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- PDB-3dlt: Snapshots of esterase D from lactobacillus rhamnosus: Insights in... -

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Basic information

Entry
Database: PDB / ID: 3dlt
TitleSnapshots of esterase D from lactobacillus rhamnosus: Insights into a rotation driven catalytic mechanism
ComponentsEsterase D
KeywordsHYDROLASE / alpha beta hydrolase / catalytic triad / rotation / esterase
Function / homology
Function and homology information


carboxylic ester hydrolase activity
Similarity search - Function
Esterase/lipase / Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
butanoic acid / Esterase D
Similarity search - Component
Biological speciesLactobacillus rhamnosus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsBennett, M.D. / Delabre, M.-L. / Holland, R. / Norris, G.E.
CitationJournal: To be Published
Title: Snapshots of esterase D from lactobacillus rhamnosus: Insights into a rotation driven catalytic mechanism
Authors: Bennett, M.D. / Delabre, M.-L. / Holland, R. / Norris, G.E.
History
DepositionJun 29, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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
A: Esterase D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5043
Polymers27,3281
Non-polymers1762
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.848, 46.848, 173.954
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Esterase D


Mass: 27327.963 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus rhamnosus (bacteria) / Strain: HN001 / Gene: EstD / Plasmid: pProExHtC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B2CZF3
#2: Chemical ChemComp-BUA / butanoic acid


Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.07 Å3/Da / Density % sol: 40.47 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 6
Details: PEG 8000, Na acetate, pH 6.0, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 21, 2006 / Details: OSMIC BLUE
RadiationMonochromator: Confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→40.57 Å / Num. all: 30410 / Num. obs: 29364 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.85 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 6.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
CrystalCleardata collection
CrystalCleardata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R1D

1r1d


Resolution: 1.9→40.57 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 1 / SU B: 6.124 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 928 5.1 %RANDOM
Rwork0.205 ---
all0.208 18460 --
obs0.208 18336 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 70.86 Å2 / Biso mean: 42.49 Å2 / Biso min: 23.35 Å2
Baniso -1Baniso -2Baniso -3
1-2.67 Å21.33 Å20 Å2
2--2.67 Å20 Å2
3----4 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1834 0 12 107 1953
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221893
X-RAY DIFFRACTIONr_bond_other_d0.0010.021224
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.9482575
X-RAY DIFFRACTIONr_angle_other_deg0.88732991
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3535238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.58224.40584
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59115282
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.667156
X-RAY DIFFRACTIONr_chiral_restr0.0780.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022143
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02388
X-RAY DIFFRACTIONr_nbd_refined0.210.2423
X-RAY DIFFRACTIONr_nbd_other0.1790.21271
X-RAY DIFFRACTIONr_nbtor_refined0.1860.2925
X-RAY DIFFRACTIONr_nbtor_other0.0880.2931
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2115
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1530.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2970.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.210
X-RAY DIFFRACTIONr_mcbond_it0.7431.51266
X-RAY DIFFRACTIONr_mcbond_other0.1511.5486
X-RAY DIFFRACTIONr_mcangle_it1.16821893
X-RAY DIFFRACTIONr_scbond_it1.7623783
X-RAY DIFFRACTIONr_scangle_it2.5214.5682
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.433 76 -
Rwork0.386 1259 -
all-1335 -
obs--100 %

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