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- PDB-5aoc: The structure of a novel thermophilic esterase from the Planctomy... -

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Basic information

Entry
Database: PDB / ID: 5aoc
TitleThe structure of a novel thermophilic esterase from the Planctomycetes species, Thermogutta terrifontis, Est2-valerate bound
ComponentsESTERASE
KeywordsHYDROLASE / CARBOXYL / CARBOXYL ESTERASE
Function / homology
Function and homology information


carboxylesterase / carboxylesterase activity / triacylglycerol lipase activity
Similarity search - Function
: / BD-FAE / : / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PENTANOIC ACID / DI(HYDROXYETHYL)ETHER / Esterase
Similarity search - Component
Biological speciesTHERMOGUTTA TERRIFONTIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsSayer, C. / Szabo, Z. / Isupov, M.N. / Ingham, C. / Littlechild, J.A.
CitationJournal: Front.Microbiol. / Year: 2015
Title: The Structure of a Novel Thermophilic Esterase from the Planctomycetes Species, Thermogutta Terrifontis Reveals an Open Active Site due to a Minimal 'CAP' Domain.
Authors: Sayer, C. / Szabo, Z. / Isupov, M.N. / Ingham, C. / Littlechild, J.A.
History
DepositionSep 10, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2May 3, 2017Group: 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 / 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: ESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,83715
Polymers31,5581
Non-polymers1,27914
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.991, 70.874, 75.932
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ESTERASE


Mass: 31557.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOGUTTA TERRIFONTIS (bacteria) / Strain: R1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0X1KHD1*PLUS, carboxylesterase

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Non-polymers , 6 types, 228 molecules

#2: Chemical ChemComp-LEA / PENTANOIC ACID / VALERIC ACID


Mass: 102.132 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10O2
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 214 / 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 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91731
DetectorType: DECTRIS PIXEL / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91731 Å / Relative weight: 1
ReflectionResolution: 1.79→51.8 Å / Num. obs: 32257 / % possible obs: 100 % / Observed criterion σ(I): 1.6 / Redundancy: 6.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.8
Reflection shellResolution: 1.79→1.9 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 1.6 / % possible all: 100

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Processing

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

1evq


Resolution: 1.79→51.81 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.692 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24096 1596 5 %RANDOM
Rwork0.18467 ---
obs0.1875 30305 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.184 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å20 Å2
2---1.51 Å20 Å2
3---0.86 Å2
Refinement stepCycle: LAST / Resolution: 1.79→51.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2151 0 83 214 2448
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192465
X-RAY DIFFRACTIONr_bond_other_d0.0020.022419
X-RAY DIFFRACTIONr_angle_refined_deg1.461.9773327
X-RAY DIFFRACTIONr_angle_other_deg0.97735588
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8145321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.80422.81121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.64615409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0331526
X-RAY DIFFRACTIONr_chiral_restr0.0890.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212790
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02584
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_it4.2046.7861161
X-RAY DIFFRACTIONr_mcbond_other4.1946.7721160
X-RAY DIFFRACTIONr_mcangle_it5.23811.3231460
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.1618.5731304
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: 1.79→1.836 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 96 -
Rwork0.327 2206 -
obs--98.46 %

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