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- PDB-8avn: Mutant of Superoxide dismutase SodFM1 from CPR Parcubacteria Wolf... -

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Entry
Database: PDB / ID: 8avn
TitleMutant of Superoxide dismutase SodFM1 from CPR Parcubacteria Wolfebacteria
ComponentsSuperoxide dismutase
KeywordsOXIDOREDUCTASE / Superoxide dismutase (SOD). Oxidoreductase. Iron. Bacterial. Metalloenzyme.
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / metal ion binding / cytoplasm
Similarity search - Function
Iron/manganese superoxide dismutase, C-terminal domain / Fe,Mn superoxide dismutase (SOD) domain / minor pseudopilin epsh fold / 3-Layer(bab) Sandwich / Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / Manganese/iron superoxide dismutase, C-terminal ...Iron/manganese superoxide dismutase, C-terminal domain / Fe,Mn superoxide dismutase (SOD) domain / minor pseudopilin epsh fold / 3-Layer(bab) Sandwich / Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Superoxide dismutase
Similarity search - Component
Biological speciesCandidatus Wolfebacteria bacterium GW2011_GWB1_47_1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsBasle, A. / Barwinska-Sendra, A. / Sendra, K.M. / Waldron, K.
Funding support United States, United Kingdom, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 AI55611 United States
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S006818/1 United Kingdom
CitationJournal: Nat Ecol Evol / Year: 2023
Title: An ancient metalloenzyme evolves through metal preference modulation.
Authors: Sendra, K.M. / Barwinska-Sendra, A. / Mackenzie, E.S. / Basle, A. / Kehl-Fie, T.E. / Waldron, K.J.
History
DepositionAug 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Jun 28, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_src_gen / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_validate_close_contact / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / struct_conn / struct_mon_prot_cis / struct_ncs_dom_lim
Item: _entity.pdbx_ec / _entity_src_gen.pdbx_gene_src_gene ..._entity.pdbx_ec / _entity_src_gen.pdbx_gene_src_gene / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2 / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc_free / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_d_res_low / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine_hist.d_res_low / _refine_ls_restr.dev_ideal / _refine_ls_restr.dev_ideal_target / _refine_ls_restr.number / _refine_ls_restr_ncs.rms_dev_position / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_low / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ncs_dom_lim.pdbx_refine_code
Description: Model orientation/position
Details: alternative AU solution representing the biological dimer rather than each chain being in two distinct symmetry related dimers.
Provider: author / Type: Coordinate replacement
Revision 3.0Aug 9, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / reflns / software / struct_conf / struct_conn / struct_mon_prot_cis / struct_ncs_dom_lim
Item: _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_nonpoly_scheme.asym_id ..._pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_assembly.details / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_all / _refine.ls_d_res_low / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine_hist.d_res_low / _refine_ls_restr_ncs.rms_dev_position / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_low / _reflns.d_resolution_low / _software.version / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_class / _struct_conf.pdbx_PDB_helix_length / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_mon_prot_cis.pdbx_omega_angle / _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 / _struct_ncs_dom_lim.pdbx_refine_code
Description: Polymer geometry / Details: please add to the list alternative AU arrangement / Provider: author / Type: Coordinate replacement
Revision 3.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Superoxide dismutase
B: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9914
Polymers46,8812
Non-polymers1102
Water3,477193
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint1 kcal/mol
Surface area17780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.490, 69.710, 58.010
Angle α, β, γ (deg.)90.000, 100.240, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 1 / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 2 - 203 / Label seq-ID: 2 - 203

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Superoxide dismutase


Mass: 23440.334 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Wolfebacteria bacterium GW2011_GWB1_47_1 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0G1X6V3
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.97 Å3/Da / Density % sol: 37.66 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 200 mM sodium chloride, 100 mM sodium acetate pH 5.0 and 20 % w/v polyethylene glycol 6000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.99987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 1.65→45.79 Å / Num. obs: 43267 / % possible obs: 98.7 % / Redundancy: 6.5 % / CC1/2: 0.999 / Net I/σ(I): 6.5
Reflection shellResolution: 1.65→1.68 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2095 / CC1/2: 0.556

