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- PDB-1yzf: Crystal structure of the lipase/acylhydrolase from Enterococcus f... -

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Basic information

Entry
Database: PDB / ID: 1yzf
TitleCrystal structure of the lipase/acylhydrolase from Enterococcus faecalis
Componentslipase/acylhydrolase
KeywordsHYDROLASE / Enterococcus faecalis / lipase/acylhydrolase / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologySGNH hydrolase / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / hydrolase activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Lipase/acylhydrolase
Function and homology information
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsZhang, R. / Hatzos, C. / Clancy, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of the lipase/acylhydrolase from Enterococcus faecalis
Authors: Zhang, R. / Hatzos, C. / Clancy, S. / Collart, F. / Joachimiak, A.
History
DepositionFeb 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 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: lipase/acylhydrolase


Theoretical massNumber of molelcules
Total (without water)21,4961
Polymers21,4961
Non-polymers00
Water4,738263
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.924, 45.924, 148.034
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThis protein existed as monomer, Molecule A represents the monomer in the assymtric unit.

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Components

#1: Protein lipase/acylhydrolase


Mass: 21495.756 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: gi:29342277 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q839J6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.013 Å3/Da / Density % sol: 36.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 30% PEG6000, 0.1M MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 18, 2005 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 15100 / % possible obs: 97.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 17.09
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 1.6 / Num. unique all: 3230 / % possible all: 74.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.9→49.33 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.496 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.163
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23901 752 5 %RANDOM
Rwork0.18355 ---
obs0.18621 14247 99.34 %-
all-14342 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.495 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20.34 Å20 Å2
2--0.68 Å20 Å2
3----1.02 Å2
Refine analyzeLuzzati coordinate error obs: 0.176 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.163 Å
Refinement stepCycle: LAST / Resolution: 1.9→49.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1502 0 0 263 1765
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221524
X-RAY DIFFRACTIONr_angle_refined_deg1.131.9932063
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3285194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.23824.61565
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.66515277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8591511
X-RAY DIFFRACTIONr_chiral_restr0.0730.2244
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021127
X-RAY DIFFRACTIONr_nbd_refined0.2070.2838
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21093
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2239
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.235
X-RAY DIFFRACTIONr_mcbond_it0.6891.5999
X-RAY DIFFRACTIONr_mcangle_it1.02221568
X-RAY DIFFRACTIONr_scbond_it1.9493575
X-RAY DIFFRACTIONr_scangle_it3.184.5495
LS refinement shellResolution: 1.896→1.945 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 39 -
Rwork0.223 926 -
obs--91.73 %

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