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- PDB-2ory: Crystal structure of M37 lipase -

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Basic information

Entry
Database: PDB / ID: 2ory
TitleCrystal structure of M37 lipase
ComponentsLipase
KeywordsHYDROLASE / alpha/beta hydrolase
Function / homology
Function and homology information


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
Biological speciesPhotobacterium sp. M37 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.2 Å
AuthorsJung, S.K. / Jeong, D.G. / Kim, S.J.
CitationJournal: Proteins / Year: 2008
Title: Structural basis for the cold adaptation of psychrophilic M37 lipase from Photobacterium lipolyticum.
Authors: Jung, S.K. / Jeong, D.G. / Lee, M.S. / Lee, J.K. / Kim, H.K. / Ryu, S.E. / Park, B.C. / Kim, J.H. / Kim, S.J.
History
DepositionFeb 5, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Lipase
B: Lipase


Theoretical massNumber of molelcules
Total (without water)77,7962
Polymers77,7962
Non-polymers00
Water3,279182
1
A: Lipase


Theoretical massNumber of molelcules
Total (without water)38,8981
Polymers38,8981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lipase


Theoretical massNumber of molelcules
Total (without water)38,8981
Polymers38,8981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-29 kcal/mol
Surface area26820 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)70.694, 95.102, 99.700
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 Lipase


Mass: 38897.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photobacterium sp. M37 (bacteria) / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / References: UniProt: Q5DRN8, triacylglycerol lipase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.15 Å3/Da / Density % sol: 42.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2M Ammonium acetate, 23-25% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 6, 2005 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 34828 / Num. obs: 34410 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rsym value: 0.052 / Net I/σ(I): 11.7
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 4898 / Rsym value: 0.215 / % possible all: 99

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS0.9refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.2→50 Å / Isotropic thermal model: isotrophic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1711 -random
Rwork0.204 ---
all0.207 34828 --
obs-34410 98.8 %-
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5363 0 0 182 5545
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.42
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.89

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