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- PDB-6sxp: STRUCTURE OF ESTER-HYDROLASE EH3 FROM THE METAGENOME OF MARINE SE... -

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Basic information

Entry
Database: PDB / ID: 6sxp
TitleSTRUCTURE OF ESTER-HYDROLASE EH3 FROM THE METAGENOME OF MARINE SEDIMENTS AT MILAZZO HARBOR (SICILY, ITALY)
ComponentsEsterase
KeywordsHYDROLASE / Ester Hydrolase
Function / homology: / Alpha/beta hydrolase fold-3 / lipase activity / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold / DI(HYDROXYETHYL)ETHER / Esterase
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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: Acs Nano / Year: 2020
Title: Tuning the Properties of Natural Promiscuous Enzymes by Engineering Their Nano-environment.
Authors: Giunta, C.I. / Cea-Rama, I. / Alonso, S. / Briand, M.L. / Bargiela, R. / Coscolin, C. / Corvini, P.F. / Ferrer, M. / Sanz-Aparicio, J. / Shahgaldian, P.
History
DepositionSep 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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)80,7395
Polymers80,4352
Non-polymers3043
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: PISA software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-4 kcal/mol
Surface area24470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.296, 51.615, 70.254
Angle α, β, γ (deg.)90.000, 93.860, 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: ILE / Beg label comp-ID: ILE / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 9 - 347 / Label seq-ID: 28 - 366

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

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Components

#1: Protein Esterase


Mass: 40217.535 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 2.26 Å3/Da / Density % sol: 45.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 24% PEG 3000, 0.2M MgCl2, 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: 1.07218 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 15, 2017 / Details: KB focusing mirrors
RadiationMonochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07218 Å / Relative weight: 1
ReflectionResolution: 2.15→45.76 Å / Num. obs: 36003 / % possible obs: 100 % / Redundancy: 5.5 % / CC1/2: 0.992 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.068 / Net I/σ(I): 8.6
Reflection shellResolution: 2.15→2.22 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.648 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 3087 / CC1/2: 0.88 / Rpim(I) all: 0.294 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimless1.11.1data scaling
MOLREP11.5.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HC0

5hc0


Resolution: 2.15→45.72 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.917 / SU B: 5.926 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.291 / ESU R Free: 0.199
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2284 1723 4.8 %RANDOM
Rwork0.2017 ---
obs0.203 34279 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 95.13 Å2 / Biso mean: 24.033 Å2 / Biso min: 11.84 Å2
Baniso -1Baniso -2Baniso -3
1-2.96 Å20 Å2-1.04 Å2
2---1.48 Å20 Å2
3----1.33 Å2
Refinement stepCycle: final / Resolution: 2.15→45.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5109 0 20 312 5441
Biso mean--44.65 28.89 -
Num. residues----674
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0135229
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174797
X-RAY DIFFRACTIONr_angle_refined_deg1.3881.6397073
X-RAY DIFFRACTIONr_angle_other_deg1.2841.57511179
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.355673
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22523.472265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.05415874
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1981530
X-RAY DIFFRACTIONr_chiral_restr0.0660.2686
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025938
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021020
Refine LS restraints NCS

Ens-ID: 1 / Number: 11025 / 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: 2.15→2.206 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 117 -
Rwork0.226 2500 -
all-2617 -
obs--99.85 %

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