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- PDB-4upd: Open conformation of O. piceae sterol esterase mutant I544W -

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Open data


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Basic information

Entry
Database: PDB / ID: 4upd
TitleOpen conformation of O. piceae sterol esterase mutant I544W
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
Chem-7P9 / TRIETHYLENE GLYCOL / Carboxylic ester hydrolase
Similarity search - Component
Biological speciesOPHIOSTOMA PICEAE (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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
DepositionJun 16, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 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
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: STEROL ESTERASE
B: STEROL ESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,2368
Polymers118,5732
Non-polymers1,6636
Water6,035335
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-7.3 kcal/mol
Surface area36500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.860, 164.860, 94.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein STEROL ESTERASE


Mass: 59286.590 Da / Num. of mol.: 2 / Fragment: RESIDUES 13-549 / Mutation: YES
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: PICHIA PASTORIS (fungus) / Strain (production host): KM71 / References: UniProt: Q2TFW1, sterol esterase
#2: Chemical ChemComp-7P9 / [(2R)-2-heptanoyloxy-3-phosphonooxy-propyl] nonanoate


Mass: 424.466 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H37O8P
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growDetails: 0.2 M SODIUM NITRATE, 0.1 M BIS-TRIS PROPANE PH 7.5, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→58.29 Å / Num. obs: 49299 / % possible obs: 99.7 % / Observed criterion σ(I): 1.9 / Redundancy: 6.8 % / Biso Wilson estimate: 39.13 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.5
Reflection shellResolution: 2.4→2.48 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 1.9 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BE9

4be9


Resolution: 2.4→58.287 Å / SU ML: 0.3 / σ(F): 1.34 / Phase error: 24.72 / Stereochemistry target values: ML
Details: RESIDUES 1-12 IN CHAIN A AND 1-13 IN CHAIN B ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.2477 2400 4.9 %
Rwork0.1962 --
obs0.1988 49284 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→58.287 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8263 0 108 335 8706
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018586
X-RAY DIFFRACTIONf_angle_d1.4811691
X-RAY DIFFRACTIONf_dihedral_angle_d15.2193060
X-RAY DIFFRACTIONf_chiral_restr0.0641303
X-RAY DIFFRACTIONf_plane_restr0.011503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4002-2.44920.29351550.25162670X-RAY DIFFRACTION97
2.4492-2.50250.28221290.23832789X-RAY DIFFRACTION100
2.5025-2.56070.31911450.23552714X-RAY DIFFRACTION100
2.5607-2.62470.3031380.22692778X-RAY DIFFRACTION100
2.6247-2.69570.26671330.21432725X-RAY DIFFRACTION100
2.6957-2.7750.26771410.20732770X-RAY DIFFRACTION100
2.775-2.86460.28081630.2032697X-RAY DIFFRACTION100
2.8646-2.9670.27781130.19562789X-RAY DIFFRACTION100
2.967-3.08580.29841500.20652741X-RAY DIFFRACTION100
3.0858-3.22620.24451360.20232785X-RAY DIFFRACTION100
3.2262-3.39630.26571260.19182771X-RAY DIFFRACTION100
3.3963-3.6090.23631530.18942731X-RAY DIFFRACTION100
3.609-3.88760.24891340.18682776X-RAY DIFFRACTION100
3.8876-4.27870.25551450.17622760X-RAY DIFFRACTION100
4.2787-4.89760.19541390.16972766X-RAY DIFFRACTION100
4.8976-6.16940.24371630.1972782X-RAY DIFFRACTION100
6.1694-58.3040.20551370.19952840X-RAY DIFFRACTION100

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