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- PDB-7v8u: Crystal structure of PsEst3 wild-type -

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Basic information

Entry
Database: PDB / ID: 7v8u
TitleCrystal structure of PsEst3 wild-type
ComponentsEsterase
KeywordsHYDROLASE / esterases
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / NITROBENZENE
Function and homology information
Biological speciesPaenibacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSon, J. / Kim, H. / Kim, H.W.
Funding support1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2021M1A5A1075524
CitationJournal: Iucrj / Year: 2023
Title: Structural and biochemical insights into PsEst3, a new GHSR-type esterase obtained from Paenibacillus sp. R4.
Authors: Son, J. / Choi, W. / Kim, H. / Kim, M. / Lee, J.H. / Shin, S.C. / Kim, H.W.
History
DepositionAug 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8663
Polymers29,6471
Non-polymers2192
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-18 kcal/mol
Surface area12230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.134, 145.134, 145.134
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein Esterase


Mass: 29647.170 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus sp. (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NBZ / NITROBENZENE


Mass: 123.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 4.3 Å3/Da / Density % sol: 71.37 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 0.1 M bis-tris pH 6.5, 2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.25→48.38 Å / Num. obs: 25533 / % possible obs: 99.9 % / Redundancy: 30.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.014 / Rrim(I) all: 0.083 / Net I/σ(I): 36.6 / Num. measured all: 785631 / Scaling rejects: 190
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.25-2.32130.2323001423000.9880.0660.24111.599.9
8.99-48.3823.10.058109914760.9970.0120.0645.696.6

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1zj4

1zj4


Resolution: 2.25→48.38 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2098 2000 7.85 %
Rwork0.1788 23484 -
obs0.1812 25484 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.86 Å2 / Biso mean: 31.4376 Å2 / Biso min: 11.43 Å2
Refinement stepCycle: final / Resolution: 2.25→48.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2040 0 14 187 2241
Biso mean--42.85 38.59 -
Num. residues----258
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.30.27021400.217116521792100
2.3-2.360.23581390.187316241763100
2.37-2.430.23281400.181116551795100
2.43-2.510.2271400.174416321772100
2.51-2.60.19651410.18116511792100
2.6-2.710.24371400.182416491789100
2.71-2.830.21021400.197816521792100
2.83-2.980.2341420.216631805100
2.98-3.170.23991420.19816691811100
3.17-3.410.23791430.188816741817100
3.41-3.750.1871430.159716811824100
3.75-4.30.18531460.148917091855100
4.3-5.410.15951480.157317361884100
5.42-48.380.22251560.20041837199399

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