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- PDB-4be9: Open conformation of O. piceae sterol esterase -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4be9
TitleOpen conformation of O. piceae sterol esterase
ComponentsSTEROL ESTERASE
KeywordsHYDROLASE / OPHIOSTOMA
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / 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 / NITRATE ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Carboxylic ester hydrolase
Similarity search - Component
Biological speciesOPHIOSTOMA PICEAE (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 6, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 26, 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
Revision 1.3Dec 20, 2023Group: 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
Revision 1.4Nov 6, 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: STEROL ESTERASE
B: STEROL ESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,66522
Polymers118,4272
Non-polymers3,23820
Water13,781765
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7760 Å2
ΔGint-3.5 kcal/mol
Surface area35420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.123, 164.123, 93.994
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

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Protein / Sugars , 2 types, 5 molecules AB

#1: Protein STEROL ESTERASE


Mass: 59213.535 Da / Num. of mol.: 2 / 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 / 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

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Non-polymers , 7 types, 782 molecules

#3: Chemical ChemComp-7P9 / [(2R)-2-heptanoyloxy-3-phosphonooxy-propyl] nonanoate


Mass: 424.466 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H37O8P
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 765 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsN-ACETYL-D-GLUCOSAMINE (NAG): COVALENTLY BOUND TO A-ASN362, A-ASN380 AND B-ASN362 RESPECTIVELY, BY ...N-ACETYL-D-GLUCOSAMINE (NAG): COVALENTLY BOUND TO A-ASN362, A-ASN380 AND B-ASN362 RESPECTIVELY, 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: 2.65 Å3/Da / Density % sol: 53.6 % / Description: NONE
Crystal growpH: 7.5
Details: 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: 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→47.28 Å / Num. obs: 84190 / % possible obs: 100 % / Observed criterion σ(I): 6 / Redundancy: 7 % / Biso Wilson estimate: 27.8 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.7
Reflection shellResolution: 2→2.11 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LPN

1lpn


Resolution: 2→43.561 Å / SU ML: 0.53 / σ(F): 1.34 / Phase error: 20.19 / Stereochemistry target values: ML
Details: THE FIRST 8 AMINO ACIDS OF THE SAMPLE (EAEAYVEF) CORRESPOND TO A PURIFICATION TAG. THIS REGION IS MAINLY DISORDERED IN THE CRYSTAL.
RfactorNum. reflection% reflection
Rfree0.2059 4204 5 %
Rwork0.1675 --
obs0.1694 84172 99.99 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.224 Å2 / ksol: 0.328 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.6444 Å20 Å20 Å2
2--1.6444 Å20 Å2
3----3.2889 Å2
Refinement stepCycle: LAST / Resolution: 2→43.561 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8251 0 212 765 9228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088743
X-RAY DIFFRACTIONf_angle_d1.05111877
X-RAY DIFFRACTIONf_dihedral_angle_d14.1183136
X-RAY DIFFRACTIONf_chiral_restr0.0731323
X-RAY DIFFRACTIONf_plane_restr0.0051527
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02280.29751270.26972662X-RAY DIFFRACTION100
2.0228-2.04660.27551440.23782653X-RAY DIFFRACTION100
2.0466-2.07150.27751290.20732656X-RAY DIFFRACTION100
2.0715-2.09770.26271310.20822655X-RAY DIFFRACTION100
2.0977-2.12530.24951440.19532690X-RAY DIFFRACTION100
2.1253-2.15450.2361310.19362628X-RAY DIFFRACTION100
2.1545-2.18520.24621300.18882669X-RAY DIFFRACTION100
2.1852-2.21780.2521500.18152663X-RAY DIFFRACTION100
2.2178-2.25250.25921430.17732674X-RAY DIFFRACTION100
2.2525-2.28940.27021530.18222617X-RAY DIFFRACTION100
2.2894-2.32890.20911190.17082647X-RAY DIFFRACTION100
2.3289-2.37130.18481270.16662686X-RAY DIFFRACTION100
2.3713-2.41690.24351390.16522657X-RAY DIFFRACTION100
2.4169-2.46620.22381340.17092682X-RAY DIFFRACTION100
2.4662-2.51980.22631480.16892636X-RAY DIFFRACTION100
2.5198-2.57840.23291430.16492630X-RAY DIFFRACTION100
2.5784-2.64290.21071440.16022661X-RAY DIFFRACTION100
2.6429-2.71430.22911380.15722665X-RAY DIFFRACTION100
2.7143-2.79420.19671630.16252636X-RAY DIFFRACTION100
2.7942-2.88440.20221380.15162672X-RAY DIFFRACTION100
2.8844-2.98740.18771340.14992690X-RAY DIFFRACTION100
2.9874-3.1070.1971290.15912664X-RAY DIFFRACTION100
3.107-3.24840.17421490.15482663X-RAY DIFFRACTION100
3.2484-3.41960.20051310.15892675X-RAY DIFFRACTION100
3.4196-3.63370.1881490.15952656X-RAY DIFFRACTION100
3.6337-3.91410.19691460.15562687X-RAY DIFFRACTION100
3.9141-4.30770.17741440.14872681X-RAY DIFFRACTION100
4.3077-4.93030.17771540.13652675X-RAY DIFFRACTION100
4.9303-6.20880.19891410.18162699X-RAY DIFFRACTION100
6.2088-43.5710.19481520.19532739X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 31.4231 Å / Origin y: 0.2326 Å / Origin z: 28.147 Å
111213212223313233
T0.007 Å20.0846 Å20.0328 Å2-0.0676 Å2-0.0178 Å2--0.0352 Å2
L0.4222 °2-0.074 °2-0.0914 °2-0.4489 °20.127 °2--0.5376 °2
S-0.0015 Å °-0.2018 Å °-0.0904 Å °0.2746 Å °0.0089 Å °-0.0598 Å °0.0889 Å °0.0832 Å °-0.0418 Å °
Refinement TLS groupSelection details: ALL

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