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2es4

Crystal structure of the Burkholderia glumae lipase-specific foldase in complex with its cognate lipase

Method: X-RAY DIFFRACTION Dmax: 111.8 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Lipase

OrganismNot specified

UniProt Q05489

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 40–358 Not recorded Lipase chaperone × 1 （Q05490） CA CALCIUM ION × 1 IOD IODIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；20 % PEG3350, 0.2 M KI, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.85 Å R-free 0.219
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 40–358 Not recorded Lipase chaperone × 1 （Q05490） CA CALCIUM ION × 1 IOD IODIDE ION × 7 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；20 % PEG3350, 0.2 M KI, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.85 Å R-free 0.219
3 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain A； UniProt 40–358 Chain B； UniProt 40–358 Not recorded Lipase chaperone × 4 （Q05490） CA CALCIUM ION × 4 IOD IODIDE ION × 16 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；20 % PEG3350, 0.2 M KI, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.85 Å R-free 0.219

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 2ES4 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CVL CRYSTAL STRUCTURE OF BACTERIAL LIPASE FROM CHROMOBACTERIUM VISCOSUM ATCC 6918 Deposited 1997-01-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 40–358（319 aa）
Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.4；PROTEIN WAS CRYSTALLIZED FROM 10-14 % PEG 4000, 10-14 % MPD, 100 MM CITRATE/PHOSPHATE BUFFER, PH 6.4
Resolution 1.60 Å
1QGE NEW CRYSTAL FORM OF PSEUDOMONAS GLUMAE (FORMERLY CHROMOBACTERIUM VISCOSUM ATCC 6918) LIPASE Deposited 1999-04-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain D 40–261（222 aa）
Chain E 262–358（97 aa）
Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；PROTEIN WAS CRYSTALLIZED FROM 10 % PEG 6000, 5 % PEG 1000, 100 MM HEPES BUFFER, PH 7.8
Resolution 1.70 Å R-free 0.228
1TAH THE CRYSTAL STRUCTURE OF TRIACYLGLYCEROL LIPASE FROM PSEUDOMONAS GLUMAE REVEALS A PARTIALLY REDUNDANT CATALYTIC ASPARTATE Deposited 1993-12-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 41–358（318 aa）
Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å R-free 0.226
1TAH THE CRYSTAL STRUCTURE OF TRIACYLGLYCEROL LIPASE FROM PSEUDOMONAS GLUMAE REVEALS A PARTIALLY REDUNDANT CATALYTIC ASPARTATE Deposited 1993-12-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 41–358（318 aa）
Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å R-free 0.226
1TAH THE CRYSTAL STRUCTURE OF TRIACYLGLYCEROL LIPASE FROM PSEUDOMONAS GLUMAE REVEALS A PARTIALLY REDUNDANT CATALYTIC ASPARTATE Deposited 1993-12-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 41–358（318 aa）
Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å R-free 0.226
1TAH THE CRYSTAL STRUCTURE OF TRIACYLGLYCEROL LIPASE FROM PSEUDOMONAS GLUMAE REVEALS A PARTIALLY REDUNDANT CATALYTIC ASPARTATE Deposited 1993-12-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 41–358（318 aa）
Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å R-free 0.226

3 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LIP_BURGL
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–319； UniProt 40–358 Author chain B； PDBConstruct 1–319； UniProt 40–358

Lipase chaperone

Burkholderia glumae

UniProt Q05490

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain D； UniProt 42–353 Fragment：periplasmic C-terminal domain Non-standard monomer：Yes (specific site not provided by mmCIF) Lipase × 1 （Q05489） CA CALCIUM ION × 1 IOD IODIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；20 % PEG3350, 0.2 M KI, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.85 Å R-free 0.219
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain E； UniProt 42–353 Fragment：periplasmic C-terminal domain Non-standard monomer：Yes (specific site not provided by mmCIF) Lipase × 1 （Q05489） CA CALCIUM ION × 1 IOD IODIDE ION × 7 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；20 % PEG3350, 0.2 M KI, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.85 Å R-free 0.219
3 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain D； UniProt 42–353 Chain E； UniProt 42–353 Fragment：periplasmic C-terminal domain Non-standard monomer：Yes (specific site not provided by mmCIF) Lipase × 4 （Q05489） CA CALCIUM ION × 4 IOD IODIDE ION × 16 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；20 % PEG3350, 0.2 M KI, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.85 Å R-free 0.219

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name LIFO_BURGL
Isoform —
PDB entities 2
Chains and sequence ranges Author chain D； PDBConstruct 22–332； UniProt 42–353 Author chain E； PDBConstruct 22–332； UniProt 42–353

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 2es4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2es4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2es4
Deposition date deposition_date2005-10-25
Structure title titleCrystal structure of the Burkholderia glumae lipase-specific foldase in complex with its cognate lipase
Keywords keywords;protein-protein complex, steric chaperone, triacylglycerol hydrolase, all alpha helix protein, a/b hydrolase fold, extensive interaction area, Hydrolase ;; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier34.96 Å
Radius of gyration Rg (electron density) rg_electron34.26 Å
Forward intensity I(0) i0258965000.00
Molecular weight molecular_weight123170.0 kDa
Excluded volume excluded_volume151300 ų
Envelope volume envelope_volume198990 ų
Hydration-shell volume shell_volume47858 ų
Envelope diameter envelope_diameter120.5 Å
Shell Rg shell_rg41.50 Å
Envelope Rg envelope_rg33.89 Å
Shape Rg shape_rg34.17 Å
Total Rg total_rg35.04 Å
Total atoms total_atoms8620
Residues n_residues1176
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax111.8 Å
Rg (real space) rg_real34.90 Å
Rg uncertainty (real space) rg_real_error0.63 Å
I(0) (real space) i0_real2.5900e+08
I(0) uncertainty (real space) i0_real_error3.6120e+06
Rg (reciprocal space) rg_reciprocal34.94 Å
I(0) (reciprocal space) i0_reciprocal259000000.0000
Solution quality estimate total_estimate0.9040
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary39.7 Å
Skewness Skewness skewness0.235
Kurtosis Kurtosis kurtosis-0.564
Angular range angular_range— – 0.2250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha41990000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.934; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.945
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd2es4a_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamilyc.69.1 — alpha/beta-Hydrolases
Family Family familyc.69.1.18 — Bacterial lipase
Domain ID domain_idd2es4b_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamilyc.69.1 — alpha/beta-Hydrolases
Family Family familyc.69.1.18 — Bacterial lipase
Domain ID domain_idd2es4d1
Class classa — All alpha proteins
Fold Fold folda.137 — Non-globular all-alpha subunits of globular proteins
Superfamily Superfamily superfamilya.137.15 — Lipase chaperone-like
Family Family familya.137.15.1 — Lipase chaperone LifO-like
Domain ID domain_idd2es4e_
Class classa — All alpha proteins
Fold Fold folda.137 — Non-globular all-alpha subunits of globular proteins
Superfamily Superfamily superfamilya.137.15 — Lipase chaperone-like
Family Family familya.137.15.1 — Lipase chaperone LifO-like

CATH v4.4 (2 domains)

Domain ID domain_id2es4A00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1820 — Alpha/Beta hydrolase fold, catalytic domain
Domain ID domain_id2es4B00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1820 — Alpha/Beta hydrolase fold, catalytic domain
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8. Citations (2)

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9. Files and Curves (10)