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- PDB-5frd: Structure of a thermophilic esterase -

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Basic information

Entry
Database: PDB / ID: 5frd
TitleStructure of a thermophilic esterase
ComponentsCARBOXYLESTERASE (EST-2)
KeywordsHYDROLASE / ESTERASE
Function / homology
Function and homology information


: / Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / CITRATE ANION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Carboxylesterase (Est-2)
Similarity search - Component
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSayer, C. / Finnigan, W. / Isupov, M.N. / Levisson, M. / Kengen, S.W.M. / van der Oost, J. / Harmer, N. / Littlechild, J.A.
CitationJournal: Sci.Rep. / Year: 2016
Title: Structural and Biochemical Characterisation of Archaeoglobus Fulgidus Esterase Reveals a Bound Coa Molecule in the Vicinity of the Active Site.
Authors: Sayer, C. / Finnigan, W. / Isupov, M.N. / Levisson, M. / Kengen, S.W. / Van Der Oost, J. / Harmer, N.J. / Littlechild, J.A.
History
DepositionDec 17, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 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 / database_2 / pdbx_database_status / 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 / _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: CARBOXYLESTERASE (EST-2)
B: CARBOXYLESTERASE (EST-2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6299
Polymers58,5782
Non-polymers2,0517
Water9,260514
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A: CARBOXYLESTERASE (EST-2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0923
Polymers29,2891
Non-polymers8032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CARBOXYLESTERASE (EST-2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5376
Polymers29,2891
Non-polymers1,2485
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.070, 67.200, 140.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.85888, 0.49359, 0.13672), (0.47064, -0.8659, 0.16947), (0.20203, -0.08121, -0.97601)
Vector: -24.40808, -0.45999, 33.27924)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein CARBOXYLESTERASE (EST-2) / ESTERASE


Mass: 29288.809 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS-RIPL / References: UniProt: O28735, carboxylesterase

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Non-polymers , 6 types, 521 molecules

#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 514 / 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: 2.31 Å3/Da / Density % sol: 46.4 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.4→70.3 Å / Num. obs: 102188 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.9
Reflection shellResolution: 1.4→1.44 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2 / % possible all: 89.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A8Q

1a8q


Resolution: 1.4→70.29 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.107 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.17347 2013 2 %RANDOM
Rwork0.15649 ---
obs0.15686 100085 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.568 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20 Å2
2--0.41 Å20 Å2
3----0.99 Å2
Refinement stepCycle: LAST / Resolution: 1.4→70.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4006 0 128 514 4648
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195024
X-RAY DIFFRACTIONr_bond_other_d0.0070.025109
X-RAY DIFFRACTIONr_angle_refined_deg1.6312.0196935
X-RAY DIFFRACTIONr_angle_other_deg1.394311981
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2365716
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.05324.473237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.495151048
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1261536
X-RAY DIFFRACTIONr_chiral_restr0.0940.2776
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025701
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021091
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6127.642287
X-RAY DIFFRACTIONr_mcbond_other3.5897.6352286
X-RAY DIFFRACTIONr_mcangle_it4.65811.4342915
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.48410.3322737
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.437 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 125 -
Rwork0.308 6538 -
obs--88.86 %

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