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- PDB-1akn: STRUCTURE OF BILE-SALT ACTIVATED LIPASE -

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Entry
Database: PDB / ID: 1akn
TitleSTRUCTURE OF BILE-SALT ACTIVATED LIPASE
DescriptorBILE-SALT ACTIVATED LIPASE
KeywordsHYDROLASE / SERINE ESTERASE / LIPID DEGRADATION / GLYCOPROTEIN / CARBOXYLIC ESTERASE / HYDROLASE()
Specimen sourceBos taurus / mammal / cattle / ウシ /
MethodX-ray diffraction (2.8 Å resolution / Molecular replacement)
AuthorsWang, X. / Zhang, X.
CitationStructure, 1997, 5, 1209-1218

Structure, 1997, 5, 1209-1218 Yorodumi Papers
The crystal structure of bovine bile salt activated lipase: insights into the bile salt activation mechanism.
Wang, X. / Wang, C.S. / Tang, J. / Dyda, F. / Zhang, X.C.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 23, 1997 / Release: May 27, 1998
RevisionDateData content typeGroupProviderType
1.0May 27, 1998Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelNon-polymer description / Version format compliance

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Assembly

Deposited unit
A: BILE-SALT ACTIVATED LIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8332
Polyers63,6111
Non-polymers2211
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)94.390, 94.390, 144.510
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP 31 2 1

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Components

#1: Polypeptide(L)BILE-SALT ACTIVATED LIPASE / CARBOXYL ESTER LIPASE / STEROL ESTERASE / CHOLESTEROL ESTERASE / PANCREATIC LYSOPHOSPHOLIPASE


Mass: 63611.363 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / mammal / ウシ / / References: UniProt: P30122, EC: 3.1.1.3

Cellular component

Molecular function

Biological process

#2: ChemicalChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 1 / Formula: C8H15NO6

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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: 2.93 / Density percent sol: 58
Crystal growpH: 7 / Details: pH 7.
Crystal grow
*PLUS
Temp: 20 K / Temp unit: ℃ / Method: Vapor diffusion, hanging drop
Crystal grow comp
*PLUS
IDConcConc unitCrystal IDCommon nameSol ID
112.5mg/ml1proteindrop
20.9M1ammonium sulfatedrop
32.5%1isopropanoldrop
40.5mM1zwittergent 3-12drop
51.8M1ammonium sulfatereservoir
65%1isopropanolreservoir
71mM1zwittergent 3-12reservoir

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Data collection

DiffractionMean temperature: 288 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Details: MIRROR / Detector: IMAGE PLATE / Collection date: Dec 1, 1996
RadiationMonochromator: NI FILTER / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 66.1 Å2 / D resolution high: 2.8 Å / D resolution low: 33.7 Å / Number obs: 18614 / Observed criterion sigma I: 0 / Rmerge I obs: 0.066 / NetI over sigmaI: 13.8 / Redundancy: 2.53 / Percent possible obs: 98.4
Reflection shellRmerge I obs: 0.39 / Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / MeanI over sigI obs: 2.8 / Redundancy: 1.3 / Percent possible all: 91.2
Reflection
*PLUS
D resolution low: 34 Å
Reflection shell
*PLUS
Percent possible obs: 99.8 / Rmerge I obs: 0.391

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ACE
Details: AT FINAL STEP, ALL DATA IN 8 - 2.8 A WERE USED TO CARRY OUT A RESTRAINED TEMPERATURE FACTOR REFINEMENT BY TNT.
R Free selection details: RANDOM
Displacement parametersB iso mean: 47.6 Å2
Least-squares processR factor R free: 0.29 / R factor R work: 0.211 / R factor obs: 0.211 / Highest resolution: 2.8 Å / Lowest resolution: 8 Å / Number reflection R free: 1706 / Number reflection obs: 17178 / Percent reflection R free: 9.3 / Percent reflection obs: 95.3
Refine hist #LASTHighest resolution: 2.8 Å / Lowest resolution: 8 Å
Number of atoms included #LASTProtein: 4261 / Nucleic acid: 0 / Ligand: 14 / Solvent: 0 / Total: 4275
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.32
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2NAG.PARNAG.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Least-squares process
*PLUS
R factor R free: 0.283 / R factor obs: 0.216
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.32

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