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- PDB-1ku0: Structure of the Bacillus stearothermophilus L1 lipase -

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Basic information

Entry
Database: PDB / ID: 1ku0
TitleStructure of the Bacillus stearothermophilus L1 lipase
ComponentsL1 lipase
KeywordsHYDROLASE / Lipase
Function / homology
Function and homology information


triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process / extracellular region / metal ion binding
Similarity search - Function
Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
triacylglycerol lipase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2 Å
AuthorsJeong, S.-T. / Kim, H.-K. / Kim, S.-J. / Chi, S.-W. / Pan, J.-G. / Oh, T.-K. / Ryu, S.-E.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Novel zinc-binding center and a temperature switch in the Bacillus stearothermophilus L1 lipase.
Authors: Jeong, S.T. / Kim, H.K. / Kim, S.J. / Chi, S.W. / Pan, J.G. / Oh, T.K. / Ryu, S.E.
History
DepositionJan 18, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 21, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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: L1 lipase
B: L1 lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5956
Polymers86,3842
Non-polymers2114
Water4,630257
1
A: L1 lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2983
Polymers43,1921
Non-polymers1052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L1 lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2983
Polymers43,1921
Non-polymers1052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.620, 85.040, 98.360
Angle α, β, γ (deg.)90.00, 99.73, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein L1 lipase


Mass: 43192.141 Da / Num. of mol.: 2 / Fragment: residues 30-417(seq db number)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: O66015, triacylglycerol lipase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.85 Å3/Da / Density % sol: 56.88 %

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2 Å / Num. all: 63638 / % possible obs: 96.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 20.2
Reflection shellHighest resolution: 2 Å / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 6.1 / % possible all: 95.2

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Processing

Software
NameVersionClassification
SHARPphasing
CNS0.9refinement
RefinementMethod to determine structure: MIR / Resolution: 2→99 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.218 3206 -RANDOM
Rwork0.185 ---
all-63638 --
obs-60432 96.9 %-
Refinement stepCycle: LAST / Resolution: 2→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6086 0 4 257 6347

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