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- PDB-1q4t: crystal structure of 4-hydroxybenzoyl CoA thioesterase from Arthr... -

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Basic information

Entry
Database: PDB / ID: 1q4t
Titlecrystal structure of 4-hydroxybenzoyl CoA thioesterase from Arthrobacter sp. strain SU complexed with 4-hydroxyphenyl CoA
ComponentsThioesterase
KeywordsHYDROLASE / thioesterase / hot-dog
Function / homology
Function and homology information


4-hydroxybenzoyl-CoA thioesterase / 4-hydroxybenzoyl-CoA thioesterase activity / 1,4-dihydroxy-2-naphthoyl-CoA thioesterase activity / phylloquinone biosynthetic process / menaquinone biosynthetic process / peroxisome / cytosol
Similarity search - Function
Phenylacetic acid degradation-related domain / Thioesterase domain / Thioesterase 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 speciesArthrobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.6 Å
AuthorsThoden, J.B. / Zhuang, Z. / Dunaway-Mariano, D. / Holden, H.M.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: The Structure of 4-Hydroxybenzoyl-CoA Thioesterase from Arthrobacter sp. strain SU
Authors: Thoden, J.B. / Zhuang, Z. / Dunaway-Mariano, D. / Holden, H.M.
History
DepositionAug 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Thioesterase
B: Thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,96411
Polymers32,8332
Non-polymers2,1319
Water5,332296
1
A: Thioesterase
B: Thioesterase
hetero molecules

A: Thioesterase
B: Thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,92822
Polymers65,6664
Non-polymers4,26318
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+2/31
Buried area18070 Å2
ΔGint-116 kcal/mol
Surface area19240 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)112.500, 112.500, 60.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Detailshomotetramer The tetramer is generated from rotation of the crystallographically independent dimer around the crystallographic 2-fold axis

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Components

#1: Protein Thioesterase / FCBC2 / 4-chlorobenzoate thioesterase


Mass: 16416.428 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter sp. (bacteria) / Strain: SU / Gene: FCBC / Plasmid: pET23b / Production host: Escherichia coli (E. coli)
References: UniProt: Q04416, 4-hydroxybenzoyl-CoA thioesterase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-4CO / 4-HYDROXYPHENACYL COENZYME A


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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 3.37 Å3/Da / Density % sol: 63.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG-3400, MOPS, LiCl, KCl, 4-hydroxyphenacyl CoA, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
118 mg/mlprotein1drop
210 mMHEPES1droppH7.5
3150 mM1dropKCl
41 mM1,4-dithio-D,L-threitol1drop
517-20 %PEG34001reservoir
6100 mMMOPS1reservoirpH7.0
7200 mM1reservoirLiCl

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: May 10, 2002 / Details: goebel optics
RadiationMonochromator: goebel optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 58147 / Num. obs: 58147 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rsym value: 0.049 / Net I/σ(I): 35.1
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 4693 / Rsym value: 0.391 / % possible all: 81
Reflection
*PLUS
Num. obs: 58417 / % possible obs: 97.1 % / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
% possible obs: 81 % / Num. unique obs: 4693 / Rmerge(I) obs: 0.391

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Processing

Software
NameClassification
TNTrefinement
SAINTdata reduction
CNSrefinement
FRAMBOdata collection
SAINTdata scaling
CNSphasing
RefinementMethod to determine structure: MIR / Resolution: 1.6→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.219 5827 -RANDOM
Rwork0.179 ---
obs0.18 58147 97.1 %-
all-58147 --
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2148 0 132 296 2576
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg2.25
Refinement
*PLUS
Num. reflection obs: 52320 / Rfactor obs: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg16.9
X-RAY DIFFRACTIONt_planar_d0.007
X-RAY DIFFRACTIONt_plane_restr0.012

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