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- PDB-6sxy: STRUCTURE OF S192A-ESTER-HYDROLASE EH3 FROM THE METAGENOME OF MAR... -

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Basic information

Entry
Database: PDB / ID: 6sxy
TitleSTRUCTURE OF S192A-ESTER-HYDROLASE EH3 FROM THE METAGENOME OF MARINE SEDIMENTS AT MILAZZO HARBOR (SICILY, ITALY) COMPLEXED WITH METHYL (2S)-2-PHENYLPROPANOATE
ComponentsEsterase
KeywordsHYDROLASE / Ester hydrolase / Complex
Function / homology: / Alpha/beta hydrolase fold-3 / lipase activity / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold / methyl (2~{S})-2-phenylpropanoate / DI(HYDROXYETHYL)ETHER / Esterase
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsCea-Rama, I. / Sanz-Aparicio, J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessProject BIO2016-76601-C3-3-R Spain
CitationJournal: Comput Struct Biotechnol J / Year: 2021
Title: Structure and evolutionary trace-assisted screening of a residue swapping the substrate ambiguity and chiral specificity in an esterase.
Authors: Cea-Rama, I. / Coscolin, C. / Katsonis, P. / Bargiela, R. / Golyshin, P.N. / Lichtarge, O. / Ferrer, M. / Sanz-Aparicio, J.
History
DepositionSep 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jun 2, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Esterase
B: Esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,32610
Polymers80,4032
Non-polymers9238
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: PISA Software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint2 kcal/mol
Surface area24590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.073, 51.707, 70.244
Angle α, β, γ (deg.)90.000, 93.760, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 11 - 346 / Label seq-ID: 30 - 365

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Esterase


Mass: 40201.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: A0A2K8JN75
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-LXH / methyl (2~{S})-2-phenylpropanoate


Mass: 164.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 29% PEG3000, 0.2M MgCl2.6H20, 0.1M Bis-Tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97924 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 28, 2018 / Details: KB focusing mirrors
RadiationMonochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.06→45.96 Å / Num. obs: 40816 / % possible obs: 99.4 % / Redundancy: 5.4 % / CC1/2: 0.986 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.066 / Net I/σ(I): 8.9
Reflection shellResolution: 2.06→2.12 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.573 / Num. unique obs: 3159 / CC1/2: 0.777 / Rpim(I) all: 0.286 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimless1.11.12data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SXP

6sxp


Resolution: 2.06→45.96 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.917 / SU B: 4.888 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.233 / ESU R Free: 0.181
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2276 2086 5.1 %RANDOM
Rwork0.1919 ---
obs0.1937 38726 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 111.23 Å2 / Biso mean: 25.842 Å2 / Biso min: 11.65 Å2
Baniso -1Baniso -2Baniso -3
1-3.22 Å20 Å20.03 Å2
2---2.2 Å20 Å2
3----1.02 Å2
Refinement stepCycle: final / Resolution: 2.06→45.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5133 0 63 326 5522
Biso mean--51.03 31.7 -
Num. residues----677
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0135306
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174870
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.6457173
X-RAY DIFFRACTIONr_angle_other_deg1.311.5811342
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5635679
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.08823.459266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.26415878
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8281530
X-RAY DIFFRACTIONr_chiral_restr0.0740.2691
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026019
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021039
Refine LS restraints NCS

Ens-ID: 1 / Number: 10978 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.06→2.114 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 152 -
Rwork0.236 2853 -
all-3005 -
obs--99.77 %

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