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- PDB-2htn: E. coli bacterioferritin in its as-isolated form -

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Basic information

Entry
Database: PDB / ID: 2htn
TitleE. coli bacterioferritin in its as-isolated form
ComponentsBacterioferritin
KeywordsMETAL BINDING PROTEIN / OXIDOREDUCTASE / four-helix bundle / ferroxidase centre / haem / protein shell / iron binding site
Function / homology
Function and homology information


ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / iron ion transport / oxidoreductase activity / iron ion binding / heme binding / protein homodimerization activity / identical protein binding ...ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / iron ion transport / oxidoreductase activity / iron ion binding / heme binding / protein homodimerization activity / identical protein binding / membrane / 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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
Authorsvan Eerde, A. / Wolterink-Van Loo, S. / Van Der Oost, J. / Dijkstra, B.W.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Fortuitous structure determination of 'as-isolated' Escherichia coli bacterioferritin in a novel crystal form.
Authors: van Eerde, A. / Wolterink-van Loo, S. / van der Oost, J. / Dijkstra, B.W.
History
DepositionJul 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Nov 12, 2014Group: Derived calculations
Revision 1.4Aug 30, 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_alt_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_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_alt_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.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_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
Remark 600HETEROGEN Authors state that the oxidation state of Fe could be an Fe(II) or FE(III) ion. Authors ...HETEROGEN Authors state that the oxidation state of Fe could be an Fe(II) or FE(III) ion. Authors also state that the FE ions could be substituted in a significant minority by ZN(II) ions.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,50428
Polymers148,1448
Non-polymers3,35920
Water1,76598
1
A: Bacterioferritin
B: Bacterioferritin
C: Bacterioferritin
D: Bacterioferritin
E: Bacterioferritin
F: Bacterioferritin
G: Bacterioferritin
H: Bacterioferritin
hetero molecules

A: Bacterioferritin
B: Bacterioferritin
C: Bacterioferritin
D: Bacterioferritin
E: Bacterioferritin
F: Bacterioferritin
G: Bacterioferritin
H: Bacterioferritin
hetero molecules

A: Bacterioferritin
B: Bacterioferritin
C: Bacterioferritin
D: Bacterioferritin
E: Bacterioferritin
F: Bacterioferritin
G: Bacterioferritin
H: Bacterioferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)454,51184
Polymers444,43224
Non-polymers10,07860
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
Buried area96780 Å2
ΔGint-1130 kcal/mol
Surface area130140 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)167.893, 167.893, 167.893
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91A
101B
111C
121D
131E
141F
151G
161H
171A
181B
191C
201D
211E
221F
231G
241H
251A
261B
271C
281D
291E
301F
311G
321H
331A
341B
351C
361D
371E
381F
391G
401H
411A
421B
431C
441D
451E
461F
471G
481H
12A
22C
32E
42G

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETASNASNAA1 - 171 - 17
211METMETASNASNBB1 - 171 - 17
311METMETASNASNCC1 - 171 - 17
411METMETASNASNDD1 - 171 - 17
511METMETASNASNEE1 - 171 - 17
611METMETASNASNFF1 - 171 - 17
711METMETASNASNGG1 - 171 - 17
811METMETASNASNHH1 - 171 - 17
921LEULEUASPASPAA19 - 5019 - 50
1021LEULEUASPASPBB19 - 5019 - 50
1121LEULEUASPASPCC19 - 5019 - 50
1221LEULEUASPASPDD19 - 5019 - 50
1321LEULEUASPASPEE19 - 5019 - 50
1421LEULEUASPASPFF19 - 5019 - 50
1521LEULEUASPASPGG19 - 5019 - 50
1621LEULEUASPASPHH19 - 5019 - 50
1731METMETLYSLYSAA52 - 5352 - 53
1831METMETLYSLYSBB52 - 5352 - 53
1931METMETLYSLYSCC52 - 5352 - 53
2031METMETLYSLYSDD52 - 5352 - 53
2131METMETLYSLYSEE52 - 5352 - 53
2231METMETLYSLYSFF52 - 5352 - 53
2331METMETLYSLYSGG52 - 5352 - 53
2431METMETLYSLYSHH52 - 5352 - 53
2541ALAALALEULEUAA55 - 9355 - 93
2641ALAALALEULEUBB55 - 9355 - 93
2741ALAALALEULEUCC55 - 9355 - 93
2841ALAALALEULEUDD55 - 9355 - 93
2941ALAALALEULEUEE55 - 9355 - 93
3041ALAALALEULEUFF55 - 9355 - 93
3141ALAALALEULEUGG55 - 9355 - 93
3241ALAALALEULEUHH55 - 9355 - 93
3351LEULEUASPASPAA95 - 12695 - 126
3451LEULEUASPASPBB95 - 12695 - 126
3551LEULEUASPASPCC95 - 12695 - 126
3651LEULEUASPASPDD95 - 12695 - 126
3751LEULEUASPASPEE95 - 12695 - 126
3851LEULEUASPASPFF95 - 12695 - 126
3951LEULEUASPASPGG95 - 12695 - 126
4051LEULEUASPASPHH95 - 12695 - 126
4161GLUGLUGLYGLYAA128 - 129128 - 129
4261GLUGLUGLYGLYBB128 - 129128 - 129
4361GLUGLUGLYGLYCC128 - 129128 - 129
4461GLUGLUGLYGLYDD128 - 129128 - 129
4561GLUGLUGLYGLYEE128 - 129128 - 129
4661GLUGLUGLYGLYFF128 - 129128 - 129
4761GLUGLUGLYGLYGG128 - 129128 - 129
4861GLUGLUGLYGLYHH128 - 129128 - 129
112METMETHEMHEMAA - K1 - 2001
212METMETHEMHEMCC - P1 - 2001
312METMETHEMHEMEE - U1 - 2001
412METMETHEMHEMGG - Z1 - 2001

