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- PDB-7cof: Cholesterol esterase from Burkholderia stabilis (orthorhombic cry... -

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Basic information

Entry
Database: PDB / ID: 7cof
TitleCholesterol esterase from Burkholderia stabilis (orthorhombic crystal form)
ComponentsAlpha/beta hydrolase
KeywordsHYDROLASE / cholesterol esterase / lipase / Burkholderia stabilis
Function / homologyalpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / metal ion binding / IMIDAZOLE / ISOPROPYL ALCOHOL / Alpha/beta hydrolase
Function and homology information
Biological speciesBurkholderia stabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.084 Å
AuthorsYasutake, Y. / Tamura, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
New Energy and Industrial Technology Development Organization (NEDO) Japan
CitationJournal: Int.J.Biol.Macromol. / Year: 2021
Title: Bacterial triacylglycerol lipase is a potential cholesterol esterase: Identification of a key determinant for sterol-binding specificity.
Authors: Yasutake, Y. / Konishi, K. / Muramatsu, S. / Yoshida, K. / Aburatani, S. / Sakasegawa, S.I. / Tamura, T.
History
DepositionAug 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6497
Polymers33,2361
Non-polymers4146
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, This protein shares ~90% aa sequence identity to Burkholderia cepacia lipase (monomeric enzyme). No oligomeric assembly is detected in the present crystallographic study.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area12970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.241, 61.365, 147.177
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-585-

HOH

21A-785-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alpha/beta hydrolase / Cholesterol esterase


Mass: 33235.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Burkholderia stabilis (bacteria) / References: UniProt: A0A1Y1BQV9

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Non-polymers , 5 types, 315 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 1.98 Å3/Da / Density % sol: 37.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Imidazole, PEG2250, 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.08→50 Å / Num. obs: 103889 / % possible obs: 93 % / Redundancy: 6.02 % / Rrim(I) all: 0.04 / Net I/σ(I): 28.9
Reflection shellResolution: 1.08→1.15 Å / Mean I/σ(I) obs: 7.13 / Num. unique obs: 11081 / Rrim(I) all: 0.22 / % possible all: 62

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YS1

1ys1


Resolution: 1.084→32.012 Å / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 8.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1181 5062 4.9 %
Rwork0.0979 --
obs0.0988 103377 92.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.084→32.012 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2345 0 26 309 2680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112500
X-RAY DIFFRACTIONf_angle_d1.3143435
X-RAY DIFFRACTIONf_dihedral_angle_d14.551877
X-RAY DIFFRACTIONf_chiral_restr0.375404
X-RAY DIFFRACTIONf_plane_restr0.01448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0842-1.09650.2093620.16561170X-RAY DIFFRACTION34
1.0965-1.10940.1541950.14061923X-RAY DIFFRACTION55
1.1094-1.12290.13561000.11882246X-RAY DIFFRACTION64
1.1229-1.13710.13231370.1122452X-RAY DIFFRACTION70
1.1371-1.15210.10091500.09672749X-RAY DIFFRACTION79
1.1521-1.16790.12651600.09373041X-RAY DIFFRACTION87
1.1679-1.18460.12171920.08843306X-RAY DIFFRACTION95
1.1846-1.20220.10371770.08533506X-RAY DIFFRACTION100
1.2022-1.2210.10811720.0813501X-RAY DIFFRACTION100
1.221-1.2410.09932020.08123501X-RAY DIFFRACTION100
1.241-1.26240.10291850.08163449X-RAY DIFFRACTION100
1.2624-1.28540.11361990.08053534X-RAY DIFFRACTION99
1.2854-1.31010.12611740.08013467X-RAY DIFFRACTION100
1.3101-1.33690.09681710.0783522X-RAY DIFFRACTION100
1.3369-1.36590.09871660.08183567X-RAY DIFFRACTION100
1.3659-1.39770.10241570.07773502X-RAY DIFFRACTION100
1.3977-1.43270.10672080.0733488X-RAY DIFFRACTION100
1.4327-1.47140.09791850.07483518X-RAY DIFFRACTION100
1.4714-1.51470.09751910.06983521X-RAY DIFFRACTION100
1.5147-1.56360.09091700.06783561X-RAY DIFFRACTION100
1.5636-1.61950.0921860.07283526X-RAY DIFFRACTION100
1.6195-1.68430.09751800.07443513X-RAY DIFFRACTION100
1.6843-1.7610.10331640.07683573X-RAY DIFFRACTION100
1.761-1.85380.10691670.08373553X-RAY DIFFRACTION100
1.8538-1.96990.10651850.08563528X-RAY DIFFRACTION100
1.9699-2.1220.10541760.09013591X-RAY DIFFRACTION100
2.122-2.33550.10851950.09353550X-RAY DIFFRACTION100
2.3355-2.67330.12121750.10213589X-RAY DIFFRACTION99
2.6733-3.36750.1321750.12123616X-RAY DIFFRACTION100
3.3675-32.0120.16782060.15613752X-RAY DIFFRACTION100

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