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- PDB-1tah: THE CRYSTAL STRUCTURE OF TRIACYLGLYCEROL LIPASE FROM PSEUDOMONAS ... -

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Basic information

Entry
Database: PDB / ID: 1tah
TitleTHE CRYSTAL STRUCTURE OF TRIACYLGLYCEROL LIPASE FROM PSEUDOMONAS GLUMAE REVEALS A PARTIALLY REDUNDANT CATALYTIC ASPARTATE
ComponentsLIPASE
KeywordsHYDROLASE(CARBOXYLIC ESTERASE)
Function / homology
Function and homology information


triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process / extracellular region / metal ion binding
Similarity search - Function
Lipases, serine active site. / 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
Triacylglycerol lipase / Triacylglycerol lipase
Similarity search - Component
Biological speciesBurkholderia glumae (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsNoble, M.E.M. / Cleasby, A. / Johnson, L.N. / Egmond, M. / Frenken, L.G.J.
Citation
Journal: FEBS Lett. / Year: 1993
Title: The crystal structure of triacylglycerol lipase from Pseudomonas glumae reveals a partially redundant catalytic aspartate.
Authors: Noble, M.E. / Cleasby, A. / Johnson, L.N. / Egmond, M.R. / Frenken, L.G.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: Crystallization and Preliminary X-Ray Study of a Lipase from Pseudomonas Glumae
Authors: Cleasby, A. / Garman, E. / Egmond, M.R. / Batenburg, M.
History
DepositionDec 21, 1993Processing site: BNL
Revision 1.0May 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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_label_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE ...SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. STRANDS 2, 3, 4, 5 OF 1A AND 1B ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: LIPASE
A: LIPASE
C: LIPASE
D: LIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,3478
Polymers132,1874
Non-polymers1604
Water00
1
B: LIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0872
Polymers33,0471
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: LIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0872
Polymers33,0471
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: LIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0872
Polymers33,0471
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: LIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0872
Polymers33,0471
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)158.160, 158.640, 63.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.91953, -0.38619, -0.07273), (-0.39168, -0.88555, -0.24979), (0.03207, 0.25819, -0.96557)-36.54662, -137.6059, 11.32877
2given(-0.53077, -0.72715, 0.43535), (0.31192, 0.31002, 0.89811), (-0.78803, 0.61249, 0.06226)-66.96497, -36.55047, 93.2341
3given(-0.87649, -0.25282, -0.40969), (-0.41783, -0.02325, 0.90823), (-0.23915, 0.96723, -0.08526)-41.48827, -43.33078, 82.01373

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Components

#1: Protein
LIPASE


Mass: 33046.625 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia glumae (bacteria)
References: UniProt: Q05489, UniProt: P0DUB8*PLUS, triacylglycerol lipase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.08 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 9 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110-20 mg/mlprotein1drop
20.1 MTris1drop
310 %(v/v)acetone1drop
527-29 %PEG80001resrvoir
4n-dodecyl-beta-D-glucopyranoside1droptrace amounts

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Data collection

Reflection
*PLUS
Num. obs: 25924 / Num. measured all: 92181 / Rmerge(I) obs: 0.046

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 3→6 Å
RfactorNum. reflection
Rfree0.226 -
Rwork0.159 -
obs0.159 21736
Refinement stepCycle: LAST / Resolution: 3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9316 0 4 0 9320
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.226 / Rfactor Rwork: 0.159
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.5

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