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

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Basic information

Entry
Database: PDB / ID: 4uhd
TitleStructural studies of a thermophilic esterase from Thermogutta terrifontis (acetate 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
ACETATE ION / DI(HYDROXYETHYL)ETHER / Esterase
Similarity search - Component
Biological speciesPLANCTOMYCETES BACTERIUM R1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07 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_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)31,5637
Polymers31,1731
Non-polymers3906
Water6,557364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.280, 43.280, 227.290
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-2085-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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): ARCTICEXPRESS (DE3)RIL / References: UniProt: A0A0M3KKY6*PLUS, carboxylesterase

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Non-polymers , 5 types, 370 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 40.3 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: DECTRIS PIXEL / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.07→37.48 Å / Num. obs: 99937 / % possible obs: 90.5 % / Observed criterion σ(I): 2 / Redundancy: 9.1 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 33.3
Reflection shellResolution: 1.07→1.1 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 5.6 / % possible all: 51.1

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Processing

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

2xua


Resolution: 1.07→37.48 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.982 / SU B: 0.521 / SU ML: 0.012 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.022 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.11203 4856 4.9 %RANDOM
Rwork0.09351 ---
obs0.09443 95076 90.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.802 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.07→37.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2108 0 24 364 2496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192775
X-RAY DIFFRACTIONr_bond_other_d0.0030.022810
X-RAY DIFFRACTIONr_angle_refined_deg1.83623866
X-RAY DIFFRACTIONr_angle_other_deg1.06236575
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8095410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.68822.397146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.92515552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8621545
X-RAY DIFFRACTIONr_chiral_restr0.1050.2425
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213271
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02646
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_it6.8572.6971276
X-RAY DIFFRACTIONr_mcbond_other6.8672.6861273
X-RAY DIFFRACTIONr_mcangle_it7.3144.6051635
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.7063.7831499
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_restr2.89635584
X-RAY DIFFRACTIONr_sphericity_free32.712541
X-RAY DIFFRACTIONr_sphericity_bonded12.17155784
LS refinement shellResolution: 1.07→1.098 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.156 232 -
Rwork0.132 3847 -
obs--50.67 %

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