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- PDB-6cl4: LipC12 - Lipase from metagenomics -

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Basic information

Entry
Database: PDB / ID: 6cl4
TitleLipC12 - Lipase from metagenomics
ComponentsLipase C12
KeywordsHYDROLASE / Lipase
Function / homology
Function and homology information


triacylglycerol lipase / triacylglycerol lipase activity
Similarity search - Function
alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsIulek, J. / Martini, V.P. / Krieger, N. / Glogauer, A. / Souza, E.M.
CitationJournal: N Biotechnol / Year: 2019
Title: Structure solution and analyses of the first true lipase obtained from metagenomics indicate potential for increased thermostability.
Authors: Martini, V.P. / Krieger, N. / Glogauer, A. / Souza, E.M. / Iulek, J.
History
DepositionMar 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 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
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 C12


Theoretical massNumber of molelcules
Total (without water)33,4341
Polymers33,4341
Non-polymers00
Water2,702150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.500, 58.500, 192.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Lipase C12


Mass: 33433.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Gene: lipc12 / Production host: Escherichia coli (E. coli) / References: UniProt: G1APT8, triacylglycerol lipase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.48 Å3/Da / Density % sol: 50.4 % / Description: needles
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.0 M sodium formate and 0.1 M bis-tris propane, pH 7.0 using a protein concentration of 10 mg / mL. Crystals grown for ten weeks

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: nitrogen stream
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.64→58.5 Å / Num. obs: 10489 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 8.82 % / Rrim(I) all: 0.14 / Net I/σ(I): 18.91
Reflection shellResolution: 2.64→2.72 Å / Redundancy: 8.38 % / Mean I/σ(I) obs: 4.29 / Num. unique obs: 851 / Rrim(I) all: 0.641 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSVERSION December 28, 2009data reduction
XSCALEVERSION January 30, 2009data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EX9

1ex9


Resolution: 2.64→48.175 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.63
RfactorNum. reflection% reflection
Rfree0.251 503 4.8 %
Rwork0.1922 --
obs0.195 10487 99.42 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.3 Å
Refinement stepCycle: LAST / Resolution: 2.64→48.175 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2181 0 0 150 2331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022250
X-RAY DIFFRACTIONf_angle_d0.4473058
X-RAY DIFFRACTIONf_dihedral_angle_d9.172807
X-RAY DIFFRACTIONf_chiral_restr0.018345
X-RAY DIFFRACTIONf_plane_restr0.002400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.64-2.90570.2831120.242423X-RAY DIFFRACTION99
2.9057-3.3260.27571440.2162419X-RAY DIFFRACTION100
3.326-4.19010.23061200.17612504X-RAY DIFFRACTION100
4.1901-48.1830.23741270.17572638X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 4.5125 Å / Origin y: 21.2 Å / Origin z: 22.0314 Å
111213212223313233
T0.1718 Å20.0669 Å20.0072 Å2-0.2189 Å20.0056 Å2--0.1874 Å2
L0.7649 °20.6386 °20.9212 °2-1.2731 °21.0468 °2--3.0022 °2
S0.0214 Å °-0.0749 Å °-0.0352 Å °-0.0523 Å °-0.001 Å °-0.0416 Å °-0.0453 Å °-0.0924 Å °-0.0238 Å °
Refinement TLS groupSelection details: chain A

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