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
xia2data reduction
XDSdata reduction
Aimlessdata scaling
Cootmodel building
BUCCANEERmodel building
MolProbitymodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GV3

1gv3


Resolution: 1.65→45.79 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.96 / SU B: 8.241 / SU ML: 0.11 / Cross valid method: FREE R-VALUE / ESU R: 0.157 / ESU R Free: 0.109
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.22 2167 5.011 %
Rwork0.1521 41078 -
all0.155 --
obs-43245 98.551 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 29.887 Å2
Baniso -1Baniso -2Baniso -3
1--1.536 Å2-0 Å2-0.153 Å2
2--3.035 Å20 Å2
3----1.355 Å2
Refinement stepCycle: LAST / Resolution: 1.65→45.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3300 0 2 193 3495
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123435
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163135
X-RAY DIFFRACTIONr_angle_refined_deg1.6591.6674688
X-RAY DIFFRACTIONr_angle_other_deg0.5551.5897247
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3285411
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.633510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.0710564
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.74210177
X-RAY DIFFRACTIONr_chiral_restr0.0820.2493
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024054
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02786
X-RAY DIFFRACTIONr_nbd_refined0.2330.2752
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.22841
X-RAY DIFFRACTIONr_nbtor_refined0.1920.21722
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21694
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2147
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0310.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2530.224
X-RAY DIFFRACTIONr_nbd_other0.2390.270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1730.217
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.110.21
X-RAY DIFFRACTIONr_mcbond_it2.682.9221624
X-RAY DIFFRACTIONr_mcbond_other2.6532.9191623
X-RAY DIFFRACTIONr_mcangle_it3.5835.2542028
X-RAY DIFFRACTIONr_mcangle_other3.5845.2552029
X-RAY DIFFRACTIONr_scbond_it3.2013.2691811
X-RAY DIFFRACTIONr_scbond_other3.23.271812
X-RAY DIFFRACTIONr_scangle_it4.2455.8392655
X-RAY DIFFRACTIONr_scangle_other4.2445.8392656
X-RAY DIFFRACTIONr_lrange_it4.96533.9354046
X-RAY DIFFRACTIONr_lrange_other4.94933.9354039
X-RAY DIFFRACTIONr_rigid_bond_restr5.36736570
X-RAY DIFFRACTIONr_ncsr_local_group_10.0840.056984
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.084410.05009
12AX-RAY DIFFRACTIONLocal ncs0.084410.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.6930.3611620.332953X-RAY DIFFRACTION97.5572
1.693-1.7390.3381570.292935X-RAY DIFFRACTION97.5702
1.739-1.7890.3131520.2462864X-RAY DIFFRACTION97.7317
1.789-1.8440.2671510.2122730X-RAY DIFFRACTION98.1267
1.844-1.9050.2761510.232681X-RAY DIFFRACTION98.0609
1.905-1.9720.3491180.2212614X-RAY DIFFRACTION97.781
1.972-2.0460.2561260.1542542X-RAY DIFFRACTION98.5593
2.046-2.1290.1891330.1342400X-RAY DIFFRACTION98.2164
2.129-2.2240.241060.1272352X-RAY DIFFRACTION98.7149
2.224-2.3320.2461090.1422258X-RAY DIFFRACTION98.5429
2.332-2.4580.2181070.1292120X-RAY DIFFRACTION99.1099
2.458-2.6060.2911100.132032X-RAY DIFFRACTION99.3506
2.606-2.7860.2221020.1291902X-RAY DIFFRACTION99.3555
2.786-3.0080.217960.1331751X-RAY DIFFRACTION99.4615
3.008-3.2940.214900.1541638X-RAY DIFFRACTION99.5965
3.294-3.680.222850.1611487X-RAY DIFFRACTION99.3051
3.68-4.2450.157720.1141324X-RAY DIFFRACTION99.7856
4.245-5.1880.167670.1161116X-RAY DIFFRACTION99.9155
5.188-7.290.149460.147872X-RAY DIFFRACTION99.6743
7.29-45.790.181270.147507X-RAY DIFFRACTION99.4413

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