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- PDB-2pzh: YbgC thioesterase (Hp0496) from Helicobacter pylori -

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Basic information

Entry
Database: PDB / ID: 2pzh
TitleYbgC thioesterase (Hp0496) from Helicobacter pylori
ComponentsHypothetical protein HP_0496
KeywordsHYDROLASE / lipid / acyl-CoA / bacterial membrane / Tol-Pal system / thioesterase / Hot-dog fold
Function / homology
Function and homology information


fatty acyl-CoA hydrolase activity / Hydrolases; Acting on ester bonds; Thioester hydrolases / lipid metabolic process
Similarity search - Function
4-hydroxybenzoyl-CoA thioesterase, active site / 4-hydroxybenzoyl-CoA thioesterase family active site. / Acyl-CoA thioester hydrolase YbgC/YbaW family / : / Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Acyl-CoA thioesterase YbgC
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAngelini, A. / Cendron, L. / Goncalves, S. / Zanotti, G. / Terradot, L.
Citation
Journal: Proteins / Year: 2008
Title: Structural and enzymatic characterization of HP0496, a YbgC thioesterase from Helicobacter pylori.
Authors: Angelini, A. / Cendron, L. / Goncalves, S. / Zanotti, G. / Terradot, L.
#1: Journal: BMC Bioinformatics / Year: 2004
Title: The Hotdog fold: wrapping up a superfamily of thioesterases and dehydratases
Authors: Dillon, S.C. / Bateman, A.
#2: Journal: J.Biol.Chem. / Year: 1998
Title: The three-dimensional structure of 4-hydroxybenzoyl-CoA thioesterase from Pseudomonas sp. Strain CBS-3
Authors: Benning, M.M. / Wesemberg, G. / Liu, R. / Taylor, K.L. / Dunway-Mariano, D. / Holden, H.M.
History
DepositionMay 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein HP_0496
C: Hypothetical protein HP_0496
D: Hypothetical protein HP_0496
B: Hypothetical protein HP_0496


Theoretical massNumber of molelcules
Total (without water)63,4174
Polymers63,4174
Non-polymers00
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9080 Å2
ΔGint-46 kcal/mol
Surface area23170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.860, 99.206, 107.288
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31D
41B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 5 / Auth seq-ID: 1 - 132 / Label seq-ID: 3 - 134

Dom-IDAuth asym-IDLabel asym-ID
1AA
2CB
3DC
4BD
DetailsThe biological assembly is the homo-tetramer (chains A,B,C,D)

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Components

#1: Protein
Hypothetical protein HP_0496


Mass: 15854.352 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: HP0496 / Plasmid: pET151/D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: P94842
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 41.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100mM Tris, 20% Ethanol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 19, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.7→45 Å / Num. all: 53355 / Num. obs: 53355 / % possible obs: 90.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 22
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.7 / Num. unique all: 6452 / % possible all: 76.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S5U

1s5u


Resolution: 1.7→45 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.924 / SU B: 2.542 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0.5 / ESU R: 0.145 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25114 2686 5 %RANDOM
Rwork0.20873 ---
obs0.21088 50627 89.8 %-
all-53355 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.851 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.7→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4419 0 0 295 4714
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224557
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.9626154
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6735539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.31923.333228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31115817
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1321532
X-RAY DIFFRACTIONr_chiral_restr0.0820.2666
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023476
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2510.32166
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3240.53216
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.5566
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2740.338
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2360.520
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.10722756
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.74734383
X-RAY DIFFRACTIONr_scbond_it1.23122002
X-RAY DIFFRACTIONr_scangle_it1.7731766
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
1A526medium positional0.260.5
2C526medium positional0.270.5
3D526medium positional0.210.5
4B526medium positional0.30.5
1A560loose positional0.765
2C560loose positional0.765
3D560loose positional0.675
4B560loose positional0.755
1A526medium thermal1.232
2C526medium thermal1.622
3D526medium thermal1.132
4B526medium thermal2.852
1A560loose thermal1.7910
2C560loose thermal2.1810
3D560loose thermal1.7210
4B560loose thermal3.6810
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 168 -
Rwork0.286 3084 -
obs--75.4 %

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