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- PDB-7cog: Cholesterol esterase from Burkholderia stabilis (monoclinic cryst... -

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Basic information

Entry
Database: PDB / ID: 7cog
TitleCholesterol esterase from Burkholderia stabilis (monoclinic 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 / Alpha/beta hydrolase
Function and homology information
Biological speciesBurkholderia stabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.098 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 1.2Oct 30, 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

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Assembly

Deposited unit
A: Alpha/beta hydrolase
B: Alpha/beta hydrolase
C: Alpha/beta hydrolase
D: Alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,1048
Polymers132,9434
Non-polymers1604
Water1,58588
1
A: Alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2762
Polymers33,2361
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area13000 Å2
MethodPISA
2
B: Alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2762
Polymers33,2361
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area13070 Å2
MethodPISA
3
C: Alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2762
Polymers33,2361
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area13430 Å2
MethodPISA
4
D: Alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2762
Polymers33,2361
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area12910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.292, 47.092, 70.082
Angle α, β, γ (deg.)90.00, 90.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Alpha/beta hydrolase / Cholesterol esterase


Mass: 33235.844 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: WP_096474789.1 / Source: (natural) Burkholderia stabilis (bacteria) / References: UniProt: A0A1Y1BQV9
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
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: 2.31 Å3/Da / Density % sol: 46.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: sodium citrate, PEG4000, 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.098→50 Å / Num. obs: 71702 / % possible obs: 99.5 % / Redundancy: 3.36 % / Rrim(I) all: 0.122 / Net I/σ(I): 8.7
Reflection shellResolution: 2.098→2.23 Å / Mean I/σ(I) obs: 2.31 / Num. unique obs: 11384 / Rrim(I) all: 0.552

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Processing

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

1ys1


Resolution: 2.098→46.497 Å / Cross valid method: THROUGHOUT / σ(F): 2.2 / Phase error: 42.52 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2517 3554 4.96 %
Rwork0.2193 --
obs0.2373 71684 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.098→46.497 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9380 0 4 88 9472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029576
X-RAY DIFFRACTIONf_angle_d0.49913120
X-RAY DIFFRACTIONf_dihedral_angle_d9.2535536
X-RAY DIFFRACTIONf_chiral_restr0.041560
X-RAY DIFFRACTIONf_plane_restr0.0031708
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0995-2.13570.29421500.29393413X-RAY DIFFRACTION94
2.1357-2.17450.33271740.29593329X-RAY DIFFRACTION94
2.1745-2.21640.35931650.29583390X-RAY DIFFRACTION95
2.2164-2.26160.29151880.28663379X-RAY DIFFRACTION94
2.2616-2.31070.30991710.27683345X-RAY DIFFRACTION95
2.3107-2.36450.27511770.27593395X-RAY DIFFRACTION95
2.3645-2.42360.25891490.26953423X-RAY DIFFRACTION96
2.4236-2.48910.29251920.26243410X-RAY DIFFRACTION95
2.4891-2.56230.27261680.24573353X-RAY DIFFRACTION95
2.5623-2.64490.30181770.24473394X-RAY DIFFRACTION95
2.6449-2.73940.26461890.24313373X-RAY DIFFRACTION95
2.7394-2.8490.2461560.23733413X-RAY DIFFRACTION96
2.849-2.97860.25451800.23493407X-RAY DIFFRACTION95
2.9786-3.13540.25721830.23573422X-RAY DIFFRACTION95
3.1354-3.33160.28261820.23353395X-RAY DIFFRACTION95
3.3316-3.58850.27352090.23023378X-RAY DIFFRACTION94
3.5885-3.94890.28131820.21273434X-RAY DIFFRACTION95
3.9489-4.51860.20351930.19433382X-RAY DIFFRACTION94
4.5186-5.68660.19931880.19913473X-RAY DIFFRACTION94
5.6866-29.95010.25171680.2213583X-RAY DIFFRACTION95

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