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- PDB-1ji3: CRYSTAL STRUCTURE OF THE FIRST THERMOSTABLE BACTERIAL LIPASE FROM... -

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Basic information

Entry
Database: PDB / ID: 1ji3
TitleCRYSTAL STRUCTURE OF THE FIRST THERMOSTABLE BACTERIAL LIPASE FROM BACILLUS STEAROTHERMOPHILUS
Componentslipase
KeywordsHYDROLASE / LIPASE / metal-binding / thermophilic
Function / homology
Function and homology information


triacylglycerol lipase / 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 / SYNCHROTRON / MIR / Resolution: 2.2 Å
AuthorsTyndall, J.D.A. / Sinchaikul, S. / Fothergill-Gilmore, L.A. / Taylor, P. / Walkinshaw, M.D.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Crystal Structure of a Thermostable Lipase from Bacillus stearothermophilus P1
Authors: Tyndall, J.D.A. / Sinchaikul, S. / Fothergill-Gilmore, L.A. / Taylor, P. / Walkinshaw, M.D.
History
DepositionJun 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 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_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_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_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_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_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: lipase
B: lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,8316
Polymers86,6202
Non-polymers2114
Water6,251347
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.500, 81.237, 99.782
Angle α, β, γ (deg.)90.00, 96.33, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

#1: Protein lipase / E.C.3.1.1.3


Mass: 43310.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Variant: P1 / Plasmid: pQE-60 / Production host: Escherichia coli (E. coli) / Strain (production host): M15[pREP4] / References: UniProt: Q9L6D3, triacylglycerol lipase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 2.75 Å3/Da / Density % sol: 55.34 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: Hepes, ammonium sulphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP at 290K
Crystal grow
*PLUS
pH: 8.5
Details: Sinchaikul, S., (2002) Acta Crystallogr., D58, 182.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 %satammonium sulfate1reservoir
20.1 MHEPES1reservoirpH6.8-7.0
315 mg/mlprotein1drop
420 mMTris-HCl1droppH8.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSRS PX14.111.48
SYNCHROTRONSRS PX9.521.2
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDFeb 4, 2001
MARRESEARCH2CCDFeb 27, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.481
21.21
ReflectionResolution: 2.2→24 Å / Num. all: 47208 / Num. obs: 47208 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.51 % / Biso Wilson estimate: 29.729 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 11.15
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 4.16 / Num. unique all: 2180 / % possible all: 91.9
Reflection
*PLUS
Num. measured all: 211130 / Rmerge(I) obs: 0.106
Reflection shell
*PLUS
% possible obs: 91.9 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 4.2

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
SOLVEphasing
REFMAC5refinement
RefinementMethod to determine structure: MIR / Resolution: 2.2→100 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2395 5.1 %RANDOM
Rwork0.166 ---
all0.1689 44812 --
obs0.1689 44812 98.66 %-
Solvent computationSolvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.6 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å20 Å20 Å2
2---0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.2→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6119 0 4 347 6470
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONr_bond_refined_d0.00562870
X-RAY DIFFRACTIONr_angle_refined_deg2.42785531.9
X-RAY DIFFRACTIONr_gen_planes_refined0.00271790
X-RAY DIFFRACTIONr_chiral_restr0.1428990.2
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4537743
X-RAY DIFFRACTIONr_nbtor_refined19.677101015
X-RAY DIFFRACTIONr_nbd_refined0.27715130.4
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1748520.5
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.234170.5
X-RAY DIFFRACTIONr_mcbond_it1.32238391.5
X-RAY DIFFRACTIONr_mcangle_it2.4361492
X-RAY DIFFRACTIONr_scbond_it3.82324483
X-RAY DIFFRACTIONr_scangle_it6.17724044.5
LS refinement shellHighest resolution: 2.2 Å / Rfactor Rfree: 0.2 / Rfactor Rwork: 0.1
Refinement
*PLUS
Lowest resolution: 40 Å / % reflection Rfree: 5 % / Rfactor obs: 0.1689 / Rfactor Rfree: 0.217 / Rfactor Rwork: 0.166
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.218
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.256
LS refinement shell
*PLUS
Rfactor Rfree: 0.2 / Rfactor Rwork: 0.1

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