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- PDB-6goc: Methylesterase BT1017 -

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Basic information

Entry
Database: PDB / ID: 6goc
TitleMethylesterase BT1017
ComponentsDUF3826 domain-containing protein
KeywordsCARBOHYDRATE / pectin / rhamnogalacturonan-II / methylesterase / human gut microbiota
Function / homologyProtein of unknown function DUF3826 / Protein of unknown function (DUF3826) / : / Alpha/Beta hydrolase fold / metal ion binding / DUF3826 domain-containing protein / DUF3826 domain-containing protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsBasle, A. / Ndeh, D. / Gilbert, H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research Council (ERC)322820 United Kingdom
CitationJournal: to be published
Title: Characterisation of a methylesterases essential for pectin rhamnogalacturonan II metabolism from the gut bacterium Bacteroides thetaiotaomicron
Authors: Ndhe, D. / Cheng-Jie, D. / Basle, A. / Gilbert, H.
History
DepositionJun 1, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 2.0Apr 22, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary
Category: atom_site / atom_sites ...atom_site / atom_sites / atom_type / chem_comp / computing / diffrn / entity / pdbx_audit_support / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_validate_close_contact / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software / struct_conf / struct_conn / struct_mon_prot_cis / struct_sheet_range / struct_site
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_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _diffrn.pdbx_serial_crystal_experiment / _entity.formula_weight / _entity.pdbx_description / _pdbx_audit_support.country / _pdbx_audit_support.funding_organization / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.auth_seq_id / _pdbx_validate_close_contact.dist / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_all / _refine.ls_R_factor_obs / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_overall_ESU_R_Free / _refine_hist.cycle_id / _reflns.d_resolution_low / _software.classification / _software.name / _software.version / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_mon_prot_cis.pdbx_omega_angle / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_site.details / _struct_site.pdbx_auth_comp_id
Description: Model completeness
Details: none of the reasons apply. Please add to the list a reason for "Atom identification correction" See communication for details.
Provider: author / Type: Coordinate replacement
Revision 2.1Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DUF3826 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1652
Polymers75,0991
Non-polymers651
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.508, 229.469, 80.709
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1055-

HOH

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Components

#1: Protein DUF3826 domain-containing protein


Mass: 75099.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: BJP75_005780, Btheta7330_02632 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0P0F0R1, UniProt: Q8A900*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 42.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20 mM 1,6-hexanediol; 20 mM 1,2-propanediol; 20 mM 1,4-butanediol; 20 mM 1-butanol; 20 mM 2-propanol; 20 mM 1,3-propanediol; 100 mM Imidazol/MES pH 6.5; 20 % ethylene glycol; 10 % PEG 8000K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97889 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97889 Å / Relative weight: 1
ReflectionResolution: 1.9→66.1 Å / Num. obs: 50611 / % possible obs: 100 % / Redundancy: 11.7 % / CC1/2: 0.998 / Net I/σ(I): 10.6
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 9.6 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 30870 / CC1/2: 0.636 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
GDAdata collection
MOSFLMdata reduction
Aimlessdata scaling
SHELXCDphasing
SHELXEmodel building
BUCCANEERmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.9→66.01 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.864 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.131
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2434 2524 4.991 %RANDOM
Rwork0.2009 ---
all0.203 ---
obs-50568 99.929 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.183 Å2
Baniso -1Baniso -2Baniso -3
1-2.741 Å20 Å20 Å2
2---3.75 Å20 Å2
3---1.008 Å2
Refinement stepCycle: LAST / Resolution: 1.9→66.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3473 0 1 279 3753
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133549
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173261
X-RAY DIFFRACTIONr_angle_refined_deg1.8351.6544801
X-RAY DIFFRACTIONr_angle_other_deg1.4721.5787560
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1155443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.85721.885191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53615569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9471525
X-RAY DIFFRACTIONr_chiral_restr0.0820.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024019
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02781
X-RAY DIFFRACTIONr_nbd_refined0.2120.2771
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.23148
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21757
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21633
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2229
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0650.23
X-RAY DIFFRACTIONr_metal_ion_refined0.3270.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0660.28
X-RAY DIFFRACTIONr_nbd_other0.1870.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0920.211
X-RAY DIFFRACTIONr_mcbond_it2.9493.3211775
X-RAY DIFFRACTIONr_mcbond_other2.9453.3191774
X-RAY DIFFRACTIONr_mcangle_it3.8294.9732217
X-RAY DIFFRACTIONr_mcangle_other3.8284.9762218
X-RAY DIFFRACTIONr_scbond_it3.7983.6551774
X-RAY DIFFRACTIONr_scbond_other3.7853.6491772
X-RAY DIFFRACTIONr_scangle_it5.4265.3242584
X-RAY DIFFRACTIONr_scangle_other5.435.3242584
X-RAY DIFFRACTIONr_lrange_it6.26739.6434068
X-RAY DIFFRACTIONr_lrange_other6.24139.5344040
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9490.3991970.4073478X-RAY DIFFRACTION99.5395
1.949-2.0030.3931780.3693425X-RAY DIFFRACTION99.8891
2.003-2.0610.3661910.3393309X-RAY DIFFRACTION99.9144
2.061-2.1240.3581790.2913240X-RAY DIFFRACTION99.9415
2.124-2.1940.3331570.2733132X-RAY DIFFRACTION100
2.194-2.2710.2671470.2323048X-RAY DIFFRACTION100
2.271-2.3560.2581470.2122949X-RAY DIFFRACTION99.9354
2.356-2.4530.2551410.1972860X-RAY DIFFRACTION99.9667
2.453-2.5620.2041480.1862683X-RAY DIFFRACTION99.9647
2.562-2.6870.2361230.1812624X-RAY DIFFRACTION100
2.687-2.8320.2531400.1762467X-RAY DIFFRACTION99.9233
2.832-3.0040.2331090.1722385X-RAY DIFFRACTION100
3.004-3.2110.2421120.1812207X-RAY DIFFRACTION99.9569
3.211-3.4680.2271060.192067X-RAY DIFFRACTION100
3.468-3.7980.2361190.1931903X-RAY DIFFRACTION100
3.798-4.2460.1861000.1561728X-RAY DIFFRACTION100
4.246-4.9020.197780.1411545X-RAY DIFFRACTION100
4.902-6.0010.183610.1581335X-RAY DIFFRACTION100
6.001-8.4750.192530.1691041X-RAY DIFFRACTION99.8175
8.475-66.010.184380.158618X-RAY DIFFRACTION100

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