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- PDB-6iey: Crystal structure of Chloramphenicol-Metabolizaing Enzyme EstDL13... -

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Basic information

Entry
Database: PDB / ID: 6iey
TitleCrystal structure of Chloramphenicol-Metabolizaing Enzyme EstDL136-Chloramphenicol complex
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
CHLORAMPHENICOL / Esterase
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.097 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
DepositionSep 18, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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
B: Esterase
A: Esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7503
Polymers68,4272
Non-polymers3231
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-45 kcal/mol
Surface area23820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.463, 152.411, 44.137
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: 34213.297 Da / Num. of mol.: 2 / Mutation: catalytic inactive mutant S156A
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-CLM / CHLORAMPHENICOL


Mass: 323.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C11H12Cl2N2O5 / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 58.25 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 500mM Ammonium fluoride (pH6.5), 30% PEG 3350, 5% glyceol 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: 2.093→50 Å / Num. obs: 46963 / % possible obs: 96.4 % / Redundancy: 6.1 % / Net I/σ(I): 263
Reflection shellResolution: 2.093→2.18 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.097→29.04 Å / SU ML: 0.27 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 25.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2614 2000 4.4 %
Rwork0.2087 --
obs0.211 45505 95.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.097→29.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4643 0 20 204 4867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084781
X-RAY DIFFRACTIONf_angle_d1.1616536
X-RAY DIFFRACTIONf_dihedral_angle_d13.0091677
X-RAY DIFFRACTIONf_chiral_restr0.044711
X-RAY DIFFRACTIONf_plane_restr0.007872
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.097-2.14940.31091180.26552550X-RAY DIFFRACTION80
2.1494-2.20750.33191390.26153037X-RAY DIFFRACTION93
2.2075-2.27250.31671370.25052982X-RAY DIFFRACTION93
2.2725-2.34580.29771380.23832997X-RAY DIFFRACTION93
2.3458-2.42960.27231370.23382992X-RAY DIFFRACTION93
2.4296-2.52680.3281380.23672996X-RAY DIFFRACTION93
2.5268-2.64170.28951400.23883058X-RAY DIFFRACTION94
2.6417-2.78090.31321430.233094X-RAY DIFFRACTION95
2.7809-2.9550.27091450.22923164X-RAY DIFFRACTION97
2.955-3.18290.28881470.22683206X-RAY DIFFRACTION99
3.1829-3.50270.26131510.21223260X-RAY DIFFRACTION100
3.5027-4.00840.25571530.18643332X-RAY DIFFRACTION100
4.0084-5.04590.2171530.17153337X-RAY DIFFRACTION100
5.0459-29.04260.1981610.17463500X-RAY DIFFRACTION100

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