NCS ensembles :
ID
1
2
DetailsThe biological assembly is a 24-mer generated from the octamer in the asymmetric unit by the operations: y+1/2,-z+1/2,-x and -z,x+1/2,-y+1/2.

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Components

#1: Protein
Bacterioferritin / BFR / Cytochrome b-1 / Cytochrome b-557


Mass: 18518.016 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: BL21 / References: UniProt: P0ABD3, ferroxidase
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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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: 2.66 Å3/Da / Density % sol: 53.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% (v/v) PEG400, 0.2M MGCl2, 0.1 M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 11, 2004
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.3→74.54 Å / Num. all: 69975 / Num. obs: 69835 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.3→2.42 Å / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BCF

1bcf


Resolution: 2.5→59.34 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.918 / SU B: 6.806 / SU ML: 0.155 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 1.045 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2) FINAL REFINEMENT WAS DONE USING DETWINNED DATA 3) the crystallographic data used for solving this structure was perfectly twinned.
RfactorNum. reflection% reflectionSelection details
Rfree0.18803 5633 10.3 %IN THIN SHELLS
Rwork0.17059 ---
all0.17243 54648 --
obs0.17243 54540 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.727 Å2
Refinement stepCycle: LAST / Resolution: 2.5→59.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10392 0 188 98 10678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02210944
X-RAY DIFFRACTIONr_bond_other_d0.0030.027320
X-RAY DIFFRACTIONr_angle_refined_deg1.1622.07214832
X-RAY DIFFRACTIONr_angle_other_deg2.027317800
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.02451256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg46.23525.27592
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.021152056
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5491572
X-RAY DIFFRACTIONr_chiral_restr0.0730.21528
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212096
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022040
X-RAY DIFFRACTIONr_nbd_refined0.2250.23291
X-RAY DIFFRACTIONr_nbd_other0.2120.27739
X-RAY DIFFRACTIONr_nbtor_refined0.1810.55546
X-RAY DIFFRACTIONr_nbtor_other0.0890.55323
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.4457
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.010.41
X-RAY DIFFRACTIONr_metal_ion_refined0.133108
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.380.269
X-RAY DIFFRACTIONr_symmetry_vdw_other0.4320.2160
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3250.428
X-RAY DIFFRACTIONr_mcbond_it6.7341.58409
X-RAY DIFFRACTIONr_mcbond_other1.591.52600
X-RAY DIFFRACTIONr_mcangle_it6.94629960
X-RAY DIFFRACTIONr_scbond_it11.93135555
X-RAY DIFFRACTIONr_scangle_it13.0094.54856
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1711tight positional00
12B1711tight positional00
13C1711tight positional00
14D1711tight positional00
15E1711tight positional00
16F1711tight positional00
17G1711tight positional00
18H1711tight positional00
21A2196tight positional00
22C2196tight positional00
23E2196tight positional00
22F2196tight positional00
11A1711tight thermal0.380.1
12B1711tight thermal0.590.1
13C1711tight thermal0.410.1
14D1711tight thermal0.580.1
15E1711tight thermal0.370.1
16F1711tight thermal0.40.1
17G1711tight thermal0.580.1
18H1711tight thermal0.570.1
21A2196tight thermal0.40.1
22C2196tight thermal0.410.1
23E2196tight thermal0.420.1
22F2196tight thermal0.470.1
LS refinement shellResolution: 2.5→2.572 Å / Total num. of bins used: 18 /
RfactorNum. reflection
Rfree0.179 -
Rwork0.199 4013

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