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

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Basic information

Entry
Database: PDB / ID: 3dkr
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
ACETATE ION / Esterase D
Similarity search - Component
Biological speciesLactobacillus rhamnosus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsBennett, M.D. / Delabre, M.-L. / Holland, R. / Norris, G.E.
CitationJournal: To be Published
Title: Crystal structure of esterase D from lactobacillus rhamnosus
Authors: Bennett, M.D. / Delabre, M.-L. / Holland, R. / Norris, G.E.
History
DepositionJun 25, 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
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
A: Esterase D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4463
Polymers27,3281
Non-polymers1182
Water4,522251
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.225, 47.225, 174.572
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-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.11 Å3/Da / Density % sol: 41.62 %
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: Dec 5, 2006 / Details: CONFOCAL
RadiationMonochromator: OSMIC BLUE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 30909 / Num. obs: 30848 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 25.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.77 Å29.84 Å
Translation1.77 Å29.84 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.4SSIdata scaling
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
CrystalCleardata collection
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R1D

1r1d


Resolution: 1.6→29.84 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.957 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.903 / SU B: 1.232 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.184 1549 5 %RANDOM
Rwork0.167 ---
all0.167 30917 --
obs0.167 30844 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 43.97 Å2 / Biso mean: 20.895 Å2 / Biso min: 13.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20.25 Å20 Å2
2--0.49 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1843 0 8 251 2102
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221899
X-RAY DIFFRACTIONr_bond_other_d0.0010.021211
X-RAY DIFFRACTIONr_angle_refined_deg1.2341.9432590
X-RAY DIFFRACTIONr_angle_other_deg0.8932960
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8655244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.85724.47185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.65115276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.755156
X-RAY DIFFRACTIONr_chiral_restr0.0770.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022175
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02392
X-RAY DIFFRACTIONr_nbd_refined0.2210.2397
X-RAY DIFFRACTIONr_nbd_other0.1790.21285
X-RAY DIFFRACTIONr_nbtor_refined0.1830.2950
X-RAY DIFFRACTIONr_nbtor_other0.0840.2914
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1070.2168
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2970.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.214
X-RAY DIFFRACTIONr_mcbond_it0.6221.51222
X-RAY DIFFRACTIONr_mcbond_other0.1581.5492
X-RAY DIFFRACTIONr_mcangle_it1.00421920
X-RAY DIFFRACTIONr_scbond_it1.6363759
X-RAY DIFFRACTIONr_scangle_it2.3354.5668
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.184 120 -
Rwork0.158 2121 -
all-2241 -
obs--99.12 %

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