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- PDB-4ypv: High-resolution structure of a metagenome-derived esterase Est8 -

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Basic information

Entry
Database: PDB / ID: 4ypv
TitleHigh-resolution structure of a metagenome-derived esterase Est8
ComponentsEst8
KeywordsHYDROLASE / esterase / Est8 / metagenome / microbial consortium
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesParvibaculum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPereira, M.R. / Maester, C.T. / Macedo Lemos, E. / Hyvonen, M. / Balan, A.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2011/09136-7 Brazil
CitationJournal: Appl. Microbiol. Biotechnol. / Year: 2017
Title: From a metagenomic source to a high-resolution structure of a novel alkaline esterase.
Authors: Pereira, M.R. / Maester, T.C. / Mercaldi, G.F. / de Macedo Lemos, E.G. / Hyvonen, M. / Balan, A.
History
DepositionMar 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: 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
Item: _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: Est8


Theoretical massNumber of molelcules
Total (without water)37,0471
Polymers37,0471
Non-polymers00
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.496, 85.496, 98.665
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Est8


Mass: 37046.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parvibaculum (bacteria) / Gene: est8 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: carboxylesterase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O

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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: 2.98 Å3/Da / Density % sol: 60.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 1% PEG 8000, 1.4 M Triammonium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.919 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919 Å / Relative weight: 1
ReflectionResolution: 1.85→27.985 Å / Num. obs: 35630 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 3.47 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 14.44
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 3.53 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 2.23 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EVQ

1evq


Resolution: 1.85→27.985 Å / SU ML: 0.17 / Cross valid method: NONE / σ(F): 1.37 / Phase error: 17.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1806 1780 5 %
Rwork0.1498 --
obs0.1513 35626 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→27.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2344 0 0 197 2541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062396
X-RAY DIFFRACTIONf_angle_d0.9863265
X-RAY DIFFRACTIONf_dihedral_angle_d11.992859
X-RAY DIFFRACTIONf_chiral_restr0.042363
X-RAY DIFFRACTIONf_plane_restr0.005436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.23721310.21222584X-RAY DIFFRACTION98
1.9-1.95590.19921280.19442535X-RAY DIFFRACTION98
1.9559-2.0190.22691370.18472544X-RAY DIFFRACTION98
2.019-2.09120.22341510.17752557X-RAY DIFFRACTION98
2.0912-2.17490.211370.16472573X-RAY DIFFRACTION99
2.1749-2.27380.17261400.1542557X-RAY DIFFRACTION99
2.2738-2.39360.17831530.15792596X-RAY DIFFRACTION99
2.3936-2.54350.18821180.1662587X-RAY DIFFRACTION98
2.5435-2.73970.17991410.16922611X-RAY DIFFRACTION99
2.7397-3.01520.20851350.16662628X-RAY DIFFRACTION99
3.0152-3.45080.19921640.15782599X-RAY DIFFRACTION99
3.4508-4.3450.16091160.13092699X-RAY DIFFRACTION99
4.345-27.98830.14941290.12522776X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.80850.461.61561.78751.12742.88530.02730.6835-0.713-0.0391-0.1016-0.25410.45680.3392-0.03640.45830.03990.04980.6237-0.24910.637212.710120.950120.2426
22.8583-1.22060.04652.3366-0.0212.46490.23880.74070.0584-0.23-0.2893-0.3484-0.07340.3538-0.03230.2519-0.01810.03290.49420.03880.35959.869740.320822.7377
32.5141-1.1265-0.14592.76920.10692.59680.050.17840.08510.1757-0.0315-0.0804-0.1753-0.02360.02050.1708-0.0263-0.010.2141-0.00020.17320.449743.055733.3564
42.3732-0.8685-0.30893.08980.45052.7199-0.17240.1605-0.84170.4265-0.04760.30810.6419-0.11680.13310.3408-0.03750.05230.2493-0.03380.423-0.079825.030934.6773
54.2062-2.1937-1.84392.84220.48253.0599-0.4193-0.5167-0.65110.95290.2245-0.01070.67750.47570.06820.50450.0817-0.04250.29120.04470.37399.49626.330142.3257
62.1135-0.7002-0.25051.93980.31661.6811-0.00450.4871-0.76230.0402-0.13140.54110.4138-0.45970.12730.2819-0.11740.03950.3967-0.14060.495-7.189427.830229.3816
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 56 )
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 175 )
4X-RAY DIFFRACTION4chain 'A' and (resid 176 through 209 )
5X-RAY DIFFRACTION5chain 'A' and (resid 210 through 232 )
6X-RAY DIFFRACTION6chain 'A' and (resid 233 through 311 )

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