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- PDB-6wpy: Crystal structure of Bacillus licheniformis lipase BlEst2 in matu... -

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Basic information

Entry
Database: PDB / ID: 6wpy
TitleCrystal structure of Bacillus licheniformis lipase BlEst2 in mature form
ComponentsBlEst2
KeywordsHYDROLASE / esterase / lipase / propetide
Function / homologyGPI inositol-deacylase PGAP1-like / PGAP1-like alpha/beta domain / hydrolase activity, acting on ester bonds / Alpha/Beta hydrolase fold / Lipase
Function and homology information
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsNakamura, A.M. / Godoy, A.S. / Kadowaki, M.A.S. / Polikarpov, I.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2015/13684-0 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)423693/2016-6 and #303988/2016-9 Brazil
CitationJournal: Febs J. / Year: 2024
Title: Structures of BlEst2 from Bacillus licheniformis in its propeptide and mature forms reveal autoinhibitory effects of the C-terminal domain
Authors: Nakamura, A.M. / Godoy, A.S. / Kadowaki, M.A.S. / Trentin, L.N. / Gonzalez, S.E.T. / Skaf, M.S. / Polikarpov, I.
History
DepositionApr 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Aug 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BlEst2
B: BlEst2
C: BlEst2
D: BlEst2
E: BlEst2
F: BlEst2


Theoretical massNumber of molelcules
Total (without water)322,4436
Polymers322,4436
Non-polymers00
Water5,026279
1
A: BlEst2


Theoretical massNumber of molelcules
Total (without water)53,7411
Polymers53,7411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BlEst2


Theoretical massNumber of molelcules
Total (without water)53,7411
Polymers53,7411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: BlEst2


Theoretical massNumber of molelcules
Total (without water)53,7411
Polymers53,7411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: BlEst2


Theoretical massNumber of molelcules
Total (without water)53,7411
Polymers53,7411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: BlEst2


Theoretical massNumber of molelcules
Total (without water)53,7411
Polymers53,7411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: BlEst2


Theoretical massNumber of molelcules
Total (without water)53,7411
Polymers53,7411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.077, 122.518, 157.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein
BlEst2


Mass: 53740.566 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / Gene: DW032_06865 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A415J7C9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 1.53 Å3/Da / Density % sol: 19.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 0.1 M MMT pH 5.0 and 25% (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4585 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4585 Å / Relative weight: 1
ReflectionResolution: 3.6→40.49 Å / Num. obs: 23568 / % possible obs: 99.31 % / Redundancy: 6.4 % / CC1/2: 0.94 / Rpim(I) all: 0.197 / Net I/σ(I): 4.8
Reflection shellResolution: 3.6→3.7 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2306 / CC1/2: 0.62 / Rpim(I) all: 0.489

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WPX

6wpx


Resolution: 3.6→40.49 Å / Cor.coef. Fo:Fc: 0.806 / Cor.coef. Fo:Fc free: 0.764 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.652
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1202 5.1 %RANDOM
Rwork0.214 ---
obs0.216 23568 99.9 %-
Displacement parametersBiso max: 181.88 Å2 / Biso mean: 38.11 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--10.0386 Å20 Å20 Å2
2---7.4826 Å20 Å2
3---17.5212 Å2
Refine analyzeLuzzati coordinate error obs: 0.5 Å
Refinement stepCycle: final / Resolution: 3.6→40.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11580 0 0 279 11859
Biso mean---38.2 -
Num. residues----1470
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3912SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes300HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1770HARMONIC5
X-RAY DIFFRACTIONt_it11976HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1464SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14600SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d11976HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg16278HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion2.83
X-RAY DIFFRACTIONt_other_torsion19.4
LS refinement shellResolution: 3.6→3.76 Å / Rfactor Rfree error: 0 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.274 137 4.84 %
Rwork0.233 2693 -
all0.235 2830 -
obs--99.93 %

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