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- PDB-7v8x: Crystal structure of PsEst3 complexed with Phenylmethylsulfonyl f... -

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Basic information

Entry
Database: PDB / ID: 7v8x
TitleCrystal structure of PsEst3 complexed with Phenylmethylsulfonyl fluoride (PMSF)
Componentsesterase
KeywordsHYDROLASE / esterases
Function / homologyphenylmethanesulfonic acid
Function and homology information
Biological speciesPaenibacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8192
Polymers29,6471
Non-polymers1721
Water99155
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint3 kcal/mol
Surface area11930 Å2
Unit cell
Length a, b, c (Å)144.773, 144.773, 144.773
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-PMS / phenylmethanesulfonic acid


Mass: 172.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 4.26 Å3/Da / Density % sol: 71.16 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting 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: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.34→50 Å / Num. obs: 22425 / % possible obs: 99.8 % / Redundancy: 30.4 % / Biso Wilson estimate: 45.29 Å2 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.013 / Rrim(I) all: 0.076 / Χ2: 1.687 / Net I/σ(I): 13.4 / Num. measured all: 681426
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.34-2.38140.52410950.3690.1370.5430.91799.8
2.38-2.4217.90.50910910.5690.1180.5241.01100
2.42-2.4719.80.50510840.6090.1120.5181.05899.9
2.47-2.52210.48811010.6460.1050.51.07999.9
2.52-2.5822.40.45410990.8070.0940.4641.171100
2.58-2.6423.30.42211080.9270.0860.4311.195100
2.64-2.725.30.38110970.9410.0740.3891.251100
2.7-2.7726.40.35311040.9630.0670.361.334100
2.77-2.8628.10.30310970.9810.0560.3081.392100
2.86-2.9529.90.26411170.990.0470.2681.47100
2.95-3.0531.70.21811140.9950.0380.2221.52299.9
3.05-3.1834.10.16811020.9970.0280.1711.66399.9
3.18-3.32360.12611110.9990.0210.1281.77199.9
3.32-3.538.30.09411270.9990.0150.0961.87499.9
3.5-3.7139.40.07611280.9990.0120.0771.87999.9
3.71-440.20.063112010.010.0642.009100
4-4.441.20.053114410.0080.0532.04999.9
4.4-5.0441.60.045115410.0070.0462.07299.7
5.04-6.3540.20.046117810.0070.0472.06399.7
6.35-5033.90.04512540.9990.0080.0462.46397.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7V8U

7v8u


Resolution: 2.34→35.11 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.48 / Phase error: 27.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2576 2000 8.93 %
Rwork0.2247 20402 -
obs0.2277 22402 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.02 Å2 / Biso mean: 54.5207 Å2 / Biso min: 23.98 Å2
Refinement stepCycle: final / Resolution: 2.34→35.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 10 55 2066
Biso mean--74.55 51.81 -
Num. residues----252
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 (%)
2.34-2.40.3931400.363914311571100
2.4-2.470.37051410.337214301571100
2.47-2.540.33951380.322914161554100
2.54-2.620.35711390.294514181557100
2.62-2.710.341400.274214261566100
2.71-2.820.29671420.270514411583100
2.82-2.950.30161400.267914441584100
2.95-3.110.30691420.253414431585100
3.11-3.30.25821420.229214491591100
3.3-3.550.2521430.216314441587100
3.56-3.910.22171440.21514711615100
3.91-4.480.20671450.188614791624100
4.48-5.640.23151460.176215031649100
5.64-35.110.22711580.19781607176599

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