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- PDB-4n5i: Crystal Structure of a C8-C4 Sn3 Inhibited Esterase B from Lactob... -

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Basic information

Entry
Database: PDB / ID: 4n5i
TitleCrystal Structure of a C8-C4 Sn3 Inhibited Esterase B from Lactobacillus Rhamnosis
ComponentsEsterase/lipase
KeywordsHYDROLASE / alpha/beta Hydrolase Fold / Esterase/Lipase Transferase / Triacylglycerase / Hydrolysis
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / (2R)-2,3-dibutoxypropyl (R)-octylphosphinate / ACETATE ION / :
Function and homology information
Biological speciesLactobacillus rhamnosus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsColbert, D.A. / Bennett, M.D. / Lun, D.J. / Loo, T.S. / Anderson, B.F. / Norris, G.E.
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of a C8-C4 Sn3 Inhibited Esterase B from Lactobacillus Rhamnosis
Authors: Colbert, D.A. / D Bennett, M. / J Lun, D. / S Loo, T. / F Anderson, B. / E Norris, G.
History
DepositionOct 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Esterase/lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2774
Polymers35,7941
Non-polymers4833
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.826, 109.826, 59.347
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Esterase/lipase


Mass: 35794.027 Da / Num. of mol.: 1 / Mutation: V210A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus rhamnosus (bacteria) / Strain: Lc 705 / Gene: LC705_02872, LRH_10360 / Plasmid: pGEX_6P3_EstB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: C7TF14
#2: Chemical ChemComp-2HD / (2R)-2,3-dibutoxypropyl (R)-octylphosphinate


Mass: 364.500 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H41O4P
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.0 M ammonium phosphate, 0.1 M TrisHCl, pH 7.2-8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 28, 2007 / Details: Capillary focusing optics and monochromator
RadiationMonochromator: capillary focusing optics and monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→27.1 Å / Num. all: 23508 / Num. obs: 23508 / % possible obs: 97 % / Observed criterion σ(I): 3 / Redundancy: 4.17 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 6.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.14 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2269 / % possible all: 95.9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.7.0029refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4N5H

4n5h


Resolution: 2→27.1 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.665 / SU ML: 0.102 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21512 1201 5.1 %RANDOM
Rwork0.1618 ---
all0.16452 22293 --
obs0.16452 22293 97.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.402 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å2-0 Å2
2---0.19 Å20 Å2
3---0.39 Å2
Refinement stepCycle: LAST / Resolution: 2→27.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2472 0 32 297 2801
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192598
X-RAY DIFFRACTIONr_bond_other_d0.0010.022403
X-RAY DIFFRACTIONr_angle_refined_deg1.7641.9463525
X-RAY DIFFRACTIONr_angle_other_deg0.92835512
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7585316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.9424.296135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.52315406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2491516
X-RAY DIFFRACTIONr_chiral_restr0.1130.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213013
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02641
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 90 -
Rwork0.225 1600 -
obs-90 95.64 %

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