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- PDB-5a2g: An esterase from anaerobic Clostridium hathewayi can hydrolyze al... -

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Basic information

Entry
Database: PDB / ID: 5a2g
TitleAn esterase from anaerobic Clostridium hathewayi can hydrolyze aliphatic aromatic polyesters
ComponentsCARBOXYLIC ESTER HYDROLASECarboxylesterase
KeywordsHYDROLASE / MICROBIAL POLYESTERASE / ANAEROBIC ESTERASE / POLYESTER BIODEGRADATION / BIOGAS BATCH / ANAEROBIC BIODEGRADATION / CLOSTRIDIUM HATHEWAYI
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / hydrolase activity
Similarity search - Function
Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Carboxylic ester hydrolase
Similarity search - Component
Biological speciesHUNGATELLA HATHEWAYI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.899 Å
AuthorsHromic, A. / Pavkov Keller, T. / Steinkellner, G. / Gruber, K. / Perz, V. / Baumschlager, A. / Bleymaier, K. / Zitzenbacher, S. / Zankel, A. / Mayrhofer, C. ...Hromic, A. / Pavkov Keller, T. / Steinkellner, G. / Gruber, K. / Perz, V. / Baumschlager, A. / Bleymaier, K. / Zitzenbacher, S. / Zankel, A. / Mayrhofer, C. / Sinkel, C. / Kueper, U. / Schlegel, K.A. / Ribitsch, D. / Guebitz, G.M.
CitationJournal: Environ.Sci.Tech. / Year: 2016
Title: An Esterase from Anaerobic Clostridium Hathewayi Can Hydrolyze Aliphatic-Aromatic Polyesters.
Authors: Perz, V. / Hromic, A. / Baumschlager, A. / Steinkellner, G. / Pavkov-Keller, T. / Gruber, K. / Bleymaier, K. / Zitzenbacher, S. / Zankel, A. / Mayrhofer, C. / Sinkel, C. / Kueper, U. / ...Authors: Perz, V. / Hromic, A. / Baumschlager, A. / Steinkellner, G. / Pavkov-Keller, T. / Gruber, K. / Bleymaier, K. / Zitzenbacher, S. / Zankel, A. / Mayrhofer, C. / Sinkel, C. / Kueper, U. / Schlegel, K. / Ribitsch, D. / Guebitz, G.M.
History
DepositionMay 19, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Mar 30, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: CARBOXYLIC ESTER HYDROLASE
B: CARBOXYLIC ESTER HYDROLASE
C: CARBOXYLIC ESTER HYDROLASE
D: CARBOXYLIC ESTER HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,4998
Polymers233,1194
Non-polymers3804
Water28,6801592
1
A: CARBOXYLIC ESTER HYDROLASE
B: CARBOXYLIC ESTER HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,7494
Polymers116,5592
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-30.7 kcal/mol
Surface area37420 Å2
MethodPISA
2
C: CARBOXYLIC ESTER HYDROLASE
D: CARBOXYLIC ESTER HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,7494
Polymers116,5592
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-30.1 kcal/mol
Surface area37370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.050, 241.830, 83.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
CARBOXYLIC ESTER HYDROLASE / Carboxylesterase / ESTERASE


Mass: 58279.691 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUNGATELLA HATHEWAYI (bacteria) / Strain: DSM 13479 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD
References: UniProt: D3AU79, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1592 / 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: 2.63 Å3/Da / Density % sol: 53.25 % / Description: NONE
Crystal growDetails: 1.0 M AMMONIUM SULFATE, 0.1 M HEPES, PH 7.0 AND 0.5 % W/V POLYETHYLENE GLYCOL 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.9→60 Å / Num. obs: 163181 / % possible obs: 84.1 % / Observed criterion σ(I): 2.1 / Redundancy: 2.9 % / Biso Wilson estimate: 20.92 Å2 / Rsym value: 0.09 / Net I/σ(I): 7.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.1 / % possible all: 74.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
XDSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OGS

2ogs


Resolution: 1.899→60.103 Å / SU ML: 0.27 / σ(F): 1.39 / Phase error: 25.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2374 8044 4.9 %
Rwork0.1886 --
obs0.191 163038 84.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.899→60.103 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15760 0 20 1592 17372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00516204
X-RAY DIFFRACTIONf_angle_d0.91422004
X-RAY DIFFRACTIONf_dihedral_angle_d13.5445904
X-RAY DIFFRACTIONf_chiral_restr0.0362320
X-RAY DIFFRACTIONf_plane_restr0.0052888
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8991-1.92070.38912200.32743914X-RAY DIFFRACTION65
1.9207-1.94330.34212450.29514625X-RAY DIFFRACTION75
1.9433-1.9670.34392500.27484672X-RAY DIFFRACTION77
1.967-1.99190.32012540.26474757X-RAY DIFFRACTION78
1.9919-2.01810.31452320.264804X-RAY DIFFRACTION79
2.0181-2.04570.30322370.25054965X-RAY DIFFRACTION80
2.0457-2.0750.31952670.24544951X-RAY DIFFRACTION81
2.075-2.10590.30322790.2354898X-RAY DIFFRACTION82
2.1059-2.13880.26622270.22435140X-RAY DIFFRACTION82
2.1388-2.17390.28212370.22964931X-RAY DIFFRACTION81
2.1739-2.21140.3122680.23315033X-RAY DIFFRACTION82
2.2114-2.25160.30162920.24394815X-RAY DIFFRACTION80
2.2516-2.29490.30332620.2264568X-RAY DIFFRACTION74
2.2949-2.34180.2942690.21635238X-RAY DIFFRACTION87
2.3418-2.39270.27982970.20895556X-RAY DIFFRACTION91
2.3927-2.44830.27232820.19915455X-RAY DIFFRACTION90
2.4483-2.50960.26972740.19895525X-RAY DIFFRACTION90
2.5096-2.57740.24953050.19965452X-RAY DIFFRACTION89
2.5774-2.65330.26712950.19735350X-RAY DIFFRACTION89
2.6533-2.73890.24232370.19745375X-RAY DIFFRACTION87
2.7389-2.83680.25562740.19935221X-RAY DIFFRACTION85
2.8368-2.95040.24772800.1954737X-RAY DIFFRACTION78
2.9504-3.08460.24743030.1975489X-RAY DIFFRACTION90
3.0846-3.24730.23132740.19045805X-RAY DIFFRACTION94
3.2473-3.45070.23112770.18135747X-RAY DIFFRACTION94
3.4507-3.71710.20822700.16425669X-RAY DIFFRACTION92
3.7171-4.09110.17172660.1465477X-RAY DIFFRACTION90
4.0911-4.68290.15973030.13085296X-RAY DIFFRACTION86
4.6829-5.89910.16232950.13585855X-RAY DIFFRACTION96
5.8991-60.13320.16632730.14425674X-RAY DIFFRACTION91

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