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- PDB-4be4: Closed conformation of O. piceae sterol esterase -

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Basic information

Entry
Database: PDB / ID: 4be4
TitleClosed conformation of O. piceae sterol esterase
ComponentsSTEROL ESTERASE
KeywordsHYDROLASE
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / lipid metabolic process / hydrolase activity
Similarity search - Function
: / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / Carboxylic ester hydrolase
Similarity search - Component
Biological speciesOPHIOSTOMA PICEAE (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGutierrez-Fernandez, J. / Vaquero, M.E. / Prieto, A. / Barriuso, J. / Gonzalez, M.J. / Hermoso, J.A.
CitationJournal: J.Struct.Biol. / Year: 2014
Title: Crystal Structures of Ophiostoma Piceae Sterol Esterase: Structural Insights Into Activation Mechanism and Product Release.
Authors: Gutierrez-Fernandez, J. / Vaquero, M.E. / Prieto, A. / Barriuso, J. / Martinez, M.J. / Hermoso, J.A.
History
DepositionMar 5, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: STEROL ESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,22119
Polymers59,2141
Non-polymers2,00718
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)119.274, 119.274, 206.774
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

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Protein / Sugars , 2 types, 3 molecules A

#1: Protein STEROL ESTERASE


Mass: 59213.535 Da / Num. of mol.: 1 / Fragment: RESIDUES 13-549
Source method: isolated from a genetically manipulated source
Details: N-ACETYLGLUCOSAMINE GLYCOSYLATIONS IN POSITIONS 362 AND 380
Source: (gene. exp.) OPHIOSTOMA PICEAE (fungus) / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): KM71 / References: UniProt: Q2TFW1, sterol esterase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 257 molecules

#3: Chemical
ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H8O2
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsN-ACETYL-D-GLUCOSAMINE (NAG): COVALENTLY BOUND TO ASN362 AND ASN380 BY N-GLYCOSIDIC LINKAGES

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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: 3.55 Å3/Da / Density % sol: 65.4 % / Description: NONE
Crystal growpH: 6.5
Details: 10% 1,4-DIOXANE, 0.1 M MES PH 6.5, 1.6 M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97908
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 2.6→46.23 Å / Num. obs: 26901 / % possible obs: 98.5 % / Observed criterion σ(I): 1.9 / Redundancy: 3.4 % / Biso Wilson estimate: 37.51 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 6.9
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 1.9 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→46.228 Å / SU ML: 0.63 / σ(F): 1.33 / Phase error: 22.23 / Stereochemistry target values: ML
Details: THE FIRST 8 AMINO ACIDS (EAEAYVEF) CORRESPOND TO A PURIFICATION TAG. ONLY THE LAST TWO AA (EF) WERE VISIBLE IN THE ELECTRON DENSITY MAP.
RfactorNum. reflection% reflection
Rfree0.2207 1344 5 %
Rwork0.164 --
obs0.1669 26656 97 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.977 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.0205 Å20 Å20 Å2
2--5.0205 Å20 Å2
3----10.0411 Å2
Refinement stepCycle: LAST / Resolution: 2.6→46.228 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4140 0 127 241 4508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074372
X-RAY DIFFRACTIONf_angle_d1.0785933
X-RAY DIFFRACTIONf_dihedral_angle_d12.581577
X-RAY DIFFRACTIONf_chiral_restr0.073656
X-RAY DIFFRACTIONf_plane_restr0.004754
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6002-2.69310.37931290.25742441X-RAY DIFFRACTION96
2.6931-2.8010.30361330.22672462X-RAY DIFFRACTION97
2.801-2.92840.28061400.20362483X-RAY DIFFRACTION97
2.9284-3.08280.29391270.19562522X-RAY DIFFRACTION98
3.0828-3.27590.23611490.17582503X-RAY DIFFRACTION98
3.2759-3.52870.20711430.15242511X-RAY DIFFRACTION97
3.5287-3.88370.16531250.13482567X-RAY DIFFRACTION98
3.8837-4.44530.17321330.11822587X-RAY DIFFRACTION98
4.4453-5.5990.17311340.12892567X-RAY DIFFRACTION97
5.599-46.23510.22931310.18942669X-RAY DIFFRACTION93
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.97340.8762-0.40332.03390.24991.4837-0.19220.6164-0.1805-0.37410.20540.2020.501-0.91990.03120.3312-0.14960.02340.3679-0.05770.2106-26.826340.0393-49.2222
22.16361.94562.53192.36981.47884.0617-0.0864-0.03710.37030.1497-0.17630.21-0.1314-0.55110.26420.26390.00360.02970.2531-0.05470.3477-25.861156.5362-32.2748
32.61680.5109-0.76240.9809-0.23051.8221-0.10510.1325-0.1618-0.175-0.02350.02870.3395-0.48330.09490.2316-0.08720.02130.2219-0.03210.1299-20.835143.5877-39.1054
41.42980.3571-0.29580.8772-0.33831.81110.0345-0.1717-0.16690.0901-0.0750.15180.5066-0.2880.08240.3585-0.1150.05510.224-0.00950.1949-20.292235.2603-31.7964
51.30590.2902-0.14290.87630.06550.5971-0.096-0.0473-0.06130.0884-0.0210.1410.4013-0.55090.04490.3468-0.15380.09660.41440.01130.2285-26.167840.2221-22.6761
60.7422-0.28180.02520.77140.19641.8715-0.0561-0.2449-0.07590.1271-0.01920.0390.22710.02540.06550.2178-0.04610.0440.20870.03150.1483-7.611148.9759-18.703
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 11:61)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 62:98)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 99:187)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 188:277)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 278:357)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 358:549)

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