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- PDB-5obb: Structure of a modified mouse H chain ferritin with a lanthanide ... -

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Basic information

Entry
Database: PDB / ID: 5obb
TitleStructure of a modified mouse H chain ferritin with a lanthanide binding motif in complex with Terbium
ComponentsFerritin heavy chain
KeywordsMETAL TRANSPORT / ferritin / lanthanide / terbium
Function / homology
Function and homology information


Iron uptake and transport / Golgi Associated Vesicle Biogenesis / iron ion sequestering activity / autolysosome / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / endocytic vesicle lumen / Neutrophil degranulation ...Iron uptake and transport / Golgi Associated Vesicle Biogenesis / iron ion sequestering activity / autolysosome / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / endocytic vesicle lumen / Neutrophil degranulation / ferric iron binding / ferrous iron binding / iron ion transport / immune response / iron ion binding / negative regulation of cell population proliferation / mitochondrion / extracellular region / identical protein binding / cytoplasm
Similarity search - Function
Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain ...Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin, core subunit, four-helix bundle / Ferritin / 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
TERBIUM(III) ION / Ferritin heavy chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å
AuthorsBaiocco, P. / Trabuco, M.C.
Funding support Italy, 1items
OrganizationGrant numberCountry
European Union637295 Italy
CitationJournal: PLoS ONE / Year: 2018
Title: Engineered ferritin for lanthanide binding.
Authors: Calisti, L. / Trabuco, M.C. / Boffi, A. / Testi, C. / Montemiglio, L.C. / des Georges, A. / Benni, I. / Ilari, A. / Taciak, B. / Bialasek, M. / Rygiel, T. / Krol, M. / Baiocco, P. / Bonamore, A.
History
DepositionJun 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: 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 / struct_conn
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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)549,70256
Polymers544,61624
Non-polymers5,08632
Water19811
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)237.251, 237.563, 237.572
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
131M
141O
151P
161Q
171R
181S
191T
201U
211V
221W
231X
241N

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A4 - 175
2114B4 - 175
3114C4 - 175
4114D4 - 175
5114E4 - 175
6114F4 - 175
7114G4 - 175
8114H4 - 175
9114I4 - 175
10114J4 - 175
11114K4 - 175
12114L4 - 175
13114M4 - 175
14114O4 - 175
15114P4 - 175
16114Q4 - 175
17114R4 - 175
18114S4 - 175
19114T4 - 175
20114U4 - 175
21114V4 - 175
22114W4 - 175
23114X4 - 175
24114N4 - 175

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.137678, -0.408065, -0.902512), (0.957568, -0.287764, -0.015967), (-0.253195, -0.866415, 0.430369)-141.259811, -25.983641, -100.381859
3given(-0.131428, 0.954951, -0.266073), (-0.401473, -0.296679, -0.866488), (-0.906392, -0.00706, 0.422379)-21.032789, -152.142517, -85.267761
4given(-0.390235, -0.25666, -0.884218), (-0.251035, -0.894315, 0.370381), (-0.885832, 0.366505, 0.284563)-145.823135, -111.303757, -68.647842
5given(0.954174, 0.063114, -0.29252), (-0.293878, 0.013216, -0.955752), (-0.056455, 0.997919, 0.031158)-15.05574, -131.833786, 4.45958
6given(0.037146, -0.918442, 0.393808), (0.999206, 0.039829, -0.001361), (-0.014435, 0.393546, 0.919192)-90.385643, -2.31121, 18.809231
7given(-0.923485, 0.080599, 0.375072), (0.078216, -0.91759, 0.389758), (0.375577, 0.389272, 0.841077)-84.964653, -92.92807, 36.651619
8given(-0.258749, 0.000311, -0.965944), (-0.908138, 0.340666, 0.243374), (0.329141, 0.940184, -0.087864)-127.024391, -79.591911, 16.244181
9given(0.099616, -0.988903, 0.110216), (0.016777, -0.109081, -0.993891), (0.994884, 0.100857, 0.005725)-107.126228, -123.848244, 7.8021
10given(0.008505, -0.149077, -0.988789), (0.2997, 0.943749, -0.139708), (0.953996, -0.295152, 0.052705)-121.849052, 5.86717, -16.450729
11given(-0.986921, -0.084972, 0.136992), (-0.090852, -0.408805, -0.908088), (0.133165, -0.908657, 0.395738)-112.352943, -143.888184, -83.033463
12given(0.037249, 0.999196, -0.014823), (-0.920142, 0.040081, 0.389527), (0.389809, -0.00087, 0.920896)5.67896, -90.893448, 17.857679
13given(0.911419, -0.229324, -0.341652), (-0.230101, -0.972391, 0.038852), (-0.341129, 0.043203, -0.939023)-38.30154, -133.734406, -125.615829
14given(-0.254035, -0.909696, 0.328511), (-0.003294, 0.340465, 0.940252), (-0.967189, 0.237774, -0.089487)-110.538933, 11.52176, -102.197723
15given(0.003391, 0.305401, 0.952218), (-0.143403, 0.94253, -0.301783), (-0.989659, -0.135527, 0.046991)14.6369, -28.619431, -119.181679
16given(0.953715, -0.295769, -0.054302), (0.06155, 0.015241, 0.997988), (-0.294347, -0.955138, 0.03274)-23.710409, -2.03757, -130.656799
17given(0.120256, 0.900919, -0.416992), (0.901216, -0.275234, -0.334747), (-0.416351, -0.335544, -0.845022)-18.33469, -45.958599, -148.714874
18given(-0.986912, 0.156746, -0.037898), (0.15769, 0.888831, -0.430248), (-0.033754, -0.430592, -0.901915)-107.15065, -21.860371, -135.593994
19given(0.095542, 0.017839, 0.995266), (-0.989792, -0.104515, 0.09689), (0.105749, -0.994363, 0.007671)4.63702, -120.47274, -111.532753
20given(0.283765, 0.942954, -0.174113), (0.37369, 0.058473, 0.925709), (0.883081, -0.327748, -0.33578)7.53734, 14.74775, -44.626869
21given(0.37744, 0.104032, 0.920172), (0.098879, -0.992516, 0.071652), (0.92074, 0.063941, -0.384902)22.297569, -114.365044, -20.6201
22given(-0.923428, 0.326365, 0.201908), (0.324769, 0.384259, 0.864217), (0.204465, 0.863615, -0.460828)-79.520271, 29.04961, -16.356819
23given(-0.195262, -0.97989, 0.041099), (-0.979633, 0.192867, -0.055876), (0.046826, -0.051173, -0.997591)-127.581772, -109.825241, -112.39315
24given(0.284377, 0.382429, 0.879135), (0.942039, 0.05881, -0.330308), (-0.178022, 0.922111, -0.343539)31.642799, -22.494591, -28.363211

