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- PDB-3i6y: Structure of an esterase from the oil-degrading bacterium Oleispi... -

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Basic information

Entry
Database: PDB / ID: 3i6y
TitleStructure of an esterase from the oil-degrading bacterium Oleispira antarctica
ComponentsEsterase APC40077
KeywordsHYDROLASE / Oleispira antarctica / lipase / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


S-formylglutathione hydrolase / S-formylglutathione hydrolase activity / formaldehyde catabolic process / carboxylic ester hydrolase activity
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
DI(HYDROXYETHYL)ETHER / S-formylglutathione hydrolase
Similarity search - Component
Biological speciesOleispira antarctica (bacteria)
MethodX-RAY DIFFRACTION / PHASER / Resolution: 1.75 Å
AuthorsSinger, A.U. / Evdokimova, E. / Kagan, O. / Edwards, A.M. / Joachimiak, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
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
DepositionJul 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 11, 2012Group: Database references
Revision 1.3Dec 9, 2015Group: Data collection
Revision 1.4Sep 6, 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Esterase APC40077
B: Esterase APC40077
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,33711
Polymers62,7882
Non-polymers5499
Water9,152508
1
A: Esterase APC40077
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6776
Polymers31,3941
Non-polymers2845
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Esterase APC40077
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6595
Polymers31,3941
Non-polymers2664
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.845, 88.179, 84.104
Angle α, β, γ (deg.)90.00, 94.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Esterase APC40077


Mass: 31393.768 Da / Num. of mol.: 2
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)-RIPL / References: UniProt: D0VWZ4*PLUS, arylesterase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 508 / 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: 2.64 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.2 M diammonium hydrogen citrate, 20% PEG 3350, Cryoprotected in Paratone-N oil, VAPOR DIFFUSION, SITTING DROP, temperature 294K, pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 23, 2009 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.7→27.94 Å / Num. all: 71147 / Num. obs: 61811 / % possible obs: 86.9 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 16.338
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 5.8 / Num. unique all: 4596 / % possible all: 64.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: PHASER
Starting model: PDB entry 1PV1

1pv1


Resolution: 1.75→27.94 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.138 / SU ML: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22898 3072 5 %RANDOM
Rwork0.18848 ---
obs0.19053 57845 92.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.966 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.03 Å2
2--0.09 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.75→27.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4358 0 33 508 4899
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0214715
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.9426434
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7615602
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59924.224232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16515718
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.391525
X-RAY DIFFRACTIONr_chiral_restr0.1040.2658
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023795
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2220.22559
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.23266
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2432
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.273
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8911.52992
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.28124687
X-RAY DIFFRACTIONr_scbond_it2.39432004
X-RAY DIFFRACTIONr_scangle_it3.434.51747
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.793 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 174 -
Rwork0.253 3436 -
obs-3610 73.7 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0950.00380.03230.28640.08090.1415-0.0077-0.0053-0.0069-0.0431-0.012-0.0003-0.0028-0.00110.0197-0.00310.00320.0082-0.00320.0035-0.0185-2.088819.894-37.5048
20.0647-0.07530.00170.39790.16960.2098-0.0086-0.0089-0.00490.0253-0.01850.01980.0025-0.01160.027-0.0191-0.00390.00270.00490.0006-0.0148-4.721335.4365-5.1982
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 279
2X-RAY DIFFRACTION2B1 - 279

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