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- PDB-3h19: Crystal structure of EstE5, was soaked by methyl alcohol -

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Basic information

Entry
Database: PDB / ID: 3h19
TitleCrystal structure of EstE5, was soaked by methyl alcohol
ComponentsEsterase/lipase
KeywordsHYDROLASE / HSL / EstE5 / esterase / lipase
Function / homology
Function and homology information


triacylglycerol lipase activity
Similarity search - Function
Lipase, GDXG, putative histidine active site / Lipolytic enzymes "G-D-X-G" family, putative histidine active site. / Lipase, GDXG, putative serine active site / Lipolytic enzymes "G-D-X-G" family, putative serine active site. / : / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold ...Lipase, GDXG, putative histidine active site / Lipolytic enzymes "G-D-X-G" family, putative histidine active site. / Lipase, GDXG, putative serine active site / Lipolytic enzymes "G-D-X-G" family, putative serine active site. / : / 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
Biological speciesUncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHwang, K.Y. / Nam, K.H.
CitationJournal: To be Published
Title: Crystal structure of EstE5, was soaked by organic solvent
Authors: Hwang, K.Y. / Nam, K.H.
History
DepositionApr 11, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Esterase/lipase


Theoretical massNumber of molelcules
Total (without water)34,6481
Polymers34,6481
Non-polymers00
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.237, 61.237, 150.575
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Esterase/lipase / EstE5


Mass: 34647.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Uncultured bacterium (environmental samples)
Description: soil Metagenome Library / Gene: estE5 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q0GMU2, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.04 Å3/Da / Density % sol: 39.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Tris-HCl pH 7.5, 2.2M ammonium sulfate, 0.2M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.23 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 20, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 12422 / % possible obs: 92.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Num. measured all: 93938
Reflection shellResolution: 2.3→2.38 Å / % possible all: 65.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FAK

3fak


Resolution: 2.3→47.51 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.893 / SU B: 16.657 / SU ML: 0.178 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.379 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24607 601 4.8 %RANDOM
Rwork0.17144 ---
all0.175 12422 --
obs0.17144 11817 92.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.332 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å20 Å2
2--0.42 Å20 Å2
3----0.83 Å2
Refinement stepCycle: LAST / Resolution: 2.3→47.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2214 0 0 59 2273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222266
X-RAY DIFFRACTIONr_angle_refined_deg2.1131.9663074
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5345291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.7572490
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.9715373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5371513
X-RAY DIFFRACTIONr_chiral_restr0.1390.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021716
X-RAY DIFFRACTIONr_nbd_refined0.230.21077
X-RAY DIFFRACTIONr_nbtor_refined0.310.21491
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2103
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2540.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3250.25
X-RAY DIFFRACTIONr_mcbond_it1.0091.51500
X-RAY DIFFRACTIONr_mcangle_it1.56322323
X-RAY DIFFRACTIONr_scbond_it2.7733888
X-RAY DIFFRACTIONr_scangle_it4.1524.5751
LS refinement shellResolution: 2.301→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 25 -
Rwork0.221 575 -
obs--61.04 %
Refinement TLS params.Method: refined / Origin x: -12.1309 Å / Origin y: 15.4148 Å / Origin z: 0.0147 Å
111213212223313233
T-0.0189 Å2-0.0205 Å2-0.0048 Å2--0.0141 Å2-0.0029 Å2---0.0173 Å2
L0.3145 °20.0426 °20.155 °2-0.2822 °2-0.0897 °2--0.5897 °2
S0.0313 Å °0.0012 Å °-0.0198 Å °0.0134 Å °0.0051 Å °-0.0041 Å °0.0308 Å °0.0221 Å °-0.0364 Å °

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