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- PDB-4ztt: Crystal structures of ferritin mutants reveal diferric-peroxo int... -

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Basic information

Entry
Database: PDB / ID: 4ztt
TitleCrystal structures of ferritin mutants reveal diferric-peroxo intermediates
Components(ferritin) x 2
KeywordsOXIDOREDUCTASE / Helicobactor pylori / Escherichia coli / Gram-negative bacteria / ferritin / iron uptake / ferroxidase center / reaction intermediate
Function / homology
Function and homology information


: / bacterial non-heme ferritin / iron ion sequestering activity / ferroxidase activity / ferric iron binding / cellular response to iron ion / ferrous iron binding / iron ion transport / response to oxidative stress / intracellular iron ion homeostasis ...: / bacterial non-heme ferritin / iron ion sequestering activity / ferroxidase activity / ferric iron binding / cellular response to iron ion / ferrous iron binding / iron ion transport / response to oxidative stress / intracellular iron ion homeostasis / DNA damage response / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Ferritin, prokaryotic-type / Ferritin / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily ...Ferritin, prokaryotic-type / Ferritin / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / : / MU-OXO-DIIRON / OXYGEN ATOM / HYDROXIDE ION / OXYGEN MOLECULE / PEROXIDE ION / Ferritin / Bacterial non-heme ferritin
Similarity search - Component
Biological speciesEscherichia coli DH1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.83 Å
AuthorsKim, S. / Park, Y.H. / Jung, S.W. / Seok, J.H. / Chung, Y.B. / Lee, D.B. / Gowda, G. / Lee, J.H. / Han, H.R. / Cho, A.E. ...Kim, S. / Park, Y.H. / Jung, S.W. / Seok, J.H. / Chung, Y.B. / Lee, D.B. / Gowda, G. / Lee, J.H. / Han, H.R. / Cho, A.E. / Lee, C. / Chung, M.S. / Kim, K.H.
CitationJournal: J. Mol. Biol. / Year: 2016
Title: Structural Basis of Novel Iron-Uptake Route and Reaction Intermediates in Ferritins from Gram-Negative Bacteria.
Authors: Kim, S. / Lee, J.H. / Seok, J.H. / Park, Y.H. / Jung, S.W. / Cho, A.E. / Lee, C. / Chung, M.S. / Kim, K.H.
History
DepositionMay 15, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Apr 5, 2017Group: Database references
Revision 1.3Feb 19, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Oct 2, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / cell ...atom_site / cell / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_database_status / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_mod_residue / pdbx_struct_special_symmetry / pdbx_validate_close_contact / software / struct_asym / struct_conn / struct_conn_type / struct_ref / struct_ref_seq / struct_ref_seq_dif / 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_alt_id / _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.occupancy / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _cell.Z_PDB / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_nonpoly.entity_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.entity_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _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.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 / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn_type.id / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.ref_id / _struct_ref_seq_dif.pdbx_seq_db_accession_code / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_evidence_code / _struct_site.pdbx_num_residues

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ferritin
B: ferritin
C: ferritin
D: ferritin
E: ferritin
F: ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,74142
Polymers117,4456
Non-polymers2,29636
Water15,907883
1
A: ferritin
B: ferritin
C: ferritin
D: ferritin
E: ferritin
F: ferritin
hetero molecules

A: ferritin
B: ferritin
C: ferritin
D: ferritin
E: ferritin
F: ferritin
hetero molecules

A: ferritin
B: ferritin
C: ferritin
D: ferritin
E: ferritin
F: ferritin
hetero molecules

A: ferritin
B: ferritin
C: ferritin
D: ferritin
E: ferritin
F: ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)478,966168
Polymers469,78124
Non-polymers9,185144
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
crystal symmetry operation3_755-y+2,x,z1
crystal symmetry operation4_575y,-x+2,z1
Buried area92580 Å2
ΔGint-1109 kcal/mol
Surface area139710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.816, 128.816, 172.247
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11E-205-

FE2

21D-414-

HOH

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Components

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Protein , 2 types, 6 molecules ABCDEF

#1: Protein
ferritin


Mass: 19571.859 Da / Num. of mol.: 5 / Mutation: S20A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli DH1 (bacteria) / Gene: ftnA, Z2960, ECs2613
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: C3T582, UniProt: P0A998*PLUS, bacterial non-heme ferritin
#2: Protein ferritin


Mass: 19585.844 Da / Num. of mol.: 1 / Mutation: S20A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli DH1 (bacteria) / Gene: ftnA, Z2960, ECs2613
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: C3T582, bacterial non-heme ferritin

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Non-polymers , 9 types, 919 molecules

#3: Chemical ChemComp-FEO / MU-OXO-DIIRON


Mass: 127.689 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: Fe2O
#4: Chemical
ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: HO
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Fe
#7: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#8: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#9: Chemical ChemComp-PER / PEROXIDE ION


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#10: Chemical ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 883 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.29 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop
Details: Lithium sulfate monohydrate, sodium citrate, ammonium sulfate

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Data collection

DiffractionMean temperature: 298.15 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 154787 / % possible obs: 91.6 % / Redundancy: 7.7 % / Net I/σ(I): 17

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata scaling
PHENIXphasing
RefinementResolution: 1.83→19.66 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.557 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.022 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19191 5691 4.7 %RANDOM
Rwork0.15644 ---
obs0.15813 115239 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.46 Å2
Baniso -1Baniso -2Baniso -3
1-4.52 Å20 Å20 Å2
2--4.52 Å20 Å2
3----9.04 Å2
Refinement stepCycle: LAST / Resolution: 1.83→19.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8085 0 115 883 9083
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0198956
X-RAY DIFFRACTIONr_bond_other_d0.0020.028136
X-RAY DIFFRACTIONr_angle_refined_deg2.0611.95312068
X-RAY DIFFRACTIONr_angle_other_deg1.057318852
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.38851085
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.55225.474475
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.791151617
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7921527
X-RAY DIFFRACTIONr_chiral_restr0.150.21274
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0210319
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022132
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_it2.5382.4184196
X-RAY DIFFRACTIONr_mcbond_other2.5322.4174195
X-RAY DIFFRACTIONr_mcangle_it3.0263.6075329
X-RAY DIFFRACTIONr_mcangle_other3.0293.6075330
X-RAY DIFFRACTIONr_scbond_it3.9952.8174758
X-RAY DIFFRACTIONr_scbond_other3.9952.8174758
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.624.0866737
X-RAY DIFFRACTIONr_long_range_B_refined7.35621.64311752
X-RAY DIFFRACTIONr_long_range_B_other7.03420.91911287
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.834→1.882 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.449 395 -
Rwork0.377 7818 -
obs--91.13 %

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