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- PDB-3dnm: Crystal Structure Hormone-Sensitive Lipase from a Metagenome Library -

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Basic information

Entry
Database: PDB / ID: 3dnm
TitleCrystal Structure Hormone-Sensitive Lipase from a Metagenome Library
ComponentsEsterase/lipase
KeywordsHYDROLASE / alpha/beta hydrolase fold
Function / homology
Function and homology information


triacylglycerol lipase activity
Similarity search - Function
Lipase, GDXG, putative histidine active site / Lipolytic enzymes "G-D-X-G" family, putative histidine active site. / Lipase, GDXG, putative serine active site / Lipolytic enzymes "G-D-X-G" family, putative serine active site. / : / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold ...Lipase, GDXG, putative histidine active site / Lipolytic enzymes "G-D-X-G" family, putative histidine active site. / Lipase, GDXG, putative serine active site / Lipolytic enzymes "G-D-X-G" family, putative serine active site. / : / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Esterase/lipase
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHwang, K.Y. / Nam, K.H.
CitationJournal: Proteins / Year: 2008
Title: Structural and functional analysis of a novel hormone-sensitive lipase from a metagenome library
Authors: Nam, K.H. / Kim, M.-Y. / Kim, S.-J. / Priyadarshi, A. / Kwon, S.-T. / Koo, B.-S. / Yoon, S.-H. / Hwang, K.Y.
History
DepositionJul 2, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 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 / 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 / _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: Esterase/lipase
B: Esterase/lipase
C: Esterase/lipase
D: Esterase/lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,68522
Polymers144,0284
Non-polymers1,65718
Water3,675204
1
A: Esterase/lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2774
Polymers36,0071
Non-polymers2703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Esterase/lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7589
Polymers36,0071
Non-polymers7518
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Esterase/lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2774
Polymers36,0071
Non-polymers2703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Esterase/lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3735
Polymers36,0071
Non-polymers3664
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
D: Esterase/lipase
hetero molecules

D: Esterase/lipase
hetero molecules

A: Esterase/lipase
hetero molecules

A: Esterase/lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,30118
Polymers144,0284
Non-polymers1,27314
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565-x,-y+3/2,z1
crystal symmetry operation2_564-x+1/2,-y+1,z-1/21
crystal symmetry operation5_454x-1/2,y+1/2,z-1/21
Buried area8080 Å2
ΔGint-136 kcal/mol
Surface area42650 Å2
MethodPISA
6
B: Esterase/lipase
C: Esterase/lipase
hetero molecules

B: Esterase/lipase
C: Esterase/lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,06926
Polymers144,0284
Non-polymers2,04222
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y+1/2,z1
Buried area9800 Å2
ΔGint-256 kcal/mol
Surface area42320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.321, 126.828, 233.393
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
DetailsThis protein works in monomer. But crystallographical data shows the dimer protein as reported in some related papers. The depositors consider that the dimer formation is crystallographical data.

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Components

#1: Protein
Esterase/lipase


Mass: 36006.938 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Description: this protein was purified from Metagenome Library(soil uncultured bacteria)
Gene: estE7 / Plasmid: pET21a / Production host: Escherichia coli (E. coli)
References: UniProt: Q0GMU1, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 3.01 Å3/Da / Density % sol: 59.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M Bis-Tris propane, pH 7.0, 0.2M ammonium sulfate, 1M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.23 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 8, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 47996 / Num. obs: 42217 / % possible obs: 88 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1
Reflection shellResolution: 2.8→2.9 Å / % possible all: 96.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LZL

1lzl


Resolution: 2.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.282 2115 RANDOM
Rwork0.233 --
obs0.233 40102 -
all-42217 -
Displacement parametersBiso mean: 47.8071 Å2
Baniso -1Baniso -2Baniso -3
1-8.879 Å20 Å20 Å2
2---21.503 Å20 Å2
3---12.624 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8839 0 86 204 9129
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.2131.5
X-RAY DIFFRACTIONc_mcangle_it2.0832
X-RAY DIFFRACTIONc_scbond_it1.7382
X-RAY DIFFRACTIONc_scangle_it2.7042.5

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