[English] 日本語
Yorodumi
- PDB-3bkn: The structure of Mycobacterial bacterioferritin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bkn
TitleThe structure of Mycobacterial bacterioferritin
ComponentsBacterioferritin
KeywordsMETAL BINDING PROTEIN / BACTERIOFERRITIN / CYTOCHROM B1 / MYCOBACTERIUM SMEGMATIS / HEME / IRON / IRON STORAGE / METAL-BINDING
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis
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 speciesMycobacterium smegmatis str. MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å
AuthorsJanowski, R. / Auerbach-Nevo, T. / Weiss, M.S.
CitationJournal: Protein Sci. / Year: 2008
Title: Bacterioferritin from Mycobacterium smegmatis contains zinc in its di-nuclear site.
Authors: Janowski, R. / Auerbach-Nevo, T. / Weiss, M.S.
History
DepositionDec 7, 2007Deposition site: RCSB / Processing site: PDBJ
SupersessionJan 22, 2008ID: 3B3H
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 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_special_symmetry / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,66457
Polymers222,01012
Non-polymers6,65345
Water73941
1
A: Bacterioferritin
B: Bacterioferritin
C: Bacterioferritin
D: Bacterioferritin
E: Bacterioferritin
F: Bacterioferritin
G: Bacterioferritin
H: Bacterioferritin
I: Bacterioferritin
J: Bacterioferritin
K: Bacterioferritin
L: Bacterioferritin
hetero molecules

A: Bacterioferritin
B: Bacterioferritin
C: Bacterioferritin
D: Bacterioferritin
E: Bacterioferritin
F: Bacterioferritin
G: Bacterioferritin
H: Bacterioferritin
I: Bacterioferritin
J: Bacterioferritin
K: Bacterioferritin
L: Bacterioferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)457,327114
Polymers444,02024
Non-polymers13,30790
Water39622
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area85460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.523, 151.520, 116.715
Angle α, β, γ (deg.)90.00, 128.08, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11K-301-

HEM

21K-301-

HEM

31K-301-

HEM

41L-301-

HEM

51L-301-

HEM

61L-301-

HEM

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 2 / Auth seq-ID: 1 - 155 / Label seq-ID: 1 - 155

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH
9II
10JJ
11KK
12LL

-
Components

-
Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Bacterioferritin


Mass: 18500.834 Da / Num. of mol.: 12 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
Strain: mc(2)155 / References: UniProt: A0QY79

-
Non-polymers , 5 types, 86 molecules

#2: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.77 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100mM HEPES pH 7.5, 10% (v/v) 2-propanol, 14% (w/v) PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.905 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 9, 2007 / Details: Si(111) monochromator
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.905 Å / Relative weight: 1
ReflectionResolution: 2.72→30 Å / Num. all: 65786 / Num. obs: 65786 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 43.7 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 10
Reflection shellResolution: 2.72→2.76 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3302 / Rsym value: 0.528 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1sof

