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- PDB-7v8v: Crystal structure of PsEst3 S128A mutant -

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Basic information

Entry
Database: PDB / ID: 7v8v
TitleCrystal structure of PsEst3 S128A mutant
Componentsesterase
KeywordsHYDROLASE / esterases
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesPaenibacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSon, J. / Kim, H. / Kim, H.W.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2021M1A5A1075524 Korea, Republic Of
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


Theoretical massNumber of molelcules
Total (without water)29,6311
Polymers29,6311
Non-polymers00
Water2,504139
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11570 Å2
Unit cell
Length a, b, c (Å)143.608, 143.608, 143.608
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-377-

HOH

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Components

#1: Protein esterase


Mass: 29631.170 Da / Num. of mol.: 1 / Mutation: S128A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus sp. (bacteria) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsthis protein is S128A mutant

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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: 4.16 Å3/Da / Density % sol: 70.45 %
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: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→47.87 Å / Num. obs: 20538 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.023 / Rrim(I) all: 0.085 / Net I/σ(I): 26.9 / Num. measured all: 279175 / Scaling rejects: 60
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
2.4-2.4913.90.792933921110.9040.2170.823.699.9
8.96-47.8711.10.018527047410.0050.0187698.7

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7V8U

7v8u


Resolution: 2.4→34.83 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.228 1998 9.77 %
Rwork0.1964 18444 -
obs0.1995 20442 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.89 Å2 / Biso mean: 45.0932 Å2 / Biso min: 22.65 Å2
Refinement stepCycle: final / Resolution: 2.4→34.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1997 0 0 139 2136
Biso mean---50.52 -
Num. residues----251
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 (%)
2.4-2.460.33981390.267312911430100
2.46-2.520.26321400.244912821422100
2.52-2.60.24791390.238212851424100
2.6-2.680.27071390.239312931432100
2.68-2.780.28541400.230512891429100
2.78-2.890.29221390.236812921431100
2.89-3.020.29791410.235312991440100
3.02-3.180.26931420.213513071449100
3.18-3.380.22791410.19861303144499
3.38-3.640.23611430.1913151458100
3.64-40.19111440.16911318146299
4-4.580.17041440.155113371481100
4.58-5.760.20191480.165713681516100
5.77-34.830.21731590.207214651624100

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