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

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Basic information

Entry
Database: PDB / ID: 3dyv
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 / aminopeptidase 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
Biological speciesLactobacillus rhamnosus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.81 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
DepositionJul 28, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 28, 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)27,3632
Polymers27,3281
Non-polymers351
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.154, 47.154, 174.226
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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.05 Å3/Da / Density % sol: 39.88 %
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: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 18, 2006 / Details: Osmic Blue
RadiationMonochromator: Osmic Blue / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.81→33.4 Å / Num. all: 41855 / Num. obs: 36866 / % possible obs: 88.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.24 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 12

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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
Crystaldata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DKR

3dkr


Resolution: 1.81→33.4 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.63 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.145 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1078 5 %RANDOM
Rwork0.195 ---
all0.197 21248 --
obs0.197 20296 99.87 %-
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: 49.67 Å2 / Biso mean: 29.854 Å2 / Biso min: 21.84 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20.52 Å20 Å2
2--1.05 Å20 Å2
3----1.57 Å2
Refinement stepCycle: LAST / Resolution: 1.81→33.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1823 0 1 171 1995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221874
X-RAY DIFFRACTIONr_bond_other_d0.0010.021200
X-RAY DIFFRACTIONr_angle_refined_deg0.9961.9442559
X-RAY DIFFRACTIONr_angle_other_deg0.86132934
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2485241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.8324.19881
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.67115274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.217156
X-RAY DIFFRACTIONr_chiral_restr0.0570.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022137
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02390
X-RAY DIFFRACTIONr_nbd_refined0.2030.2378
X-RAY DIFFRACTIONr_nbd_other0.1730.21245
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2927
X-RAY DIFFRACTIONr_nbtor_other0.0830.2865
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1030.2135
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2520.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2910.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1040.27
X-RAY DIFFRACTIONr_mcbond_it0.3951.51254
X-RAY DIFFRACTIONr_mcbond_other0.0671.5487
X-RAY DIFFRACTIONr_mcangle_it0.63221901
X-RAY DIFFRACTIONr_scbond_it0.9343756
X-RAY DIFFRACTIONr_scangle_it1.3114.5657
LS refinement shellResolution: 1.81→1.857 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 90 -
Rwork0.214 1438 -
all-1528 -
obs--100 %

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