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- PDB-3umj: Crystal Structure of D311E Lipase -

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Basic information

Entry
Database: PDB / ID: 3umj
TitleCrystal Structure of D311E Lipase
ComponentsThermostable lipase
KeywordsHYDROLASE / thermostable D311E 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 zalihae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRuslan, R. / Rahman, R.N.Z.R.A. / Leow, T.C. / Ali, M.S.M. / Basri, M. / Salleh, A.B.
CitationJournal: Int J Mol Sci / Year: 2012
Title: Improvement of Thermal Stability via Outer-Loop Ion Pair Interaction of Mutated T1 Lipase from Geobacillus zalihae Strain T1
Authors: Ruslan, R. / Rahman, R.N.Z.R.A. / Leow, T.C. / Ali, M.S.M. / Basri, M. / Salleh, A.B.
History
DepositionNov 13, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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 / 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_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

Downloads & links

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Assembly

Deposited unit
A: Thermostable lipase
B: Thermostable lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,01013
Polymers86,4062
Non-polymers60411
Water11,205622
1
A: Thermostable lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5517
Polymers43,2031
Non-polymers3486
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thermostable lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4596
Polymers43,2031
Non-polymers2565
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.323, 81.162, 100.140
Angle α, β, γ (deg.)90.00, 96.49, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-389-

HOH

21B-620-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Thermostable lipase


Mass: 43203.094 Da / Num. of mol.: 2 / Fragment: UNP residues 30-416 / Mutation: D311E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus zalihae (bacteria) / Plasmid: PGEX/T1S / Production host: Escherichia coli (E. coli) / References: UniProt: Q842J9, triacylglycerol lipase

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Non-polymers , 6 types, 633 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 622 / 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: 2.74 Å3/Da / Density % sol: 55.13 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M MES, 0.1M Sodium phosphate, 0.1M Potassium phosphate, 1.5M NaCl, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jun 4, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→37.57 Å / Num. obs: 88705 / % possible obs: 96.9 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 4.9 / Redundancy: 2.93 % / Rmerge(I) obs: 0.0833 / Rsym value: 0.092
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 2.15 % / Rmerge(I) obs: 0.1946 / Mean I/σ(I) obs: 4.01 / % possible all: 91.4

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Processing

Software
NameVersionClassification
PROTEUM PLUSdata collection
XPREPdata reduction
REFMAC5.5.0109refinement
SAINTdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DSN

2dsn


Resolution: 2.1→33.17 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.905 / SU B: 4.106 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21163 2677 5.1 %RANDOM
Rwork0.15518 ---
obs0.15806 50139 96.78 %-
all-88705 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.722 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.01 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.1→33.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6102 0 26 622 6750
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0216285
X-RAY DIFFRACTIONr_angle_refined_deg1.7861.9358543
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.435771
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.82223.121314
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.68115951
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4831550
X-RAY DIFFRACTIONr_chiral_restr0.1280.2893
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214956
X-RAY DIFFRACTIONr_mcbond_it1.0641.53825
X-RAY DIFFRACTIONr_mcangle_it1.81726124
X-RAY DIFFRACTIONr_scbond_it3.10832460
X-RAY DIFFRACTIONr_scangle_it4.8224.52419
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 185 -
Rwork0.21 3443 -
obs--91.04 %

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