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- PDB-3l1j: Crystal structure of EstE5, was soaked by ZnSO4 -

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Basic information

Entry
Database: PDB / ID: 3l1j
TitleCrystal structure of EstE5, was soaked by ZnSO4
ComponentsEsterase/lipase
KeywordsHYDROLASE / HSL / EstE5 / esterase / lipase
Function / homology
Function and homology information


Lipase, GDXG, putative histidine active site / Lipase, GDXG, putative serine active site / Lipolytic enzymes "G-D-X-G" family, putative histidine 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 / Lipase, GDXG, putative serine active site / Lipolytic enzymes "G-D-X-G" family, putative histidine 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 / molecular replacement / Resolution: 2 Å
AuthorsNam, K.H. / Hwang, K.Y.
CitationJournal: To be Published
Title: Structural insights into the noninvasive inhibition of HSL-homolog EstE5 by organic solvents and metal ions
Authors: Nam, K.H. / Hwang, K.Y.
History
DepositionDec 11, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 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
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.114, 61.114, 150.674
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 / Production host: Escherichia coli (E. coli)
References: UniProt: Q0GMU2, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.03 Å3/Da / Density % sol: 39.42 %
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 21, 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→50 Å / Num. obs: 18624 / % possible obs: 92.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Num. measured all: 111658
Reflection shellResolution: 2→2.07 Å / % possible all: 52.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.5.0072refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FAK

3fak


Resolution: 2→43.21 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 1 / SU B: 4.441 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.219 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1898 10.2 %RANDOM
Rwork0.184 ---
all0.19 18624 --
obs0.19 18597 92.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 66.81 Å2 / Biso mean: 29.38 Å2 / Biso min: 14.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20 Å2
2--0.27 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 2→43.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2222 0 0 97 2319
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222274
X-RAY DIFFRACTIONr_angle_refined_deg1.8061.9663084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.495292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1122490
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.66515376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7351513
X-RAY DIFFRACTIONr_chiral_restr0.1330.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211720
X-RAY DIFFRACTIONr_mcbond_it0.9961.51462
X-RAY DIFFRACTIONr_mcangle_it1.70322331
X-RAY DIFFRACTIONr_scbond_it3.0183812
X-RAY DIFFRACTIONr_scangle_it4.4424.5753
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 70 -
Rwork0.268 606 -
all-676 -
obs--46.27 %

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