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- PDB-3ngm: Crystal structure of lipase from Gibberella zeae -

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Basic information

Entry
Database: PDB / ID: 3ngm
TitleCrystal structure of lipase from Gibberella zeae
ComponentsExtracellular lipase
KeywordsHYDROLASE / secret lipase / Gibberella zeae
Function / homology
Function and homology information


triacylglycerol lipase / triacylglycerol lipase activity / lipid metabolic process
Similarity search - Function
Fungal lipase-like domain / Lipase (class 3) / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Extracellular lipase
Similarity search - Component
Biological speciesGibberella zeae (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLou, Z.Y. / Li, M. / Sun, Y.N. / Liu, Y. / Liu, Z. / Rao, Z.H.
CitationJournal: Protein Cell / Year: 2010
Title: Crystal structure of a secreted lipase from Gibberella zeae reveals a novel "double-lock" mechanism
Authors: Lou, Z.Y. / Li, M. / Sun, Y.N. / Liu, Y. / Liu, Z. / Wu, W.P. / Rao, Z.H.
History
DepositionJun 12, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Extracellular lipase
B: Extracellular lipase
C: Extracellular lipase
D: Extracellular lipase


Theoretical massNumber of molelcules
Total (without water)135,1984
Polymers135,1984
Non-polymers00
Water3,927218
1
A: Extracellular lipase


Theoretical massNumber of molelcules
Total (without water)33,8001
Polymers33,8001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Extracellular lipase


Theoretical massNumber of molelcules
Total (without water)33,8001
Polymers33,8001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Extracellular lipase


Theoretical massNumber of molelcules
Total (without water)33,8001
Polymers33,8001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Extracellular lipase


Theoretical massNumber of molelcules
Total (without water)33,8001
Polymers33,8001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.417, 91.001, 195.802
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Extracellular lipase


Mass: 33799.562 Da / Num. of mol.: 4 / Fragment: residues 1-319
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gibberella zeae (fungus) / Gene: FGL1 / Plasmid: pLIZG7 / Production host: Pichia pastoris (fungus) / Strain (production host): KM71 / References: UniProt: Q6WER3, triacylglycerol lipase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.58 Å3/Da / Density % sol: 52.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 3, 2008 / Details: osmic mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 35284 / Num. obs: 34080 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.101

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EIN

1ein


Resolution: 2.8→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.264 2906 random
Rwork0.238 --
all-34080 -
obs-29217 -
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8792 0 0 218 9010
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg0.006
X-RAY DIFFRACTIONc_bond_d1.097

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