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- PDB-1bvq: THREE-DIMENSIONAL STRUCTURE OF 4-HYDROXYBENZOYL COA THIOESTERASE ... -

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Basic information

Entry
Database: PDB / ID: 1bvq
TitleTHREE-DIMENSIONAL STRUCTURE OF 4-HYDROXYBENZOYL COA THIOESTERASE FROM PSEUDOMONAS SP. STRAIN CBS-3.
ComponentsPROTEIN (4-HYDROXYBENZOYL COA THIOESTERASE)
KeywordsHYDROLASE
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-hydroxybenzoyl-CoA thioesterase
Similarity search - Component
Biological speciesPseudomonas sp. CBS3 (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2 Å
AuthorsHolden, H.M. / Benning, M.M. / Dunaway-Mariano, D.
CitationJournal: J.Biol.Chem. / Year: 1998
Title: The three-dimensional structure of 4-hydroxybenzoyl-CoA thioesterase from Pseudomonas sp. Strain CBS-3.
Authors: Benning, M.M. / Wesenberg, G. / Liu, R. / Taylor, K.L. / Dunaway-Mariano, D. / Holden, H.M.
History
DepositionSep 16, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 23, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: PROTEIN (4-HYDROXYBENZOYL COA THIOESTERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3792
Polymers16,1401
Non-polymers2381
Water1,18966
1
A: PROTEIN (4-HYDROXYBENZOYL COA THIOESTERASE)
hetero molecules

A: PROTEIN (4-HYDROXYBENZOYL COA THIOESTERASE)
hetero molecules

A: PROTEIN (4-HYDROXYBENZOYL COA THIOESTERASE)
hetero molecules

A: PROTEIN (4-HYDROXYBENZOYL COA THIOESTERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5158
Polymers64,5624
Non-polymers9534
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
crystal symmetry operation3_755-x+2,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Unit cell
Length a, b, c (Å)49.600, 56.000, 93.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein PROTEIN (4-HYDROXYBENZOYL COA THIOESTERASE)


Mass: 16140.452 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas sp. CBS3 (bacteria) / Strain: CBS-3 / References: UniProt: P56653, EC: 3.8.1.6
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.03 Å3/Da / Density % sol: 39 %
Crystal growpH: 7
Details: 0.9 M AMMONIUM SULFATE 1.0 % 2-METHYL-2,4-PENTADIOL 50 MM HEPES PH 7.0
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.9 Mammonium sulfate11
21 %(v/v)MPD11
350 mMHEPES11
45 mM11NaN3

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Mar 15, 1997 / Details: 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: 2→30 Å / Num. obs: 8775 / % possible obs: 96 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.04
Reflection shellResolution: 2→2.09 Å / Rmerge(I) obs: 0.135 / % possible all: 90
Reflection shell
*PLUS
% possible obs: 90 %

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Processing

Software
NameVersionClassification
TNT5Erefinement
XDSdata reduction
XCALIBREdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2→30 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO /
Num. reflection% reflection
obs8775 96 %
Solvent computationBsol: 377 Å2 / ksol: 0.9129 e/Å3
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1115 0 15 66 1196
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_bond_d0.015
X-RAY DIFFRACTIONt_angle_deg2.65
X-RAY DIFFRACTIONt_dihedral_angle_d18.5
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.005
X-RAY DIFFRACTIONt_gen_planes0.004
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.04822
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / σ(F): 0 / Rfactor obs: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.65
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg18.5
X-RAY DIFFRACTIONt_planar_d0.005
X-RAY DIFFRACTIONt_plane_restr0.004

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