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- PDB-6z68: A novel metagenomic alpha/beta-fold esterase -

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Basic information

Entry
Database: PDB / ID: 6z68
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 / DI(HYDROXYETHYL)ETHER / Acetyl esterase/lipase
Function and homology information
Biological speciesPseudonocardia thermophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)81,6527
Polymers81,0272
Non-polymers6255
Water16,862936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint6 kcal/mol
Surface area24950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.710, 77.190, 162.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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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-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#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.: 936 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.27 Å3/Da / Density % sol: 45.87 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop
Details: 0.25 M magnesium chloride, 0.1 M Tris pH 8.5 and 35 % (w/v) PEG 4000 with 0.01 M TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976246 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976246 Å / Relative weight: 1
ReflectionResolution: 1.35→55.28 Å / Num. obs: 155980 / % possible obs: 96.69 % / Redundancy: 6.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Net I/σ(I): 16.64
Reflection shellResolution: 1.353→1.402 Å / Rmerge(I) obs: 0.488 / Num. unique obs: 10966 / CC1/2: 0.804

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
Auto-Rickshawphasing
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: xxxx

Resolution: 1.35→55.28 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.968 / SU B: 3.086 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.049 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1841 1994 1.3 %RANDOM
Rwork0.1376 ---
obs0.1381 153608 96.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 126.09 Å2 / Biso mean: 18.011 Å2 / Biso min: 7.23 Å2
Baniso -1Baniso -2Baniso -3
1--2.99 Å20 Å20 Å2
2--1.85 Å20 Å2
3---1.13 Å2
Refinement stepCycle: final / Resolution: 1.35→55.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5428 0 41 936 6405
Biso mean--41.14 34.47 -
Num. residues----720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0135702
X-RAY DIFFRACTIONr_bond_other_d0.0050.0175307
X-RAY DIFFRACTIONr_angle_refined_deg2.0061.6497776
X-RAY DIFFRACTIONr_angle_other_deg1.6171.57112254
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2345746
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.620.095316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.67315837
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8581559
X-RAY DIFFRACTIONr_chiral_restr0.1160.2717
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.026577
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021252
X-RAY DIFFRACTIONr_rigid_bond_restr7.916311009
LS refinement shellResolution: 1.353→1.388 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 88 -
Rwork0.3 6671 -
all-6759 -
obs--57.39 %

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