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- PDB-1jfr: CRYSTAL STRUCTURE OF THE STREPTOMYCES EXFOLIATUS LIPASE AT 1.9A R... -

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Basic information

Entry
Database: PDB / ID: 1jfr
TitleCRYSTAL STRUCTURE OF THE STREPTOMYCES EXFOLIATUS LIPASE AT 1.9A RESOLUTION: A MODEL FOR A FAMILY OF PLATELET-ACTIVATING FACTOR ACETYLHYDROLASES
ComponentsLIPASE
KeywordsSERINE HYDROLASE / LIPASE
Function / homology
Function and homology information


carboxylic ester hydrolase activity
Similarity search - Function
Platelet-activating factor acetylhydrolase, isoform II / Cutinase / PET hydrolase-like / : / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Triacylglycerol acylhydrolase
Similarity search - Component
Biological speciesStreptomyces exfoliatus (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.9 Å
AuthorsWei, Y. / Derewenda, Z.S.
CitationJournal: Structure / Year: 1998
Title: Structure of a microbial homologue of mammalian platelet-activating factor acetylhydrolases: Streptomyces exfoliatus lipase at 1.9 A resolution.
Authors: Wei, Y. / Swenson, L. / Castro, C. / Derewenda, U. / Minor, W. / Arai, H. / Aoki, J. / Inoue, K. / Servin-Gonzalez, L. / Derewenda, Z.S.
History
DepositionJul 11, 1997Processing site: BNL
Revision 1.0Jul 15, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LIPASE
B: LIPASE


Theoretical massNumber of molelcules
Total (without water)55,9342
Polymers55,9342
Non-polymers00
Water11,025612
1
A: LIPASE


Theoretical massNumber of molelcules
Total (without water)27,9671
Polymers27,9671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LIPASE


Theoretical massNumber of molelcules
Total (without water)27,9671
Polymers27,9671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.500, 53.000, 81.100
Angle α, β, γ (deg.)90.00, 95.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein LIPASE


Mass: 27967.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces exfoliatus (bacteria) / Gene: STREPTOMYCES EXFOLIATUS / Gene (production host): STREPTOMYCES EXFOLIATUS / Production host: Escherichia coli (E. coli) / References: UniProt: Q56008
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 612 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 8

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 54 %
Crystal growpH: 7.75 / Details: pH 7.75
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mMTris-HCl1drop
25.0-7.0 mg/mlprotein1drop
330 %ammonium sulfate1reservoir
410 %MME20001reservoir
56 %PEG60001reservoir
6200 mMphosphate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Jul 8, 1996 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 49042 / % possible obs: 95.4 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 14.75
Reflection
*PLUS
Num. measured all: 235302 / Rmerge(I) obs: 0.054

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CCP4data reduction
SHELX-90model building
SHELX-90refinement
CCP4data scaling
SHELX-90phasing
RefinementMethod to determine structure: MIR / Resolution: 1.9→8 Å / σ(F): 0 /
RfactorNum. reflection
Rfree0.186 -
Rwork0.14 -
obs-48642
Refine analyzeLuzzati coordinate error obs: 0.01 Å
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3924 0 0 607 4531
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.0280.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0520.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.3012
X-RAY DIFFRACTIONp_mcangle_it3.393
X-RAY DIFFRACTIONp_scbond_it2.8462
X-RAY DIFFRACTIONp_scangle_it4.2163
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor9.237
X-RAY DIFFRACTIONp_staggered_tor2115
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor1815
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.14 / Rfactor Rwork: 0.14
Solvent computation
*PLUS
Displacement parameters
*PLUS

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