1sof


Resolution: 2.72→29.64 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.885 / SU B: 21.95 / SU ML: 0.218 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: TLS and NCS used
RfactorNum. reflection% reflectionSelection details
Rfree0.22828 2649 4 %RANDOM
Rwork0.17947 ---
all0.18144 63129 --
obs0.18144 63129 98.78 %-
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: 46.756 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å2-0.71 Å2
2---0.24 Å20 Å2
3----0.99 Å2
Refinement stepCycle: LAST / Resolution: 2.72→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15564 0 367 41 15972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02216455
X-RAY DIFFRACTIONr_angle_refined_deg1.7152.07922429
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.64651926
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.27725.018843
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.814152910
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.70115120
X-RAY DIFFRACTIONr_chiral_restr0.1150.22427
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212540
X-RAY DIFFRACTIONr_nbd_refined0.2280.27670
X-RAY DIFFRACTIONr_nbtor_refined0.3130.211152
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2473
X-RAY DIFFRACTIONr_metal_ion_refined0.1210.248
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.2164
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.219
X-RAY DIFFRACTIONr_mcbond_it1.02829913
X-RAY DIFFRACTIONr_mcangle_it1.695315474
X-RAY DIFFRACTIONr_scbond_it1.75227337
X-RAY DIFFRACTIONr_scangle_it3.03106928
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A618tight positional0.050.05
2B618tight positional0.050.05
3C618tight positional0.050.05
4D618tight positional0.060.05
5E618tight positional0.050.05
6F618tight positional0.050.05
7G618tight positional0.060.05
8H618tight positional0.050.05
9I618tight positional0.050.05
10J618tight positional0.060.05
11K618tight positional0.050.05
12L618tight positional0.050.05
1A627medium positional0.490.5
2B627medium positional0.470.5
3C627medium positional0.340.5
4D627medium positional0.50.5
5E627medium positional0.370.5
6F627medium positional0.370.5
7G627medium positional0.320.5
8H627medium positional0.320.5
9I627medium positional0.350.5
10J627medium positional0.390.5
11K627medium positional0.390.5
12L627medium positional0.330.5
1A618tight thermal0.130.5
2B618tight thermal0.130.5
3C618tight thermal0.130.5
4D618tight thermal0.120.5
5E618tight thermal0.120.5
6F618tight thermal0.120.5
7G618tight thermal0.130.5
8H618tight thermal0.130.5
9I618tight thermal0.120.5
10J618tight thermal0.120.5
11K618tight thermal0.110.5
12L618tight thermal0.110.5
1A627medium thermal0.922
2B627medium thermal1.032
3C627medium thermal0.962
4D627medium thermal1.032
5E627medium thermal0.912
6F627medium thermal0.832
7G627medium thermal0.982
8H627medium thermal0.922
9I627medium thermal0.882
10J627medium thermal1.082
11K627medium thermal0.932
12L627medium thermal0.922
LS refinement shellResolution: 2.72→2.866 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.273 349 -
Rwork0.243 8839 -
obs--95.39 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8415-0.9261-0.08012.05560.15260.67930.01720.0206-0.0667-0.17630.10620.0031-0.12030.0122-0.1235-0.1161-0.0029-0.0243-0.1610.0388-0.089611.53832.4771-39.2363
20.9129-0.3857-0.62421.15771.0091.74440.06890.10750.0359-0.1627-0.00690.0692-0.1825-0.1617-0.062-0.08940.0359-0.0124-0.05430.059-0.1423-12.9702-2.8147-41.905
31.00280.10980.70030.67520.38782.5758-0.0292-0.04810.1058-0.067-0.0466-0.0296-0.07210.30470.0758-0.1948-0.0344-0.016-0.05810.0029-0.024743.3668-10.9179-17.4794
40.5093-0.0295-0.25610.69960.07532.6899-0.0088-0.04980.06820.02710.0363-0.0029-0.11610.2144-0.0276-0.1183-0.09550.004-0.1049-0.0234-0.041632.485910.6049-10.8567
50.6376-0.0238-0.03891.20790.52141.1138-0.0475-0.18-0.0393-0.01190.0331-0.19340.06720.30530.0144-0.12030.0641-0.03280.07730.0291-0.092433.4405-31.869934.1989
61.1233-0.7008-0.04851.82080.15320.4749-0.0149-0.1670.01250.13060.0049-0.0245-0.04960.33590.01-0.1564-0.0045-0.02970.11270.0051-0.071144.0377-15.324918.648
72.26170.56030.14630.41910.2210.71240.01810.2631-0.0354-0.0707-0.04-0.06440.1101-0.08330.0218-0.0868-0.0394-0.0132-0.1254-0.0218-0.11510.3913-36.1232-46.8555
81.66730.2008-0.43220.3406-0.15130.9535-0.0030.0703-0.04070.0109-0.0235-0.00420.232-0.0820.02650.0267-0.06410.0535-0.1309-0.0692-0.1148-1.7817-57.7398-34.2745
90.7360.2792-0.26512.107-0.94031.1625-0.14470.0281-0.0696-0.00650.0614-0.14930.15050.07350.0832-0.0660.08320.0167-0.12290.0067-0.088232.2575-49.5629-25.0651
100.62030.2265-0.36021.2784-0.57931.6135-0.1021-0.0533-0.0438-0.0030.048-0.10640.17540.14490.0541-0.14320.14610.01160.00090.0482-0.062343.5695-44.3006-3.3187
112.58710.57450.18710.65640.11380.76230.14410.02990.18980.0203-0.04520.0289-0.2844-0.0806-0.09890.00180.01310.0392-0.15820.0194-0.0648-1.512423.3908-12.4667
120.75810.25320.83830.81370.59272.1672-0.1191-0.0657-0.1460.0636-0.0681-0.01260.46610.01530.18710.08980.04850.1152-0.13840.0032-0.048212.1043-70.538-3.2689
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1611 - 161
2X-RAY DIFFRACTION2BB1 - 1611 - 161
3X-RAY DIFFRACTION3CC1 - 1611 - 161
4X-RAY DIFFRACTION4DD1 - 1611 - 161
5X-RAY DIFFRACTION5EE1 - 1611 - 161
6X-RAY DIFFRACTION6FF1 - 1611 - 161
7X-RAY DIFFRACTION7GG1 - 1611 - 161
8X-RAY DIFFRACTION8HH1 - 1611 - 161
9X-RAY DIFFRACTION9II1 - 1611 - 161
10X-RAY DIFFRACTION10JJ1 - 1611 - 161
11X-RAY DIFFRACTION11KK1 - 1611 - 161
12X-RAY DIFFRACTION12LL1 - 1611 - 161

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlc1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more