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- PDB-3s8y: Bromide soaked structure of an esterase from the oil-degrading ba... -

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Basic information

Entry
Database: PDB / ID: 3s8y
TitleBromide soaked structure of an esterase from the oil-degrading bacterium Oleispira antarctica
ComponentsEsterase APC40077
KeywordsHYDROLASE / Rossmann fold
Function / homology
Function and homology information


S-formylglutathione hydrolase / S-formylglutathione hydrolase activity / formaldehyde catabolic process / carboxylic ester hydrolase activity / cytosol
Similarity search - Function
S-formylglutathione hydrolase / Esterase-like / Putative esterase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / S-formylglutathione hydrolase
Similarity search - Component
Biological speciesOleispira antarctica (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPetit, P. / Dong, A. / Kagan, O. / Savchenko, A. / Yakunin, A.F.
CitationJournal: Biochem.J. / Year: 2012
Title: Structure and activity of the cold-active and anion-activated carboxyl esterase OLEI01171 from the oil-degrading marine bacterium Oleispira antarctica.
Authors: Lemak, S. / Tchigvintsev, A. / Petit, P. / Flick, R. / Singer, A.U. / Brown, G. / Evdokimova, E. / Egorova, O. / Gonzalez, C.F. / Chernikova, T.N. / Yakimov, M.M. / Kube, M. / Reinhardt, R. ...Authors: Lemak, S. / Tchigvintsev, A. / Petit, P. / Flick, R. / Singer, A.U. / Brown, G. / Evdokimova, E. / Egorova, O. / Gonzalez, C.F. / Chernikova, T.N. / Yakimov, M.M. / Kube, M. / Reinhardt, R. / Golyshin, P.N. / Savchenko, A. / Yakunin, A.F.
History
DepositionMay 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 18, 2012Group: Database references
Revision 1.3Sep 13, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Esterase APC40077
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1452
Polymers31,0661
Non-polymers801
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.532, 84.451, 88.051
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Esterase APC40077


Mass: 31065.502 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Thrombin Cleavage / Source: (gene. exp.) Oleispira antarctica (bacteria) / Gene: olei01171 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D0VWZ4, arylesterase
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.66 Å3/Da / Density % sol: 53.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 0.4M Di-Ammonium citrate, 22% PEG3350, Soaking step: KBr 0.8M, 30s. , pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Apr 15, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→19.73 Å / Num. obs: 19720 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Rmerge(I) obs: 0.09 / Rsym value: 0.083 / Net I/σ(I): 17
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 6.3 / Num. unique all: 2775 / Rsym value: 0.27 / % possible all: 97

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3I6Y

3i6y


Resolution: 2.1→19.69 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 15.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1847 959 5.02 %RANDOM
Rwork0.1542 ---
obs0.1557 19117 95.54 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.681 Å2 / ksol: 0.406 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.4264 Å20 Å2-0 Å2
2--2.5964 Å20 Å2
3----7.0228 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2161 0 1 181 2343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082222
X-RAY DIFFRACTIONf_angle_d1.0433026
X-RAY DIFFRACTIONf_dihedral_angle_d12.684787
X-RAY DIFFRACTIONf_chiral_restr0.073314
X-RAY DIFFRACTIONf_plane_restr0.004402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.21060.23021270.16812451X-RAY DIFFRACTION92
2.2106-2.34890.20411260.16232445X-RAY DIFFRACTION91
2.3489-2.52990.20081320.15122537X-RAY DIFFRACTION95
2.5299-2.78380.20941510.14072583X-RAY DIFFRACTION96
2.7838-3.18520.16171470.14052631X-RAY DIFFRACTION97
3.1852-4.00750.1621350.13692715X-RAY DIFFRACTION99
4.0075-19.69640.181410.17752796X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -4.8407 Å / Origin y: 15.6966 Å / Origin z: -7.7503 Å
111213212223313233
T0.0532 Å20.0008 Å20.002 Å2-0.055 Å2-0.0063 Å2--0.0594 Å2
L0.2087 °2-0.0883 °20.0117 °2-0.2956 °2-0.1561 °2--0.4278 °2
S-0.0023 Å °0.0109 Å °0.0095 Å °-0.001 Å °-0.0015 Å °0.0218 Å °0.0073 Å °-0.0326 Å °0.0012 Å °
Refinement TLS groupSelection details: all

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