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

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Basic information

Entry
Database: PDB / ID: 6syl
TitleSTRUCTURE OF ESTER-HYDROLASE EH3 FROM THE METAGENOME OF MARINE SEDIMENTS AT MILAZZO HARBOR (SICILY, ITALY) COMPLEXED WITH A DERIVATIVE OF BUTYL 4-NITROPHENYL HEXYLPHOSPHONATE
ComponentsEsterase
KeywordsHYDROLASE / Ester Hydrolase / Complex
Function / homology: / Alpha/beta hydrolase fold-3 / lipase activity / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold / butoxy(hexyl)phosphinic acid / Esterase
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 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 30, 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)80,8804
Polymers80,4352
Non-polymers4452
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: PISA software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-8 kcal/mol
Surface area23930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.624, 51.316, 70.400
Angle α, β, γ (deg.)90.000, 93.890, 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: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 9 - 346 / Label seq-ID: 28 - 365

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-H7N / butoxy(hexyl)phosphinic acid


Mass: 222.262 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H23O3P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.19 Å3/Da / Density % sol: 43.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 26% PEG 3000, 0.1M Bis-Tris pH 6.5, 0.2M MgCl2x6H2O

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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: 2.95→45.84 Å / Num. obs: 13962 / % possible obs: 99.3 % / Redundancy: 5.6 % / CC1/2: 0.97 / Rmerge(I) obs: 0.243 / Rpim(I) all: 0.111 / Net I/σ(I): 6.3
Reflection shellResolution: 2.95→3.13 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.641 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 2236 / CC1/2: 0.901 / Rpim(I) all: 0.289 / % possible all: 99.9

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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: 2.95→45.84 Å / Cor.coef. Fo:Fc: 0.875 / Cor.coef. Fo:Fc free: 0.811 / SU B: 25.191 / SU ML: 0.475 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.576
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.305 732 5.2 %RANDOM
Rwork0.2518 ---
obs0.2547 13230 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 75.49 Å2 / Biso mean: 23.406 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1-4.95 Å20 Å2-0.33 Å2
2---3.59 Å20 Å2
3----1.3 Å2
Refinement stepCycle: final / Resolution: 2.95→45.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5174 0 0 23 5197
Biso mean---8.28 -
Num. residues----679
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0135276
X-RAY DIFFRACTIONr_bond_other_d0.0090.0174851
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.6487141
X-RAY DIFFRACTIONr_angle_other_deg1.2811.5911305
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8445677
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.33823.459266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.13915878
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8731530
X-RAY DIFFRACTIONr_chiral_restr0.070.2692
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025981
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021029
Refine LS restraints NCS

Ens-ID: 1 / Number: 10998 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.95→3.027 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 55 -
Rwork0.293 985 -
all-1040 -
obs--99.9 %

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