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- PDB-6z69: A novel metagenomic alpha/beta-fold esterase -

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Basic information

Entry
Database: PDB / ID: 6z69
TitleA novel metagenomic alpha/beta-fold esterase
ComponentsAcetyl esterase/lipase
KeywordsHYDROLASE / alpha/beta-fold hydrolase / esterase / metagenome / inhibitor-bound / substrate promiscuity
Function / homologyAlpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold / hydrolase activity / 7-hydroxy-4-methyl-2H-chromen-2-one / N-HEXYLPHOSPHONATE ETHYL ESTER / Acetyl esterase/lipase
Function and homology information
Biological speciesPseudonocardia thermophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsBollinger, A. / Thies, S. / Hoeppner, A. / Kobus, S. / Jaeger, K.-E. / Smits, S.H.J.
CitationJournal: Febs J. / Year: 2021
Title: Crystal structures of a novel family IV esterase in free and substrate-bound form.
Authors: Hoppner, A. / Bollinger, A. / Kobus, S. / Thies, S. / Coscolin, C. / Ferrer, M. / Jaeger, K.E. / Smits, S.H.J.
History
DepositionMay 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: 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

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Assembly

Deposited unit
A: Acetyl esterase/lipase
B: Acetyl esterase/lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,9878
Polymers81,0272
Non-polymers9596
Water17,330962
1
A: Acetyl esterase/lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2545
Polymers40,5141
Non-polymers7414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Acetyl esterase/lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7323
Polymers40,5141
Non-polymers2192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.410, 86.700, 110.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Acetyl esterase/lipase


Mass: 40513.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudonocardia thermophila (bacteria) / Gene: SAMN05443637_118146 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1M6Y2K1
#2: Chemical ChemComp-HEE / N-HEXYLPHOSPHONATE ETHYL ESTER


Mass: 194.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H19O3P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-4MU / 7-hydroxy-4-methyl-2H-chromen-2-one / 4-methylumbelliferone / Hymecromone


Mass: 176.169 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 962 / 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: 2.13 Å3/Da / Density % sol: 42.33 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium chloride, 0.1 M Tris pH 8.5, 30 % (w/v) PEG 4000, 2 mM methyl 4-methylumbelliferyl hexylphosphat

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.81→43.39 Å / Num. obs: 63348 / % possible obs: 98.93 % / Redundancy: 4.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.117 / Net I/σ(I): 10.3
Reflection shellResolution: 1.811→1.875 Å / Rmerge(I) obs: 0.555 / Num. unique obs: 6223 / CC1/2: 0.82

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Z68

6z68


Resolution: 1.81→43.39 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.787 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1922 3152 5 %RANDOM
Rwork0.1509 ---
obs0.153 59945 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.78 Å2 / Biso mean: 15.82 Å2 / Biso min: 3.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å20 Å2
2--0.55 Å20 Å2
3----0.24 Å2
Refinement stepCycle: final / Resolution: 1.81→43.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5436 0 58 962 6456
Biso mean--20.33 26.81 -
Num. residues----721
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0135659
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175250
X-RAY DIFFRACTIONr_angle_refined_deg1.6481.6637713
X-RAY DIFFRACTIONr_angle_other_deg1.4421.58612098
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0945727
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.42419.968313
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54115819
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4741560
X-RAY DIFFRACTIONr_chiral_restr0.0860.2709
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026513
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021249
LS refinement shellResolution: 1.811→1.858 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 200 -
Rwork0.227 4430 -
all-4630 -
obs--99.27 %

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