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- PDB-6aae: Crystal structure of Chloramphenicol-Metabolizaing Enzyme EstDL136 -

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Basic information

Entry
Database: PDB / ID: 6aae
TitleCrystal structure of Chloramphenicol-Metabolizaing Enzyme EstDL136
ComponentsEsterase
KeywordsHYDROLASE / Chloramphenicol / metagenome / hornome sensitive lipase / HSL / EstDL136 / esterase
Function / homology
Function and homology information


carboxylesterase / carboxylesterase activity
Similarity search - Function
: / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Esterase
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.641 Å
AuthorsKim, S.H. / Kang, P.A. / Han, K.T. / Lee, S.W. / Rhee, S.K.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
Rural Development AdministrationPJ01325801 Korea, Republic Of
National Research Foundation (Korea)2017R1A2B4002860 Korea, Republic Of
Rural Development AdministrationPJ 0109390 Korea, Republic Of
CitationJournal: PLoS ONE / Year: 2019
Title: Crystal structure of chloramphenicol-metabolizing enzyme EstDL136 from a metagenome.
Authors: Kim, S.H. / Kang, P.A. / Han, K.T. / Lee, S.W. / Rhee, S.K.
History
DepositionJul 18, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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: Esterase
B: Esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,26821
Polymers68,4592
Non-polymers2,80919
Water8,773487
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10590 Å2
ΔGint-15 kcal/mol
Surface area24360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.943, 153.586, 44.243
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Esterase


Mass: 34229.297 Da / Num. of mol.: 2 / Mutation: 37-39 deletion
Source method: isolated from a genetically manipulated source
Details: To make EstDL136 crystal, internal residues from P37 to P39 were deleted
Source: (gene. exp.) uncultured bacterium (environmental samples)
Gene: estDL136 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: G3CR02, carboxylesterase
#2: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 487 / Source method: isolated from a natural source / Formula: H2O

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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: 2.95 Å3/Da / Density % sol: 58.33 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 500mM Ammonium fluoride (pH6.5), 30% PEG3350, 5% glycerol and 120mM TCEP

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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: Jun 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 100067 / % possible obs: 100 % / Redundancy: 14.3 % / Net I/σ(I): 23
Reflection shellResolution: 1.64→1.7 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U4N

1u4n


Resolution: 1.641→32.258 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.16
RfactorNum. reflection% reflection
Rfree0.2201 1999 2 %
Rwork0.1893 --
obs0.1899 99964 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.641→32.258 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4704 0 187 487 5378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074994
X-RAY DIFFRACTIONf_angle_d1.0686747
X-RAY DIFFRACTIONf_dihedral_angle_d15.371795
X-RAY DIFFRACTIONf_chiral_restr0.043716
X-RAY DIFFRACTIONf_plane_restr0.005882
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.641-1.68210.30761380.28646783X-RAY DIFFRACTION98
1.6821-1.72760.26071410.26886875X-RAY DIFFRACTION100
1.7276-1.77840.29581420.2576983X-RAY DIFFRACTION100
1.7784-1.83580.29271410.24266920X-RAY DIFFRACTION100
1.8358-1.90140.31341420.2646917X-RAY DIFFRACTION100
1.9014-1.97750.29271420.26466944X-RAY DIFFRACTION100
1.9775-2.06750.23351410.22026927X-RAY DIFFRACTION100
2.0675-2.17650.22571420.20826976X-RAY DIFFRACTION100
2.1765-2.31280.27691430.22416986X-RAY DIFFRACTION100
2.3128-2.49130.2431440.18937024X-RAY DIFFRACTION100
2.4913-2.74190.221430.18957014X-RAY DIFFRACTION100
2.7419-3.13840.20251440.18467077X-RAY DIFFRACTION100
3.1384-3.95290.20151460.15917121X-RAY DIFFRACTION100
3.9529-32.26380.17061500.14687418X-RAY DIFFRACTION100

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