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- PDB-4po3: Crystal structure of a C4-C4 SN3 tributyrin phosphonate inhibited... -

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Basic information

Entry
Database: PDB / ID: 4po3
TitleCrystal structure of a C4-C4 SN3 tributyrin phosphonate inhibited by ESTERASE B from LACTOBACILLUS RHAMNOSIS
ComponentsEsterase B
KeywordsHYDROLASE / Esterase/Lipase / Triacylglycerase / Hydrolysis
Function / homology
Function and homology information


: / BD-FAE / : / 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
Chem-HY4 / Esterase B
Similarity search - Component
Biological speciesLactobacillus rhamnosus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsBennett, M.D. / Anderson, B.F. / Norris, G.E. / Colbert, D.A.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of a C4-C4 SN3 tributyrin phodphonate inhibited ESTERASE B from LACTOBACILLUS RHAMNOSIS
Authors: Bennett, M.D. / Colbert, D.A. / Anderson, B.F. / Norris, G.E.
History
DepositionFeb 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Esterase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1042
Polymers35,7941
Non-polymers3101
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.853, 109.853, 59.335
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11X-660-

HOH

21X-678-

HOH

31X-689-

HOH

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Components

#1: Protein Esterase B / Esterase/lipase


Mass: 35794.027 Da / Num. of mol.: 1 / Mutation: V218A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus rhamnosus (bacteria) / Strain: HN001 / Gene: LRH_10360 / Plasmid: pGEX_6P3_EstB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: B2CZF4
#2: Chemical ChemComp-HY4 / (2R)-2,3-dibutoxypropyl hydrogen (S)-propylphosphonate


Mass: 310.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H31O5P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 50.81 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.0 ammonium phosphate, 0.1M TrisHCL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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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: Jul 20, 2006
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: 1.44→38.84 Å / Num. obs: 24173 / % possible obs: 89.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.73 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 7.3
Reflection shellResolution: 1.44→1.49 Å / Redundancy: 1.26 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 1.4 / % possible all: 25.5

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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: 1.96→38.84 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.67 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20807 1249 4.9 %RANDOM
Rwork0.16421 ---
obs0.16636 24173 99.51 %-
all-25546 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.301 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.96→38.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2450 0 19 191 2660
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192551
X-RAY DIFFRACTIONr_bond_other_d0.0010.022346
X-RAY DIFFRACTIONr_angle_refined_deg1.8641.9433466
X-RAY DIFFRACTIONr_angle_other_deg0.90435382
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3525313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.13624.545132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.13615399
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2211514
X-RAY DIFFRACTIONr_chiral_restr0.1210.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212950
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02624
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.96→2.011 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 89 -
Rwork0.238 1796 -
obs--100 %

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