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- PDB-5wh9: Structure of BH1999 gentisyl-coenzyme A thioesterase -

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Basic information

Entry
Database: PDB / ID: 5wh9
TitleStructure of BH1999 gentisyl-coenzyme A thioesterase
Components4-hydroxybenzoyl-CoA thioesterase
KeywordsHYDROLASE / Gentisyl CoA Thioesterase / Hotdog Fold
Function / homologyAcyl-CoA thioester hydrolase YbgC/YbaW family / thiolester hydrolase activity / : / Thioesterase-like superfamily / Thioesterase superfamily / HotDog domain superfamily / 4-hydroxybenzoyl-CoA thioesterase
Function and homology information
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFinci, L.I. / Allen, K.N.
CitationJournal: To Be Published
Title: Structure of BH1999 gentisyl-coenzyme A thioesterase
Authors: Finci, L.I. / Allen, K.N.
History
DepositionJul 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
C: 4-hydroxybenzoyl-CoA thioesterase
D: 4-hydroxybenzoyl-CoA thioesterase


Theoretical massNumber of molelcules
Total (without water)63,0534
Polymers63,0534
Non-polymers00
Water2,918162
1
A: 4-hydroxybenzoyl-CoA thioesterase
B: 4-hydroxybenzoyl-CoA thioesterase

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


Theoretical massNumber of molelcules
Total (without water)63,0534
Polymers63,0534
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area6570 Å2
ΔGint-56 kcal/mol
Surface area21230 Å2
MethodPISA
2
C: 4-hydroxybenzoyl-CoA thioesterase
D: 4-hydroxybenzoyl-CoA thioesterase

C: 4-hydroxybenzoyl-CoA thioesterase
D: 4-hydroxybenzoyl-CoA thioesterase


Theoretical massNumber of molelcules
Total (without water)63,0534
Polymers63,0534
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_576x,-y+2,-z+11
Buried area7240 Å2
ΔGint-65 kcal/mol
Surface area21410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.656, 80.758, 120.282
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

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Components

#1: Protein
4-hydroxybenzoyl-CoA thioesterase


Mass: 15763.230 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125) (bacteria)
Strain: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125
Gene: BH1999 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KBC9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.07 Å3/Da / Density % sol: 40.48 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 100 mM MOPS buffer with 200 mM NaCl and an equal volume of 0.24 M malonate pH 5.8, 18% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Dec 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→38.3 Å / Num. obs: 21470 / % possible obs: 90 % / Redundancy: 2.46 % / Net I/σ(I): 13.7

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
SAINTdata reduction
PROTEUM PLUSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BVQ

1bvq


Resolution: 2.3→38.28 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2635 1090 5.08 %
Rwork0.2206 --
obs0.2227 21469 89.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→38.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4008 0 0 163 4171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0194132
X-RAY DIFFRACTIONf_angle_d1.9655582
X-RAY DIFFRACTIONf_dihedral_angle_d14.9951468
X-RAY DIFFRACTIONf_chiral_restr0.107595
X-RAY DIFFRACTIONf_plane_restr0.011699
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.40470.37061000.30012058X-RAY DIFFRACTION73
2.4047-2.53140.31451110.28252209X-RAY DIFFRACTION79
2.5314-2.690.31941370.26362341X-RAY DIFFRACTION84
2.69-2.89760.32031220.2532560X-RAY DIFFRACTION92
2.8976-3.18910.27981490.24262731X-RAY DIFFRACTION97
3.1891-3.65030.24491740.19962765X-RAY DIFFRACTION98
3.6503-4.59770.21711540.18122814X-RAY DIFFRACTION98
4.5977-38.28490.24781430.20652901X-RAY DIFFRACTION96

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