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

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Basic information

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


carboxylesterase / carboxylesterase activity
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
CACODYLIC ACID / DI(HYDROXYETHYL)ETHER / Alpha/beta hydrolase fold
Similarity search - Component
Biological speciesPLANCTOMYCETES BACTERIUM R1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.06 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 / 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)30,4954
Polymers30,2161
Non-polymers2803
Water8,251458
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.310, 43.310, 226.850
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-2103-

HOH

21A-2259-

HOH

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Components

#1: Protein ESTERASE


Mass: 30215.900 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: A0A0H4B872*PLUS, carboxylesterase
#2: Chemical ChemComp-CAD / CACODYLIC ACID / HYDROXYDIMETHYLARSINE OXIDE


Mass: 137.997 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H7AsO2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 458 / 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 Å3/Da / Density % sol: 40 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949
DetectorType: DECTRIS PIXEL / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.06→37.81 Å / Num. obs: 113560 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.5
Reflection shellResolution: 1.06→1.09 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.1 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XUA

2xua


Resolution: 1.06→37.81 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.983 / SU B: 0.66 / SU ML: 0.015 / Cross valid method: THROUGHOUT / ESU R: 0.021 / ESU R Free: 0.022 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.12312 5507 4.9 %RANDOM
Rwork0.10295 ---
obs0.10393 107919 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.171 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.02 Å20 Å2
2--0.04 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.06→37.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2104 0 13 458 2575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192631
X-RAY DIFFRACTIONr_bond_other_d0.0010.022658
X-RAY DIFFRACTIONr_angle_refined_deg1.6992.0033650
X-RAY DIFFRACTIONr_angle_other_deg0.90436198
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9275381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.51422.422128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.49115507
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6481538
X-RAY DIFFRACTIONr_chiral_restr0.1020.2409
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213059
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_it1.7052.7161241
X-RAY DIFFRACTIONr_mcbond_other1.6512.7071240
X-RAY DIFFRACTIONr_mcangle_it2.2234.6321585
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.9583.8111390
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_restr2.78535288
X-RAY DIFFRACTIONr_sphericity_free31.17527
X-RAY DIFFRACTIONr_sphericity_bonded11.04255614
LS refinement shellResolution: 1.06→1.088 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 393 -
Rwork0.224 7542 -
obs--95.75 %

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