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- PDB-6lkp: Crystal structure of Dps1 from the thermophilic non-heterocystous... -

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Basic information

Entry
Database: PDB / ID: 6lkp
TitleCrystal structure of Dps1 from the thermophilic non-heterocystous filamentous cyanobacterium Thermoleptolyngbya sp. O-77
ComponentsDNA protection during starvation protein
KeywordsDNA BINDING PROTEIN / The DNA-binding protein from starved cells / Dps / ferritin superfamily / dodecamer
Function / homology
Function and homology information


Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / ferric iron binding
Similarity search - Function
Dps protein family signature 2. / DNA-binding protein Dps, conserved site / DNA-binding protein Dps / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / DNA protection during starvation protein
Similarity search - Component
Biological speciesLeptolyngbya sp. O-77 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMinato, T. / Teramoto, T. / Kakuta, Y. / Ogo, S. / Yoon, K.S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JPMJCR18R2 Japan
CitationJournal: Febs Open Bio / Year: 2020
Title: Biochemical and structural characterization of a thermostable Dps protein with His-type ferroxidase centers and outer metal-binding sites.
Authors: Minato, T. / Teramoto, T. / Kakuta, Y. / Ogo, S. / Yoon, K.S.
History
DepositionDec 19, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 2.0Apr 1, 2020Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_nonpoly_scheme / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_asym / 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.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.vector[3] / _struct_asym.entity_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id / _struct_site_gen.label_seq_id / _struct_site_gen.pdbx_num_res / _struct_site_gen.site_id / _struct_site_gen.symmetry
Revision 2.1Sep 30, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_atom_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_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry
Revision 2.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: DNA protection during starvation protein
B: DNA protection during starvation protein
C: DNA protection during starvation protein
D: DNA protection during starvation protein
E: DNA protection during starvation protein
F: DNA protection during starvation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,48230
Polymers124,0276
Non-polymers1,45524
Water00
1
A: DNA protection during starvation protein
B: DNA protection during starvation protein
C: DNA protection during starvation protein
D: DNA protection during starvation protein
E: DNA protection during starvation protein
F: DNA protection during starvation protein
hetero molecules

A: DNA protection during starvation protein
B: DNA protection during starvation protein
C: DNA protection during starvation protein
D: DNA protection during starvation protein
E: DNA protection during starvation protein
F: DNA protection during starvation protein
hetero molecules


  • defined by author&software
  • Evidence: gel filtration
  • 251 kDa, 12 polymers
Theoretical massNumber of molelcules
Total (without water)250,96560
Polymers248,05412
Non-polymers2,91048
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556-x,y,-z+11
Buried area59930 Å2
ΔGint-1410 kcal/mol
Surface area59630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.787, 92.787, 261.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Space group name HallP4cw2c
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNVALVAL(chain 'A' and (resid 17 through 92 or resid 97 through 173))AA17 - 9217 - 92
12LYSLYSSERSER(chain 'A' and (resid 17 through 92 or resid 97 through 173))AA97 - 17397 - 173
21ASNASNVALVAL(chain 'B' and (resid 17 through 92 or resid 97 through 173))BB17 - 9217 - 92
22LYSLYSSERSER(chain 'B' and (resid 17 through 92 or resid 97 through 173))BB97 - 17397 - 173
31ASNASNVALVAL(chain 'C' and (resid 17 through 92 or resid 97 through 173))CC17 - 9217 - 92
32LYSLYSSERSER(chain 'C' and (resid 17 through 92 or resid 97 through 173))CC97 - 17397 - 173
41ASNASNVALVAL(chain 'D' and (resid 17 through 92 or resid 97 through 173))DD17 - 9217 - 92
42LYSLYSSERSER(chain 'D' and (resid 17 through 92 or resid 97 through 173))DD97 - 17397 - 173
51ASNASNVALVAL(chain 'E' and (resid 17 through 92 or resid 97 through 173))EE17 - 9217 - 92
52LYSLYSSERSER(chain 'E' and (resid 17 through 92 or resid 97 through 173))EE97 - 17397 - 173
61ASNASNVALVALchain 'F'FF17 - 9217 - 92
62LYSLYSSERSERchain 'F'FF97 - 17397 - 173

