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- PDB-4uhe: Structural studies of a thermophilic esterase from Thermogutta te... -

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Basic information

Entry
Database: PDB / ID: 4uhe
TitleStructural studies of a thermophilic esterase from Thermogutta terrifontis (malate bound)
ComponentsESTERASE
KeywordsHYDROLASE / ALPHA BETA HYDROLASE
Function / homology
Function and homology information


carboxylesterase / carboxylesterase activity / metal ion binding
Similarity search - Function
: / Epoxide hydrolase-like / alpha/beta hydrolase fold / 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
D-MALATE / TRIETHYLENE GLYCOL / Esterase
Similarity search - Component
Biological speciesPLANCTOMYCETES BACTERIUM R1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
AuthorsSayer, C. / Isupov, M.N. / Bonch-Osmolovskaya, E. / Littlechild, J.A.
CitationJournal: FEBS J. / Year: 2015
Title: Structural Studies of a Thermophilic Esterase from a New Planctomycetes Species, Thermogutta Terrifontis.
Authors: Sayer, C. / Isupov, M.N. / Bonch-Osmolovskaya, E. / Littlechild, J.A.
History
DepositionMar 24, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Jan 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 / pdbx_struct_special_symmetry / 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

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Assembly

Deposited unit
A: ESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5285
Polymers31,1731
Non-polymers3554
Water8,323462
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.330, 43.330, 227.060
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-2100-

HOH

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Components

#1: Protein ESTERASE


Mass: 31172.900 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLANCTOMYCETES BACTERIUM R1 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ARCTICEXPRESS RIL / References: UniProt: A0A0M3KKY6*PLUS, carboxylesterase
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / 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: 2.06 Å3/Da / Density % sol: 40.4 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.16→37.52 Å / Num. obs: 86054 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 9.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.2
Reflection shellResolution: 1.16→1.19 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 2.2 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XUA

2xua


Resolution: 1.16→37.52 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.101 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.14224 4255 4.9 %RANDOM
Rwork0.10679 ---
obs0.10854 81741 98.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.146 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.16→37.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2087 0 21 462 2570
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192589
X-RAY DIFFRACTIONr_bond_other_d0.0020.022610
X-RAY DIFFRACTIONr_angle_refined_deg1.8341.9993587
X-RAY DIFFRACTIONr_angle_other_deg1.07236087
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6075379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.39822.308130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.35815503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1511540
X-RAY DIFFRACTIONr_chiral_restr0.1060.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213015
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02595
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_it2.1772.9091214
X-RAY DIFFRACTIONr_mcbond_other1.812.8971213
X-RAY DIFFRACTIONr_mcangle_it2.5064.9571548
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.0184.0021375
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_restr2.1635198
X-RAY DIFFRACTIONr_sphericity_free41.582521
X-RAY DIFFRACTIONr_sphericity_bonded13.4855538
LS refinement shellResolution: 1.16→1.19 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 298 -
Rwork0.208 5754 -
obs--95.05 %

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