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- PDB-3r34: Crystal structure of Arthrobacter sp. strain SU 4-hydroxybenzoyl ... -

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Basic information

Entry
Database: PDB / ID: 3r34
TitleCrystal structure of Arthrobacter sp. strain SU 4-hydroxybenzoyl CoA thioesterase mutant E73D complexed with CoA
Components4-hydroxybenzoyl-CoA thioesterase
KeywordsHYDROLASE / THIOESTERASE / HOTDOG-fold / 4-Hydroxybenzoyl-CoA
Function / homology
Function and homology information


4-hydroxybenzoyl-CoA thioesterase / 4-hydroxybenzoyl-CoA thioesterase activity / 1,4-dihydroxy-2-naphthoyl-CoA thioesterase activity / 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
COENZYME A / 4-hydroxybenzoyl-CoA thioesterase
Similarity search - Component
Biological speciesArthrobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHolden, H.M. / Thoden, J.B. / Song, F. / Zhuang, Z. / Trujillo, M. / Dunaway-Mariano, D.
CitationJournal: Biochemistry / Year: 2012
Title: The Catalytic Mechanism of the Hotdog-fold Enzyme Superfamily 4-Hydroxybenzoyl-CoA Thioesterase from Arthrobacter sp. Strain SU.
Authors: Song, F. / Thoden, J.B. / Zhuang, Z. / Latham, J. / Trujillo, M. / Holden, H.M. / Dunaway-Mariano, D.
History
DepositionMar 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Sep 19, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 13, 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
B: 4-hydroxybenzoyl-CoA thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4025
Polymers32,8052
Non-polymers1,5973
Water4,035224
1
A: 4-hydroxybenzoyl-CoA thioesterase
B: 4-hydroxybenzoyl-CoA thioesterase
hetero molecules

A: 4-hydroxybenzoyl-CoA thioesterase
B: 4-hydroxybenzoyl-CoA thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,80410
Polymers65,6104
Non-polymers3,1946
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+2/31
Buried area14740 Å2
ΔGint-11 kcal/mol
Surface area20340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.700, 112.700, 59.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein 4-hydroxybenzoyl-CoA thioesterase / 4-HBA-CoA thioesterase


Mass: 16402.402 Da / Num. of mol.: 2 / Mutation: E73D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter sp. (bacteria) / Gene: fcbC, fcbC1 / Plasmid: pET23B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q04416, 4-hydroxybenzoyl-CoA thioesterase
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 3.35 Å3/Da / Density % sol: 63.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG3400, 200 mM LiCl, 100 mM MOPS, 1 mM 4-Hydroxybenzoyl-CoA, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Sep 8, 2002 / Details: goebel mirrors
RadiationMonochromator: ni-filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→100 Å / Num. all: 37116 / Num. obs: 37116 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 32.1
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2243 / Rsym value: 0.264 / % possible all: 78.6

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Processing

Software
NameVersionClassification
FRAMBOdata collection
AMoREphasing
REFMAC5.5.0066refinement
SAINTdata reduction
SAINTdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Q4S

1q4s


Resolution: 1.8→97.6 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.592 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2174 1960 5 %RANDOM
Rwork0.18954 ---
all0.19095 33116 --
obs0.19095 37116 95.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.032 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å2-0.57 Å20 Å2
2---1.13 Å20 Å2
3---1.7 Å2
Refinement stepCycle: LAST / Resolution: 1.8→97.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2141 0 100 224 2465
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212306
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1211.9773151
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6845279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.18222.475101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76615339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3161522
X-RAY DIFFRACTIONr_chiral_restr0.1650.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211736
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.6821.51395
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.54622245
X-RAY DIFFRACTIONr_scbond_it4.0843911
X-RAY DIFFRACTIONr_scangle_it5.9164.5906
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 114 -
Rwork0.331 2243 -
obs--78.59 %

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