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- PDB-2es4: Crystal structure of the Burkholderia glumae lipase-specific fold... -

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Basic information

Entry
Database: PDB / ID: 2es4
TitleCrystal structure of the Burkholderia glumae lipase-specific foldase in complex with its cognate lipase
Components
  • Lipase
  • Lipase chaperone
KeywordsHYDROLASE / protein-protein complex / steric chaperone / triacylglycerol hydrolase / all alpha helix protein / a/b hydrolase fold / extensive interaction area
Function / homology
Function and homology information


triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process / unfolded protein binding / protein folding / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
Lipase chaperone / Proteobacterial lipase chaperone protein / 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
IODIDE ION / Triacylglycerol lipase / Triacylglycerol lipase / Lipase-specific foldase
Similarity search - Component
Biological speciesBurkholderia glumae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPauwels, K. / Wyns, L. / Tommassen, J. / Savvides, S.N. / Van Gelder, P.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Structure of a membrane-based steric chaperone in complex with its lipase substrate.
Authors: Pauwels, K. / Lustig, A. / Wyns, L. / Tommassen, J. / Savvides, S.N. / Van Gelder, P.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Crystallization and crystal manipulation of a steric chaperone in complex with its lipase substrate
Authors: Pauwels, K. / Loris, R. / Vandenbussche, G. / Ruysschaert, J.-M. / Wyns, L. / Van Gelder, P.
History
DepositionOct 25, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Aug 23, 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_conn_type / 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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.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 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.7Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipase
D: Lipase chaperone
B: Lipase
E: Lipase chaperone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,80314
Polymers136,7084
Non-polymers1,09510
Water15,187843
1
A: Lipase
D: Lipase chaperone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5214
Polymers68,3542
Non-polymers1672
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-37 kcal/mol
Surface area24530 Å2
MethodPISA
2
B: Lipase
E: Lipase chaperone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,28210
Polymers68,3542
Non-polymers9288
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-42 kcal/mol
Surface area24540 Å2
MethodPISA
3
B: Lipase
E: Lipase chaperone
hetero molecules

B: Lipase
E: Lipase chaperone
hetero molecules

A: Lipase
D: Lipase chaperone
hetero molecules

A: Lipase
D: Lipase chaperone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)275,60728
Polymers273,4168
Non-polymers2,19120
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
crystal symmetry operation3_445x-1/2,y-1/2,z1
crystal symmetry operation4_545-x+1/2,y-1/2,-z1
Buried area31920 Å2
ΔGint-188 kcal/mol
Surface area89570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.000, 75.700, 116.600
Angle α, β, γ (deg.)90.00, 117.60, 90.00
Int Tables number5
Space group name H-MC121
DetailsThere are 2 biological units in the asymmetric unit (chains A & D and chains B & E)

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Components

#1: Protein Lipase / Triacylglycerol lipase


Mass: 33117.703 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Burkholderia glumae (bacteria) / Cellular location: extracellular / Strain: PG1
References: UniProt: Q05489, UniProt: P0DUB8*PLUS, triacylglycerol lipase
#2: Protein Lipase chaperone / Lipase foldase / Lipase helper protein / Lipase activator protein / Lipase modulator


Mass: 35236.238 Da / Num. of mol.: 2 / Fragment: periplasmic C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia glumae (bacteria) / Gene: lifO, lipB / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: Q05490
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 843 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 52.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20 % PEG3350, 0.2 M KI, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.85→40 Å / Num. all: 119154 / Num. obs: 120503 / % possible obs: 99 % / Redundancy: 7 % / Rmerge(I) obs: 0.072 / Χ2: 1.077 / Net I/σ(I): 15.4
Reflection shellResolution: 1.85→1.92 Å / % possible obs: 91.3 % / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 3.85 / Num. measured obs: 10920 / Χ2: 1.034 / % possible all: 91.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT1.7data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CVL

1cvl


Resolution: 1.85→40 Å
RfactorNum. reflection
Rfree0.219 5974
Rwork0.199 -
obs-119309
Displacement parametersBiso mean: 34.93 Å2
Refinement stepCycle: LAST / Resolution: 1.85→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8611 0 10 843 9464

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