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- PDB-6i8f: STRUCTURE OF ESTER-HYDROLASE EH1AB1 FROM THE METAGENOME OF LAKE ARREO -

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Basic information

Entry
Database: PDB / ID: 6i8f
TitleSTRUCTURE OF ESTER-HYDROLASE EH1AB1 FROM THE METAGENOME OF LAKE ARREO
ComponentsEH1AB1
KeywordsHYDROLASE / Ester Hydrolase
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsCea-Rama, I. / Sanz-Aparicio, J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessProject BIO2016-76601-C3-3R Spain
CitationJournal: Nat Catal / Year: 2020
Title: Genetically engineered proteins with two active sites for enhanced biocatalysis and synergistic chemo- and biocatalysis
Authors: Alonso, S. / Santiago, G. / Cea-Rama, I. / Fernandez-Lopez, L. / Coscolin, C. / Modregger, J. / Ressmann, A.K. / Martinez-Martinez, M. / Marrero, H. / Bargiela, R. / Pita, M. / Gonzalez- ...Authors: Alonso, S. / Santiago, G. / Cea-Rama, I. / Fernandez-Lopez, L. / Coscolin, C. / Modregger, J. / Ressmann, A.K. / Martinez-Martinez, M. / Marrero, H. / Bargiela, R. / Pita, M. / Gonzalez-Alfonso, J.L. / Briand, M.L. / Rojo, D. / Barbas, C. / Plou, F.J. / Golyshin, P.N. / Shahgaldian, P. / Sanz-Aparicio, J. / Guallar, V. / Ferrer, M.
History
DepositionNov 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 15, 2020Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 2.0Oct 14, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref_seq / struct_sheet_range / struct_site_gen
Item: _atom_site.label_seq_id / _entity.formula_weight ..._atom_site.label_seq_id / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_host_org_vector_type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id / _struct_site_gen.label_seq_id
Revision 2.1Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.2Oct 26, 2022Group: Database references / Category: citation / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EH1AB1
B: EH1AB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,23824
Polymers71,2082
Non-polymers2,03122
Water6,161342
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.226, 86.045, 98.166
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETARGARGAA1 - 1815 - 32
21METMETARGARGBB1 - 1815 - 32
12LYSLYSVALVALAA34 - 20248 - 216
22LYSLYSVALVALBB34 - 20248 - 216
13TRPTRPTHRTHRAA219 - 315233 - 329
23TRPTRPTHRTHRBB219 - 315233 - 329

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.487908, -0.023057, 0.872591), (-0.041977, -0.997875, -0.049839), (0.871885, -0.060946, 0.485903)-39.46196, 1.93466, 23.48877

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Components

#1: Protein EH1AB1


Mass: 35603.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: uncultured bacterium from the metagenome of Lake Arreo, an evaporite karstic lake in Spain
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli BL21 (bacteria)
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 2.56 Å3/Da / Density % sol: 52.08 % / Description: Thin bars
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 45 % PEG P400, 0.1 M BIS-TRIS pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.11→43.02 Å / Num. obs: 40731 / % possible obs: 99.9 % / Redundancy: 5.8 % / Biso Wilson estimate: 19.653 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.057 / Net I/σ(I): 10.6
Reflection shellResolution: 2.11→2.17 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.641 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 3301 / CC1/2: 0.776 / Rpim(I) all: 0.296 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata reduction
Aimless1.11.12data scaling
MOLREP11.6.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JD4

5jd4


Resolution: 2.11→43.02 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.046 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.157 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19771 2081 5.1 %RANDOM
Rwork0.16012 ---
obs0.16208 38599 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.487 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20 Å20 Å2
2---0.4 Å20 Å2
3----0.4 Å2
Refinement stepCycle: 1 / Resolution: 2.11→43.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4770 0 130 343 5243
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0145008
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174408
X-RAY DIFFRACTIONr_angle_refined_deg1.1921.6856766
X-RAY DIFFRACTIONr_angle_other_deg0.9041.68110318
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0655628
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.42820.515272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.90215718
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5011546
X-RAY DIFFRACTIONr_chiral_restr0.0630.2638
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025710
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02938
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_it1.8932.8332518
X-RAY DIFFRACTIONr_mcbond_other1.8932.8332517
X-RAY DIFFRACTIONr_mcangle_it3.2084.2443144
X-RAY DIFFRACTIONr_mcangle_other3.2084.2443145
X-RAY DIFFRACTIONr_scbond_it2.2513.1712490
X-RAY DIFFRACTIONr_scbond_other2.2513.1742485
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6094.6043613
X-RAY DIFFRACTIONr_long_range_B_refined7.16935.7735677
X-RAY DIFFRACTIONr_long_range_B_other7.16935.7825678
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4060 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.430.5
medium thermal3.682
LS refinement shellResolution: 2.11→2.165 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 145 -
Rwork0.194 2847 -
obs--99.97 %

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