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- PDB-3ise: Structure of mineralized Bfrb (double soak) from Pseudomonas aeru... -

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Basic information

Entry
Database: PDB / ID: 3ise
TitleStructure of mineralized Bfrb (double soak) from Pseudomonas aeruginosa to 2.8A Resolution
ComponentsBacterioferritin
KeywordsELECTRON TRANSPORT / iron storage / Heme / Iron / Metal-binding
Function / homology
Function and homology information


iron ion sequestering activity / ferritin complex / ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis / iron ion binding / heme binding / cytosol
Similarity search - Function
Bacterioferritin signature. / Bacterioferritin / 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 ...Bacterioferritin signature. / Bacterioferritin / 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
: / PROTOPORPHYRIN IX CONTAINING FE / : / Bacterioferritin BfrB
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsLovell, S. / Weeratunga, S.K. / Battaile, K.P. / Rivera, M.
CitationJournal: Biochemistry / Year: 2010
Title: Structural Studies of Bacterioferritin B from Pseudomonas aeruginosa Suggest a Gating Mechanism for Iron Uptake via the Ferroxidase Center
Authors: Weeratunga, S.K. / Lovell, S. / Yao, H. / Battaile, K.P. / Fischer, C.J. / Gee, C.E. / Rivera, M.
History
DepositionAug 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bacterioferritin
B: Bacterioferritin
C: Bacterioferritin
D: Bacterioferritin
E: Bacterioferritin
F: Bacterioferritin
G: Bacterioferritin
H: Bacterioferritin
I: Bacterioferritin
J: Bacterioferritin
K: Bacterioferritin
L: Bacterioferritin
M: Bacterioferritin
N: Bacterioferritin
O: Bacterioferritin
P: Bacterioferritin
Q: Bacterioferritin
R: Bacterioferritin
S: Bacterioferritin
T: Bacterioferritin
U: Bacterioferritin
V: Bacterioferritin
W: Bacterioferritin
X: Bacterioferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)454,89766
Polymers445,92424
Non-polymers8,97342
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area84120 Å2
ΔGint-862 kcal/mol
Surface area134120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.712, 203.206, 207.865
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
131M
141N
151O
161P
171Q
181R
191S
201T
211U
221V
231W
241X

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 4 / Auth seq-ID: 3 - 156 / Label seq-ID: 3 - 156

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH
9II
10JJ
11KK
12LL
13MM
14NN
15OO
16PP
17QQ
18RR
19SS
20TT
21UU
22VV
23WW
24XX

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Components

#1: Protein ...
Bacterioferritin


Mass: 18580.168 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: bfrB, PA3531 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): Arctic express RIL / References: UniProt: Q9HY79
#2: Chemical...
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C34H32FeN4O4

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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: 2.98 Å3/Da / Density % sol: 58.68 %
Crystal growTemperature: 277 K / pH: 6
Details: 35% MPD, 100mM MES, 200mM Li2SO4, pH 6.0, vapor diffusion, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1.6531
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 15, 2009
Diffraction measurementDetails: 1.00 degrees, 20.0 sec, detector distance 140.00 mm
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6531 Å / Relative weight: 1
ReflectionAv R equivalents: 0.17 / Number: 955818
ReflectionResolution: 2.8→47.51 Å / Num. obs: 131241 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.17 / Rsym value: 0.17 / Net I/σ(I): 12.97
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.753 / Mean I/σ(I) obs: 2.25 / Rsym value: 0.753 / % possible all: 100
Cell measurementReflection used: 955818

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefmac_5.5.0066refinement
PDB_EXTRACT3.005data extraction
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3IS7

3is7


Resolution: 2.8→47.51 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.898 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 11.598 / SU ML: 0.225 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 3.672 / ESU R Free: 0.337 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.237 6600 5 %RANDOM
Rwork0.195 ---
obs0.197 131148 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20 Å20 Å2
2---1.32 Å20 Å2
3---0.73 Å2
Refinement stepCycle: LAST / Resolution: 2.8→47.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30414 0 546 0 30960
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02131518
X-RAY DIFFRACTIONr_bond_other_d00.0228325
X-RAY DIFFRACTIONr_angle_refined_deg1.5532.01542614
X-RAY DIFFRACTIONr_angle_other_deg0.716366167
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.29653676
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.06725.8571680
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.916156082
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.68715120
X-RAY DIFFRACTIONr_chiral_restr0.0750.24612
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0234516
X-RAY DIFFRACTIONr_gen_planes_other00.025572
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_it0.4911.518284
X-RAY DIFFRACTIONr_mcbond_other0.1261.57640
X-RAY DIFFRACTIONr_mcangle_it1.024229305
X-RAY DIFFRACTIONr_scbond_it1.718313234
X-RAY DIFFRACTIONr_scangle_it3.0234.513309
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2424 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.270.5
2Bmedium positional0.280.5
3Cmedium positional0.280.5
4Dmedium positional0.280.5
5Emedium positional0.270.5
6Fmedium positional0.260.5
7Gmedium positional0.250.5
8Hmedium positional0.350.5
9Imedium positional0.270.5
10Jmedium positional0.30.5
11Kmedium positional0.280.5
12Lmedium positional0.290.5
13Mmedium positional0.270.5
14Nmedium positional0.280.5
15Omedium positional0.290.5
16Pmedium positional0.260.5
17Qmedium positional0.290.5
18Rmedium positional0.280.5
19Smedium positional0.290.5
20Tmedium positional0.280.5
21Umedium positional0.270.5
22Vmedium positional0.30.5
23Wmedium positional0.260.5
24Xmedium positional0.250.5
1Amedium thermal0.522
2Bmedium thermal0.522
3Cmedium thermal0.442
4Dmedium thermal0.492
5Emedium thermal0.452
6Fmedium thermal0.512
7Gmedium thermal0.462
8Hmedium thermal0.682
9Imedium thermal0.452
10Jmedium thermal0.452
11Kmedium thermal0.462
12Lmedium thermal0.442
13Mmedium thermal0.442
14Nmedium thermal0.482
15Omedium thermal0.542
16Pmedium thermal0.432
17Qmedium thermal0.572
18Rmedium thermal0.62
19Smedium thermal0.492
20Tmedium thermal0.482
21Umedium thermal0.452
22Vmedium thermal0.542
23Wmedium thermal0.522
24Xmedium thermal0.532
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 496 -
Rwork0.309 8967 -
obs--99.17 %

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