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- PDB-8dc1: Structural and biochemical characterization of L. interrogans Lsa... -

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Basic information

Entry
Database: PDB / ID: 8dc1
TitleStructural and biochemical characterization of L. interrogans Lsa45 reveals a penicillin-binding protein with esterase activity
ComponentsLsa45
KeywordsHYDROLASE / Leptospira / esterase / PBP / Beta-Lactamase
Function / homology
Function and homology information


: / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / DI(HYDROXYETHYL)ETHER / Putative lipoprotein
Similarity search - Component
Biological speciesLeptospira interrogans serovar Copenhageni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.62 Å
AuthorsSantos, J.C. / Nascimento, A.L.T.O.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)14/50981-0 Brazil
Sao Paulo Research Foundation (FAPESP)2019/17488-2 Brazil
CitationJournal: Process Biochem / Year: 2023
Title: Structural and biochemical characterization of Leptospira interrogans Lsa45 reveals a penicillin-binding protein with esterase activity.
Authors: Santos, J.C. / Handa, S. / Fernandes, L.G.V. / Bleicher, L. / Gandin, C.A. / de Oliveira-Neto, M. / Ghosh, P. / Nascimento, A.L.T.O.
History
DepositionJun 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed ..._citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lsa45
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,96219
Polymers38,8291
Non-polymers2,13418
Water3,855214
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.141, 74.862, 113.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lsa45


Mass: 38828.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira interrogans serovar Copenhageni (bacteria)
Strain: Fiocruz L1-130 / Gene: LIC_10731 / Production host: Escherichia coli (E. coli) / References: UniProt: Q72UC8
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: I / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.42 Å3/Da / Density % sol: 49.11 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Solution consisting of 100 mM Tris-HCl, pH 8.5, 30% PEG 1500 and 8% MPD

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.5499 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 15, 2018
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5499 Å / Relative weight: 1
ReflectionResolution: 1.62→45.22 Å / Num. obs: 48588 / % possible obs: 99.7 % / Redundancy: 31.5 % / Biso Wilson estimate: 17.64 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.033 / Rrim(I) all: 0.184 / Net I/σ(I): 21.9
Reflection shellResolution: 1.62→1.65 Å / Redundancy: 20.9 % / Rmerge(I) obs: 2.786 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2223 / CC1/2: 0.524 / Rpim(I) all: 0.619 / Rrim(I) all: 2.858 / % possible all: 94.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.62→41.17 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.485 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21059 2405 5 %RANDOM
Rwork0.18474 ---
obs0.186 46108 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.489 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å2-0 Å2-0 Å2
2--0.04 Å2-0 Å2
3---1.01 Å2
Refinement stepCycle: LAST / Resolution: 1.62→41.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2734 0 30 216 2980
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0182818
X-RAY DIFFRACTIONr_bond_other_d0.0010.0192753
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.8923802
X-RAY DIFFRACTIONr_angle_other_deg1.1092.7136360
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6475345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96622.153144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.40715520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8081519
X-RAY DIFFRACTIONr_chiral_restr0.0880.2418
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023120
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02630
X-RAY DIFFRACTIONr_mcbond_it2.7860.6871371
X-RAY DIFFRACTIONr_mcbond_other2.7860.6871370
X-RAY DIFFRACTIONr_mcangle_it3.3961.0321713
X-RAY DIFFRACTIONr_mcangle_other3.3951.0321714
X-RAY DIFFRACTIONr_scbond_it6.6531.1811447
X-RAY DIFFRACTIONr_scbond_other6.6521.1841448
X-RAY DIFFRACTIONr_scangle_other7.7631.5472088
X-RAY DIFFRACTIONr_long_range_B_refined8.59710.0143245
X-RAY DIFFRACTIONr_long_range_B_other8.5829.5883210
LS refinement shellResolution: 1.62→1.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 172 -
Rwork0.265 3232 -
obs--96.43 %
Refinement TLS params.Method: refined / Origin x: 5.354 Å / Origin y: 46.933 Å / Origin z: 81.809 Å
111213212223313233
T0.1089 Å20.0084 Å2-0.0033 Å2-0.0614 Å20.0173 Å2--0.0067 Å2
L1.146 °20.3864 °2-0.6761 °2-1.3542 °2-0.4022 °2--1.5146 °2
S0.0096 Å °-0.0589 Å °-0.0211 Å °0.2417 Å °-0.0257 Å °0.0103 Å °-0.0239 Å °0.0366 Å °0.0161 Å °

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