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Components

#1: Protein
DNA protection during starvation protein


Mass: 20671.207 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: SF file contains Friedel pairs. / Source: (natural) Leptolyngbya sp. O-77 (bacteria)
References: UniProt: A0A0X8WZ56, Oxidoreductases; Oxidizing metal ions
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
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: 2.26 Å3/Da / Density % sol: 45.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.15 M Cesium chloride and 18% Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1.25 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.25 Å / Relative weight: 1
ReflectionResolution: 2.9→46.39 Å / Num. obs: 48249 / % possible obs: 100 % / Redundancy: 14 % / Biso Wilson estimate: 83.84 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.035 / Rrim(I) all: 0.133 / Net I/σ(I): 12.1
Reflection shellResolution: 2.9→3 Å / Redundancy: 13.3 % / Rmerge(I) obs: 1.606 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4857 / CC1/2: 0.627 / Rpim(I) all: 0.455 / Rrim(I) all: 1.669 / % possible all: 100

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Processing

Software
NameVersionClassification
Coot1.17.1_3660model building
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HJH

5hjh


Resolution: 2.9→46.39 Å / SU ML: 0.4672 / Cross valid method: FREE R-VALUE / Phase error: 33.5539
RfactorNum. reflection% reflection
Rfree0.3149 3662 7.59 %
Rwork0.2527 --
obs0.2574 48249 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 95 Å2
Refinement stepCycle: LAST / Resolution: 2.9→46.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7968 0 24 0 7992
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00488152
X-RAY DIFFRACTIONf_angle_d0.812111012
X-RAY DIFFRACTIONf_chiral_restr0.04581186
X-RAY DIFFRACTIONf_plane_restr0.00511460
X-RAY DIFFRACTIONf_dihedral_angle_d26.08962946
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.940.3261410.30571685X-RAY DIFFRACTION100
2.94-2.980.38171430.31261729X-RAY DIFFRACTION100
2.98-3.020.39171410.34081693X-RAY DIFFRACTION100
3.02-3.070.40031400.32241736X-RAY DIFFRACTION100
3.07-3.110.38071440.33031722X-RAY DIFFRACTION100
3.11-3.160.37621390.32651692X-RAY DIFFRACTION100
3.17-3.220.42411400.33311737X-RAY DIFFRACTION100
3.22-3.280.41231430.34071694X-RAY DIFFRACTION100
3.28-3.340.37591430.28621730X-RAY DIFFRACTION100
3.34-3.410.34781360.26271712X-RAY DIFFRACTION100
3.41-3.480.32471440.24291708X-RAY DIFFRACTION100
3.48-3.560.28481410.25881748X-RAY DIFFRACTION100
3.56-3.650.29931410.2511683X-RAY DIFFRACTION100
3.65-3.750.3541450.23841731X-RAY DIFFRACTION100
3.75-3.860.33151420.22981737X-RAY DIFFRACTION100
3.86-3.990.33281360.2221676X-RAY DIFFRACTION100
3.99-4.130.26461440.22681728X-RAY DIFFRACTION100
4.13-4.290.31591370.20861706X-RAY DIFFRACTION100
4.29-4.490.24831410.18761715X-RAY DIFFRACTION100
4.49-4.730.27141420.18391725X-RAY DIFFRACTION100
4.73-5.020.25611470.19361706X-RAY DIFFRACTION100
5.02-5.410.26731470.23351706X-RAY DIFFRACTION100
5.41-5.950.35251360.25511732X-RAY DIFFRACTION100
5.95-6.810.28571350.2631719X-RAY DIFFRACTION100
6.81-8.570.26761370.22131725X-RAY DIFFRACTION100
8.58-46.390.36321370.32521712X-RAY DIFFRACTION99.25
Refinement TLS params.Method: refined / Origin x: 16.8517334527 Å / Origin y: 43.9456390718 Å / Origin z: 130.057071425 Å
111213212223313233
T0.516592957272 Å20.10794701442 Å2-0.011700332166 Å2-0.60743864154 Å2-0.0660973676661 Å2--0.651402289844 Å2
L1.5713188939 °2-0.00264335462849 °2-0.871948898925 °2-0.935173343853 °20.136971354839 °2--2.02338343999 °2
S-0.30766051376 Å °-0.265081414217 Å °0.203733208865 Å °-0.00176006601086 Å °0.254659594823 Å °-0.315184181176 Å °0.443899201327 Å °0.614804138353 Å °0.0267484547409 Å °
Refinement TLS groupSelection details: all

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