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- PDB-1jkm: BREFELDIN A ESTERASE, A BACTERIAL HOMOLOGUE OF HUMAN HORMONE SENS... -

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Basic information

Entry
Database: PDB / ID: 1jkm
TitleBREFELDIN A ESTERASE, A BACTERIAL HOMOLOGUE OF HUMAN HORMONE SENSITIVE LIPASE
ComponentsBREFELDIN A ESTERASE
KeywordsSERINE HYDROLASE / DEGRADATION OF BREFELDIN A / ALPHA/BETA HYDROLASE FAMILY
Function / homology
Function and homology information


: / 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
: / Brefeldin A esterase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.85 Å
AuthorsWei, Y. / Contreras, A.J. / Sheffield, P. / Osterlund, T. / Derewenda, U. / Matern, U.O. / Derewenda, Z.S.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: Crystal structure of brefeldin A esterase, a bacterial homolog of the mammalian hormone-sensitive lipase.
Authors: Wei, Y. / Contreras, J.A. / Sheffield, P. / Osterlund, T. / Derewenda, U. / Kneusel, R.E. / Matern, U. / Holm, C. / Derewenda, Z.S.
History
DepositionFeb 4, 1998Processing site: BNL
Revision 1.0Feb 16, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BREFELDIN A ESTERASE
B: BREFELDIN A ESTERASE


Theoretical massNumber of molelcules
Total (without water)77,1262
Polymers77,1262
Non-polymers00
Water9,566531
1
A: BREFELDIN A ESTERASE
B: BREFELDIN A ESTERASE

A: BREFELDIN A ESTERASE
B: BREFELDIN A ESTERASE


Theoretical massNumber of molelcules
Total (without water)154,2524
Polymers154,2524
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)140.700, 82.600, 81.500
Angle α, β, γ (deg.)90.00, 112.50, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein BREFELDIN A ESTERASE


Mass: 38563.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Cell line: 293 / Production host: Escherichia coli (E. coli) / Strain (production host): 293 / References: GenBank: 3025874, UniProt: O68884*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 531 / 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: 20

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop
Details: drop contained equal volume of protein and reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.0 mg/mlprotein1drop
240 %satammonium sulfate1reservoir
3100 mMammonium acetate1reservoir
45.0 mMpotassium phosphate1reservoir
50.5 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.54
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. obs: 62664 / % possible obs: 86 % / Redundancy: 1.8 % / Rsym value: 0.108 / Net I/σ(I): 9.4
Reflection
*PLUS
% possible obs: 85.8 % / Num. measured all: 206345 / Rmerge(I) obs: 0.108
Reflection shell
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 1.88 Å / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2.5

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Processing

Software
NameClassification
SHELX-90model building
SHELX-90refinement
XENGENdata reduction
DENZOdata reduction
SCALEPACKdata scaling
CCP4data scaling
SHELX-90phasing
RefinementMethod to determine structure: MIR / Resolution: 1.85→8 Å / Cross valid method: FREE R / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.206 -5 %
Rwork0.169 --
obs0.17 62664 85.8 %
Displacement parametersBiso mean: 18.1 Å2
Refinement stepCycle: LAST / Resolution: 1.85→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5012 0 0 524 5536
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0280.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0330.05
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_tor9.27
X-RAY DIFFRACTIONp_staggered_tor2115
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.4

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