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- PDB-3r3b: Crystal structure of Arthrobacter sp. strain SU 4-hydroxybenzoyl ... -

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Basic information

Entry
Database: PDB / ID: 3r3b
TitleCrystal structure of Arthrobacter sp. strain SU 4-hydroxybenzoyl CoA thioesterase mutant Q58A complexed with 4-hydroxyphenacyl 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
4-HYDROXYPHENACYL 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

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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)34,5224
Polymers32,7192
Non-polymers1,8032
Water4,648258
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)69,0448
Polymers65,4384
Non-polymers3,6074
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+2/31
Buried area15610 Å2
ΔGint-65 kcal/mol
Surface area19700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.500, 112.500, 59.500
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: 16359.376 Da / Num. of mol.: 2 / Mutation: Q58A
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-4CO / 4-HYDROXYPHENACYL COENZYME A


Mass: 901.666 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H42N7O18P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 3.32 Å3/Da / Density % sol: 62.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG3400, 100 mM MOPS, 200 mM LiCl, 1mM 4-HYDROXYPHENACYL 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: 1.54178 Å
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: May 23, 2002 / Details: goebel mirrors
RadiationMonochromator: ni-filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.8→100 Å / Num. all: 36193 / Num. obs: 36193 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 34.9
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 3.1 / Num. unique all: 2347 / Rsym value: 0.251 / % possible all: 83.3

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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→97.43 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.49 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22119 1899 5 %RANDOM
Rwork0.18265 ---
all0.18457 36193 --
obs0.18457 36193 94.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.176 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å2-0.22 Å20 Å2
2---0.45 Å20 Å2
3---0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.8→97.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2135 0 116 258 2509
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212332
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0341.9873190
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8515279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.31322.2100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.43215342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7411523
X-RAY DIFFRACTIONr_chiral_restr0.1540.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211757
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_it1.5221.51399
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.41522255
X-RAY DIFFRACTIONr_scbond_it3.7973933
X-RAY DIFFRACTIONr_scangle_it5.4454.5935
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
Rfree0.323 119 -
Rwork0.287 2347 -
obs--83.25 %

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