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- PDB-6wpx: Crystal structure of Bacillus licheniformis lipase BlEst2 in prop... -

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Basic information

Entry
Database: PDB / ID: 6wpx
TitleCrystal structure of Bacillus licheniformis lipase BlEst2 in propetide 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 / IODIDE ION / Lipase
Function and homology information
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 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 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,52726
Polymers107,4812
Non-polymers3,04624
Water7,963442
1
A: BlEst2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,39014
Polymers53,7411
Non-polymers1,65013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BlEst2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,13712
Polymers53,7411
Non-polymers1,39611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.890, 78.315, 166.486
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein BlEst2


Mass: 53740.566 Da / Num. of mol.: 2
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: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.03 Å3/Da / Density % sol: 39.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.2 M calcium chloride, 0.1 M Tris pH 8.0 and 28% (w/v) polyethylene glycol (PEG)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 2→20.16 Å / Num. obs: 59739 / % possible obs: 99 % / Redundancy: 6.9 % / CC1/2: 0.99 / Rpim(I) all: 0.077 / Net I/σ(I): 12.88
Reflection shellResolution: 2→2.07 Å / Num. unique obs: 5862 / CC1/2: 0.61 / Rpim(I) all: 0.618

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2→20.16 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.913 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.202 / SU Rfree Blow DPI: 0.162 / SU Rfree Cruickshank DPI: 0.161
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1983 3.32 %RANDOM
Rwork0.196 ---
obs0.197 59727 99.8 %-
Displacement parametersBiso max: 100.67 Å2 / Biso mean: 29.07 Å2 / Biso min: 7.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.1976 Å20 Å20 Å2
2--2.3601 Å20 Å2
3----3.5578 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: final / Resolution: 2→20.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7010 0 24 442 7476
Biso mean--57.55 32.57 -
Num. residues----901
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2428SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes185HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1058HARMONIC5
X-RAY DIFFRACTIONt_it7205HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion920SEMIHARMONIC5
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_contact8995SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7205HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg9760HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion3.6
X-RAY DIFFRACTIONt_other_torsion15.72
LS refinement shellResolution: 2→2.05 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 144 3.31 %
Rwork0.222 4200 -
all0.223 4344 -
obs--99.52 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2898-1.3081-0.49041.85320.96821.0601-0.1636-0.1198-0.12150.12830.11050.13360.03060.10220.0531-0.08150.0407-0.03-0.0682-0.0082-0.0308-4.473710.2828-22.1752
20.84740.2188-0.05921.6228-0.26780.3230.0444-0.0760.0259-0.06680.0162-0.0655-0.0105-0.0201-0.0606-0.0366-0.0636-0.0051-0.02210.003-0.0894-29.12210.4069-62.0619
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A29 - 482
2X-RAY DIFFRACTION2{ B|* }B28 - 482

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