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 626 / 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: 2.09 Å3/Da / Density % sol: 47 % / 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: 1.71→75.94 Å / Num. obs: 75585 / % possible obs: 99.3 % / Observed criterion σ(I): 2.1 / Redundancy: 7.7 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 8.2
Reflection shellResolution: 1.71→1.75 Å / Redundancy: 8 % / Rmerge(I) obs: 1.18 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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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: 1.71→75.94 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / SU B: 5.348 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19366 3771 5 %RANDOM
Rwork0.15787 ---
obs0.15967 71707 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.653 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20 Å2
2---0.66 Å20 Å2
3---1.33 Å2
Refinement stepCycle: LAST / Resolution: 1.71→75.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5683 0 50 626 6359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0195901
X-RAY DIFFRACTIONr_bond_other_d0.0050.025520
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.9617966
X-RAY DIFFRACTIONr_angle_other_deg1.204312624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.925744
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.74522.624282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.72115866
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0721560
X-RAY DIFFRACTIONr_chiral_restr0.0810.2847
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216818
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021442
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_it0.8231.0962982
X-RAY DIFFRACTIONr_mcbond_other0.8211.0962981
X-RAY DIFFRACTIONr_mcangle_it1.0521.6463726
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.951.2412918
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.005311421
X-RAY DIFFRACTIONr_sphericity_free17.345160
X-RAY DIFFRACTIONr_sphericity_bonded3.899511719
LS refinement shellResolution: 1.714→1.759 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 267 -
Rwork0.239 5227 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0345-2.0296-2.42265.45223.37625.5629-0.0529-0.18560.00510.1250.0842-0.17230.04210.2287-0.03140.02030.0034-0.03450.14550.01780.0655-8.78432.32222.9786
23.0244-0.3494-1.86453.2873-0.25825.9515-0.0914-0.4105-0.08480.2916-0.00630.05670.36670.06230.09770.1225-0.0104-0.00350.07670.01130.1356-11.6341-1.739-6.0176
33.64011.97750.0571.4619-0.23280.20110.0040.0164-0.2229-0.0421-0.0144-0.16260.07620.0320.01040.1060.0355-0.02150.05990.00590.0954-12.46190.155519.2004
41.74810.64240.05643.20881.57563.1349-0.03370.1026-0.23-0.1122-0.0201-0.01240.2354-0.03080.05380.05930.0231-0.00780.0990.01510.0736-17.7159-4.687817.106
52.8174-0.0328-1.09783.47910.3264.10560.0053-0.0807-0.02470.07040.0350.14510.1424-0.0894-0.04030.0088-0.0033-0.00850.02020.01440.0591-26.3048-0.494219.3216
61.36170.3804-0.62850.7399-0.63421.42510.0059-0.08730.1440.1020.04230.1065-0.0956-0.0799-0.04810.01910.01340.00690.0198-0.00960.03-26.646215.182415.6343
73.34691.2611-1.36350.8886-0.83143.080.0611-0.1580.1710.1143-0.05650.0066-0.15180.0662-0.00460.04780.0154-0.0230.0287-0.01090.0285-12.052714.650321.1809
83.23220.1358-0.91761.7013-0.60431.43020.0475-0.20250.35880.09440.00120.1307-0.1941-0.0299-0.04870.1098-0.0012-0.02140.0261-0.02480.0617-22.24627.5368.4158
95.5411-1.70723.71012.111-2.36735.62010.05280.0713-0.1735-0.1885-0.08490.01880.1064-0.03980.03210.11570.01480.01110.0133-0.01660.0737-0.41159.9557-23.0215
102.7348-0.9968-0.59382.2604-0.38346.70180.06850.2189-0.0014-0.38140.0026-0.108-0.17990.3563-0.0710.1052-0.0257-0.01090.1202-0.01380.13423.270313.42716.0992
112.29761.74010.04033.16320.23930.12210.077-0.1763-0.03290.1871-0.0215-0.18060.02810.0596-0.05550.07550.04130.00080.075-0.00090.10944.716715.4931-16.0559
122.13110.07230.56522.06310.2952.46450.0533-0.03380.04280.0245-0.0141-0.23110.07470.0755-0.03930.02090.0120.02280.01040.0150.06183.354121.3716-19.2036
130.64280.2149-0.24381.3027-0.25011.17680.02370.06840.0364-0.1076-0.02640.0231-0.0242-0.01930.00270.01830.0043-0.00990.01060.00820.019-12.194325.4254-17.7289
141.5164-0.6923-1.32272.23951.51531.6354-0.04970.2179-0.1813-0.2231-0.18570.3211-0.0118-0.25220.23540.1103-0.0059-0.06160.09660.00570.0931-25.344514.0085-9.4438
152.76160.3707-0.50543.3403-0.40136.7539-0.03980.1643-0.0445-0.1832-0.03370.0649-0.134-0.19030.07350.080.0259-0.01710.06650.03210.1056-24.094735.1557-18.2481
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 17
2X-RAY DIFFRACTION2A18 - 36
3X-RAY DIFFRACTION3A37 - 84
4X-RAY DIFFRACTION4A85 - 141
5X-RAY DIFFRACTION5A142 - 173
6X-RAY DIFFRACTION6A174 - 296
7X-RAY DIFFRACTION7A297 - 337
8X-RAY DIFFRACTION8A338 - 371
9X-RAY DIFFRACTION9B2 - 17
10X-RAY DIFFRACTION10B18 - 35
11X-RAY DIFFRACTION11B36 - 101
12X-RAY DIFFRACTION12B102 - 168
13X-RAY DIFFRACTION13B169 - 332
14X-RAY DIFFRACTION14B333 - 358
15X-RAY DIFFRACTION15B359 - 377

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