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Components

#1: Protein ...
Ferritin heavy chain / / Ferritin H subunit


Mass: 22692.334 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fth1, Fth / Production host: Escherichia coli (E. coli) / References: UniProt: P09528, ferroxidase
#2: Chemical...
ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: Tb
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 3.49 Å3/Da / Density % sol: 64.75 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: ammonium sulphate, TRIS-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.4 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.376
11K, -L, -H20.349
11-L, -H, K30.274
ReflectionResolution: 2.65→48.48 Å / Num. obs: 191449 / % possible obs: 99.2 % / Redundancy: 6.7 % / Net I/σ(I): 12.6
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 8966 / % possible all: 94.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WNW

3wnw


Resolution: 2.65→48.48 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.926 / SU B: 6.461 / SU ML: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.043
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1735 9591 5 %RANDOM
Rwork0.1676 ---
obs0.1679 181854 98.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 101.96 Å2 / Biso mean: 53.195 Å2 / Biso min: 13.71 Å2
Baniso -1Baniso -2Baniso -3
1-12.81 Å20 Å20 Å2
2---14.33 Å20 Å2
3---1.52 Å2
Refinement stepCycle: final / Resolution: 2.65→48.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34067 0 32 11 34110
Biso mean--78.55 33.49 -
Num. residues----4177
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01934807
X-RAY DIFFRACTIONr_bond_other_d0.0010.0232512
X-RAY DIFFRACTIONr_angle_refined_deg0.6281.94846806
X-RAY DIFFRACTIONr_angle_other_deg0.634374930
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.78854163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.43324.8361925
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.445156404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.115197
X-RAY DIFFRACTIONr_chiral_restr0.0350.24881
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.0239786
X-RAY DIFFRACTIONr_gen_planes_other0.0010.028355
Refine LS restraints NCS

Ens-ID: 1 / Number: 2710 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.270.5
2BMEDIUM POSITIONAL0.360.5
3CMEDIUM POSITIONAL0.30.5
4DMEDIUM POSITIONAL0.250.5
5EMEDIUM POSITIONAL0.310.5
6FMEDIUM POSITIONAL0.290.5
7GMEDIUM POSITIONAL0.30.5
8HMEDIUM POSITIONAL0.310.5
9IMEDIUM POSITIONAL0.310.5
0JMEDIUM POSITIONAL0.230.5
1KMEDIUM POSITIONAL0.30.5
2LMEDIUM POSITIONAL0.310.5
3MMEDIUM POSITIONAL0.350.5
4NMEDIUM POSITIONAL0.290.5
5OMEDIUM POSITIONAL0.30.5
6PMEDIUM POSITIONAL0.310.5
7QMEDIUM POSITIONAL0.30.5
8RMEDIUM POSITIONAL0.30.5
9SMEDIUM POSITIONAL0.280.5
0TMEDIUM POSITIONAL0.310.5
1UMEDIUM POSITIONAL0.240.5
2VMEDIUM POSITIONAL0.290.5
3WMEDIUM POSITIONAL0.270.5
4XMEDIUM POSITIONAL0.250.5
1AMEDIUM THERMAL3.142
2BMEDIUM THERMAL5.152
3CMEDIUM THERMAL3.762
4DMEDIUM THERMAL3.432
5EMEDIUM THERMAL2.482
6FMEDIUM THERMAL3.582
7GMEDIUM THERMAL2.592
8HMEDIUM THERMAL2.582
9IMEDIUM THERMAL2.32
0JMEDIUM THERMAL5.912
1KMEDIUM THERMAL1.882
2LMEDIUM THERMAL5.062
3MMEDIUM THERMAL5.782
4NMEDIUM THERMAL4.152
5OMEDIUM THERMAL42
6PMEDIUM THERMAL7.512
7QMEDIUM THERMAL5.552
8RMEDIUM THERMAL4.712
9SMEDIUM THERMAL1.812
0TMEDIUM THERMAL2.752
1UMEDIUM THERMAL4.332
2VMEDIUM THERMAL2.582
3WMEDIUM THERMAL1.932
4XMEDIUM THERMAL3.712
LS refinement shellResolution: 2.647→2.715 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 611 -
Rwork0.274 12100 -
all-12711 -
obs--89.43 %

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