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- PDB-1lo7: X-ray structure of 4-Hydroxybenzoyl CoA Thioesterase complexed wi... -

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Basic information

Entry
Database: PDB / ID: 1lo7
TitleX-ray structure of 4-Hydroxybenzoyl CoA Thioesterase complexed with 4-hydroxyphenacyl CoA
Components4-hydroxybenzoyl-CoA Thioesterase
KeywordsHYDROLASE / Thioesterase / hot dog fold / catalytic mechanism
Function / homology
Function and homology information


4-hydroxybenzoyl-CoA thioesterase / 4-hydroxybenzoyl-CoA thioesterase activity
Similarity search - Function
4-hydroxybenzoyl-CoA thioesterase, active site / 4-hydroxybenzoyl-CoA thioesterase family active site. / Thioesterase-like superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
4-HYDROXYPHENACYL COENZYME A / 4-hydroxybenzoyl-CoA thioesterase
Similarity search - Component
Biological speciesPseudomonas sp. CBS3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsThoden, J.B. / Holden, H.M. / Zhuang, Z. / Dunaway-Mariano, D.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: X-ray crystallographic analyses of inhibitor and substrate complexes of wild-type and mutant 4-hydroxybenzoyl-CoA thioesterase.
Authors: Thoden, J.B. / Holden, H.M. / Zhuang, Z. / Dunaway-Mariano, D.
History
DepositionMay 6, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / 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 / _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: 4-hydroxybenzoyl-CoA Thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1664
Polymers16,1401
Non-polymers1,0263
Water3,117173
1
A: 4-hydroxybenzoyl-CoA Thioesterase
hetero molecules

A: 4-hydroxybenzoyl-CoA Thioesterase
hetero molecules

A: 4-hydroxybenzoyl-CoA Thioesterase
hetero molecules

A: 4-hydroxybenzoyl-CoA Thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,66516
Polymers64,5624
Non-polymers4,10312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)51.500, 55.200, 93.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Cell settingorthorhombic
Space group name H-MI222

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Components

#1: Protein 4-hydroxybenzoyl-CoA Thioesterase / / E.C.3.1.2.23


Mass: 16140.452 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. CBS3 (bacteria) / Strain: CBS-3 / Gene: 4HBT_PSESP / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3)
References: UniProt: P56653, 4-hydroxybenzoyl-CoA thioesterase
#2: Chemical ChemComp-4CO / 4-HYDROXYPHENACYL COENZYME A


Mass: 901.666 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H42N7O18P3S
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.06 Å3/Da / Density % sol: 40.22 %
Crystal growTemperature: 277 K / Method: batch / pH: 5
Details: PEG 8000, potassium chloride, succinate, 4-hydroxyphenacyl CoA, pH 5.0, batch at 277K
Crystal grow
*PLUS
Temperature: 4 R.T. / pH: 7 / Method: sparse matrix screening
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
114 mg/mlprotein1drop
210 mMHEPES1droppH7.0
3200 mM1dropKCl
45 mM4-hydroxyphenacyl-CoA1drop
510 %PEG80001reservoir
62 %1reservoirMe2SO
7100 mMsuccinate1reservoirpH5.0

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.981 Å
DetectorType: SBC-2 / Detector: CCD / Date: Mar 28, 2001
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.981 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. all: 20139 / Num. obs: 20139 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rsym value: 0.038 / Net I/σ(I): 30.6
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 4 / Num. unique all: 1828 / Rsym value: 0.173 / % possible all: 87
Reflection
*PLUS
Rmerge(I) obs: 0.038
Reflection shell
*PLUS
% possible obs: 87 % / Num. unique obs: 1828 / Rmerge(I) obs: 0.173

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Processing

Software
NameVersionClassification
AMoREphasing
TNT5Frefinement
d*TREKdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BVQ

1bvq


Resolution: 1.5→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.198 2014 -RANDOM
Rwork0.161 ---
all0.163 20139 --
obs0.163 20139 94.1 %-
Refinement stepCycle: LAST / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1136 0 66 173 1375
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.013
X-RAY DIFFRACTIONt_angle_deg2.31
Refinement
*PLUS
Num. reflection obs: 18125 / Rfactor all: 0.163 / Rfactor Rfree: 0.198 / Rfactor Rwork: 0.161
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg15.8
X-RAY DIFFRACTIONt_planar_d0.008
X-RAY DIFFRACTIONt_plane_restr0.011

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