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- PDB-1t4m: STRUCTURE OF A THERMOSTABLE DOUBLE MUTANT OF BACILLUS SUBTILIS LI... -

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Basic information

Entry
Database: PDB / ID: 1t4m
TitleSTRUCTURE OF A THERMOSTABLE DOUBLE MUTANT OF BACILLUS SUBTILIS LIPASE OBTAINED THROUGH DIRECTED EVOLUTION
ComponentsLIPASE A
KeywordsHYDROLASE / ALPHA/BETA HYDROLASE
Function / homology
Function and homology information


lipase activity / triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process / extracellular region
Similarity search - Function
Lipase EstA/Esterase EstB / Lipase (class 2) / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRajakumara, E. / Sankaranarayanan, R.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Structural basis of selection and thermostability of laboratory evolved Bacillus subtilis lipase
Authors: Acharya, P. / Rajakumara, E. / Sankaranarayanan, R. / Rao, N.M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystallization and preliminary x-ray crystallographic investigations on several thermostable forms of a bacillus subtilis lipase
Authors: Rajakumara, E. / Acharya, P. / Ahamad, S. / Shanmugam, V.M. / Rao, N.M. / Sankaranarayanan, R.
History
DepositionApr 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LIPASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5152
Polymers19,4761
Non-polymers391
Water3,297183
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.015, 76.015, 103.093
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Cell settingrhombohedral
Space group name H-MH3

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Components

#1: Protein LIPASE A / E.C.3.1.1.3 / Triacylglycerol lipase


Mass: 19475.918 Da / Num. of mol.: 1 / Mutation: A132D, N166Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: Lip A / Plasmid: pET-21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P37957, triacylglycerol lipase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 3 Å3/Da / Density % sol: 58.9 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 9.5
Details: PEG 3350, ethanolamine, n-octyl-beta-D-glucoside, sodium sulfate., pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 100K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 3, 2003 / Details: osmic
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 14102 / Num. obs: 14102 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 27.9 Å2 / Rsym value: 0.044 / Net I/σ(I): 19
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 793 / Rsym value: 0.241 / % possible all: 63.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPCCP4phasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I6W

1i6w


Resolution: 2→24.19 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1544171.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: THE ION PRESENT IN THE COORDINATES WAS NAMED POTASSIUM BASED ON THE B-FACTOR DURING REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.257 712 5 %RANDOM
Rwork0.206 ---
all0.207 14102 --
obs0.207 14102 94.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 77.4203 Å2 / ksol: 0.341969 e/Å3
Displacement parametersBiso mean: 32.2 Å2
Baniso -1Baniso -2Baniso -3
1-3.8 Å23.77 Å20 Å2
2--3.8 Å20 Å2
3----7.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2→24.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1358 0 1 183 1542
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d0.7
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.352 51 5.5 %
Rwork0.32 873 -
all-924 -
obs-924 61.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMCNS_ION.TOP

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