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- PDB-4fbl: LipS and LipT, two metagenome-derived lipolytic enzymes increase ... -

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Basic information

Entry
Database: PDB / ID: 4fbl
TitleLipS and LipT, two metagenome-derived lipolytic enzymes increase the diversity of known lipase and esterase families
ComponentsLipS lipolytic enzyme
KeywordsHYDROLASE / thermostable / Structural Genomics / Enzyme Function Initiative / Structural Proteomics in Europe / SPINE / alpha/beta hydrolase / lipase
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / SPERMIDINE
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsChow, J. / Krauss, U. / Dall Antonia, Y. / Fersini, F. / Schmeisser, C. / Schmidt, M. / Menyes, I. / Bornscheuer, U. / Lauinger, B. / Bongen, P. ...Chow, J. / Krauss, U. / Dall Antonia, Y. / Fersini, F. / Schmeisser, C. / Schmidt, M. / Menyes, I. / Bornscheuer, U. / Lauinger, B. / Bongen, P. / Pietruszka, J. / Eckstein, M. / Thum, O. / Liese, A. / Mueller-Dieckmann, J. / Jaeger, K.-E. / Kovacic, F. / Streit, W.R. / Structural Proteomics in Europe (SPINE)
CitationJournal: Plos One / Year: 2012
Title: The Metagenome-Derived Enzymes LipS and LipT Increase the Diversity of Known Lipases.
Authors: Chow, J. / Kovacic, F. / Dall Antonia, Y. / Krauss, U. / Fersini, F. / Schmeisser, C. / Lauinger, B. / Bongen, P. / Pietruszka, J. / Schmidt, M. / Menyes, I. / Bornscheuer, U.T. / Eckstein, ...Authors: Chow, J. / Kovacic, F. / Dall Antonia, Y. / Krauss, U. / Fersini, F. / Schmeisser, C. / Lauinger, B. / Bongen, P. / Pietruszka, J. / Schmidt, M. / Menyes, I. / Bornscheuer, U.T. / Eckstein, M. / Thum, O. / Liese, A. / Mueller-Dieckmann, J. / Jaeger, K.E. / Streit, W.R.
History
DepositionMay 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LipS lipolytic enzyme
B: LipS lipolytic enzyme
C: LipS lipolytic enzyme
D: LipS lipolytic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,66811
Polymers121,0914
Non-polymers5787
Water10,953608
1
A: LipS lipolytic enzyme
C: LipS lipolytic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9076
Polymers60,5452
Non-polymers3614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-35 kcal/mol
Surface area17830 Å2
MethodPISA
2
B: LipS lipolytic enzyme
D: LipS lipolytic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7625
Polymers60,5452
Non-polymers2163
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-40 kcal/mol
Surface area17730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.270, 105.270, 120.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4
Components on special symmetry positions
IDModelComponents
11D-500-

HOH

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Components

#1: Protein
LipS lipolytic enzyme


Mass: 30272.713 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: protein identified by using functional metagenomic screenings
Source: (gene. exp.) unidentified (others) / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H19N3
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 608 / 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: 2.64 Å3/Da / Density % sol: 53.38 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 4.5
Details: 0.1 M NaAcetate, 3 M NaCl,0.01 M spermidine, pH 4.5, VAPOR DIFFUSION, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 9, 2011
Details: Monochromator (horizontally side diffracting Silicon 111 crystal)
RadiationMonochromator: horizontally diffracting monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.99→40.3 Å / Num. all: 90469 / Num. obs: 85910 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.8
Reflection shellResolution: 1.99→2.1 Å / Redundancy: 5 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2 / Num. unique all: 13179 / % possible all: 100

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TQH

1tqh


Resolution: 1.99→40.3 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.687 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.138 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21679 4534 5 %RANDOM
Rwork0.17602 ---
obs0.17805 85910 99.95 %-
all-90469 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.736 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å20 Å2
2--0.9 Å20 Å2
3----1.8 Å2
Refinement stepCycle: LAST / Resolution: 1.99→40.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7418 0 34 608 8060
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0227659
X-RAY DIFFRACTIONr_angle_refined_deg2.1931.97910438
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5335985
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.33423.537294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.412151205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0961547
X-RAY DIFFRACTIONr_chiral_restr0.1630.21189
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0225807
X-RAY DIFFRACTIONr_mcbond_it1.3061.54921
X-RAY DIFFRACTIONr_mcangle_it2.1627915
X-RAY DIFFRACTIONr_scbond_it3.64132738
X-RAY DIFFRACTIONr_scangle_it5.6584.52523
LS refinement shellResolution: 1.988→2.04 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 334 -
Rwork0.292 6324 -
obs--99.95 %

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