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- PDB-6rky: STRUCTURE OF ESTER-HYDROLASE EH1AB1 FROM THE METAGENOME OF LAKE A... -

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Entry
Database: PDB / ID: 6rky
TitleSTRUCTURE OF ESTER-HYDROLASE EH1AB1 FROM THE METAGENOME OF LAKE ARREO COMPLEXED WITH A DERIVATIVE OF BIPYRIDINE PHOSPHONATE
ComponentsEH1AB1
KeywordsHYDROLASE / Ester Hydrolase / Complex
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / DI(HYDROXYETHYL)ETHER / Chem-ZK8
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsCea-Rama, I. / Sanz-Aparicio, J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessProject BIO2016-76601-C3-3-R 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
DepositionApr 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
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_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 / _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.ptnr1_label_seq_id / _struct_conn.ptnr2_label_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 3.0Jun 30, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / struct_conf / struct_conn / struct_ref_seq / struct_sheet_range / struct_site_gen
Item: _atom_site.label_seq_id / _chem_comp.formula ..._atom_site.label_seq_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.mon_nstd_flag / _chem_comp.type / _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 / _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_leaving_atom_flag / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_seq_id / _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 3.1Oct 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 4.0Jul 5, 2023Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_poly / entity_poly_seq / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_validate_torsion / struct_asym / struct_conf / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_torsion.auth_comp_id / _struct_conf.beg_auth_comp_id / _struct_conf.beg_label_comp_id
Revision 4.1Feb 7, 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
C: EH1AB1
D: EH1AB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,73818
Polymers142,4154
Non-polymers2,32214
Water1,29772
1
A: EH1AB1
C: EH1AB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,47510
Polymers71,2082
Non-polymers1,2678
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-1 kcal/mol
Surface area23260 Å2
MethodPISA
2
B: EH1AB1
D: EH1AB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2638
Polymers71,2082
Non-polymers1,0556
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-4 kcal/mol
Surface area23090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.766, 201.920, 90.637
Angle α, β, γ (deg.)90.00, 112.19, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: THR / End label comp-ID: THR / Refine code: _ / Auth seq-ID: 1 - 315 / Label seq-ID: 15 - 329

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
EH1AB1


Mass: 35603.793 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli BL21 (bacteria)
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-ZK8 / hexyl-[2-(3-oxidanylpyridin-2-yl)pyridin-3-yl]oxy-phosphinic acid


Mass: 336.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H21N2O4P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.85 Å3/Da / Density % sol: 56.78 % / Description: prism
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 3350, 0.1M Bis-Tris propane pH 7.5, 0.2 M NaF

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 28, 2019 / Details: KB focusing mirrors
RadiationMonochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.79→49.08 Å / Num. obs: 37139 / % possible obs: 99.1 % / Redundancy: 3.8 % / Biso Wilson estimate: 51.388 Å2 / CC1/2: 0.919 / Rmerge(I) obs: 0.277 / Rpim(I) all: 0.161 / Net I/σ(I): 2.7
Reflection shellResolution: 2.79→2.91 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4557 / CC1/2: 0.752 / Rpim(I) all: 0.327 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimless1.11.17data scaling
MOLREP11.6.04phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6I8F

6i8f


Resolution: 2.79→49.08 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.888 / SU B: 18.657 / SU ML: 0.382 / Cross valid method: THROUGHOUT / ESU R Free: 0.413 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27602 1823 4.9 %RANDOM
Rwork0.23905 ---
obs0.24092 35315 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 48.362 Å2
Baniso -1Baniso -2Baniso -3
1-2 Å20 Å2-2 Å2
2--1.6 Å20 Å2
3----1.47 Å2
Refinement stepCycle: LAST / Resolution: 2.79→49.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9628 0 64 72 9764
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0139922
X-RAY DIFFRACTIONr_bond_other_d0.0030.0179028
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.66413462
X-RAY DIFFRACTIONr_angle_other_deg1.2511.58920824
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.53351256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.69820.515544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.826151432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1961592
X-RAY DIFFRACTIONr_chiral_restr0.0760.21260
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211440
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022268
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_it3.8464.9025036
X-RAY DIFFRACTIONr_mcbond_other3.8424.9015035
X-RAY DIFFRACTIONr_mcangle_it5.8627.3556288
X-RAY DIFFRACTIONr_mcangle_other5.8637.3556289
X-RAY DIFFRACTIONr_scbond_it4.6395.4984886
X-RAY DIFFRACTIONr_scbond_other4.6395.4994887
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.2998.0347175
X-RAY DIFFRACTIONr_long_range_B_refined9.92358.310513
X-RAY DIFFRACTIONr_long_range_B_other9.91958.30310512
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A102340.02
12B102340.02
21A101600.02
22C101600.02
31A101630.03
32D101630.03
41B101760.02
42C101760.02
51B101780.03
52D101780.03
61C101800.03
62D101800.03
LS refinement shellResolution: 2.79→2.862 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 119 -
Rwork0.264 2649 -
obs--99.28 %

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