PDB-6ts0: Crystal structure of human L ferritin (HuLf) triple variant E60A-...

ID or keywords:

Entry

Database: PDB / ID: 6ts0

Title

Crystal structure of human L ferritin (HuLf) triple variant E60A-E61A-E64A Fe(III)-loaded for 30 minutes

Components

Ferritin light chain

Keywords

METAL BINDING PROTEIN / human L ferritin / HuLf / E60A-E61A-E64A / Fe(III) / trinuclear Fe(III) cluster

Function / homology

Function and homology information

ferritin complex / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / autolysosome / ferric iron binding / autophagosome / iron ion transport / Iron uptake and transport / ferrous iron binding / azurophil granule lumen ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Pozzi, C. / Ciambellotti, S. / Turano, P. / Mangani, S.

Citation

Journal: Chemistry / Year: 2020
Title: Iron Biomineral Growth from the Initial Nucleation Seed in L-Ferritin.
Authors: Ciambellotti, S. / Pozzi, C. / Mangani, S. / Turano, P.

History

Deposition	Dec 19, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 19, 2020	Provider: repository / Type: Initial release
Revision 1.1	May 20, 2020	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2	Jan 24, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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_symmetry

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6ts0.cif.gz	82.2 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6ts0_validation.pdf.gz	3.9 MB	Display	wwPDB validaton report
Full document	6ts0_full_validation.pdf.gz	3.9 MB	Display
Data in XML	6ts0_validation.xml.gz	10.1 KB	Display
Data in CIF	6ts0_validation.cif.gz	14.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ts/6ts0 ftp://data.pdbj.org/pub/pdb/validation_reports/ts/6ts0	HTTPS FTP

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Related structure data

Related structure data	6tr9C 6trzC 6ts1C 6tsaC 6tsfC 6tsjC 6tssC 6tsxC 5lg8S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6tsa-1 6tsf-1 6tsj-1 6u8j-d 2900 4n78-d 3p8c-d 3a6p-d 5wab-d 2465 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#35 - Nov 2002 Ferritin and Transferrin similarity (11) #111 - Mar 2009 Hydrogenase similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #237 - Sep 2019 Nanodiscs and HDL similarity (1) #114 - Jun 2009 Vaults similarity (1) #57 - Sep 2004 Catalase similarity (1)

Deposited unit

AAA: Ferritin light chain

hetero molecules

20.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

AAA: Ferritin light chain

hetero molecules

AAA: Ferritin light chain

hetero molecules

AAA: Ferritin light chain

hetero molecules

AAA: Ferritin light chain

hetero molecules

AAA: Ferritin light chain

hetero molecules

AAA: Ferritin light chain

hetero molecules

AAA: Ferritin light chain

hetero molecules

AAA: Ferritin light chain

hetero molecules

AAA: Ferritin light chain

hetero molecules

AAA: Ferritin light chain

hetero molecules

AAA: Ferritin light chain

hetero molecules

AAA: Ferritin light chain

hetero molecules

AAA: Ferritin light chain

hetero molecules

AAA: Ferritin light chain

hetero molecules

AAA: Ferritin light chain

hetero molecules

AAA: Ferritin light chain

hetero molecules

AAA: Ferritin light chain

hetero molecules

AAA: Ferritin light chain

hetero molecules

AAA: Ferritin light chain

hetero molecules

AAA: Ferritin light chain

hetero molecules

AAA: Ferritin light chain

hetero molecules

AAA: Ferritin light chain

hetero molecules

AAA: Ferritin light chain

hetero molecules

AAA: Ferritin light chain

hetero molecules

defined by author
Evidence: gel filtration
492 kDa, 24 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_555	-x,-y,z	1
crystal symmetry operation	3_555	-x,y,-z	1
crystal symmetry operation	4_555	x,-y,-z	1
crystal symmetry operation	5_555	z,x,y	1
crystal symmetry operation	6_555	z,-x,-y	1
crystal symmetry operation	7_555	-z,-x,y	1
crystal symmetry operation	8_555	-z,x,-y	1
crystal symmetry operation	9_555	y,z,x	1
crystal symmetry operation	10_555	-y,z,-x	1
crystal symmetry operation	11_555	y,-z,-x	1
crystal symmetry operation	12_555	-y,-z,x	1
crystal symmetry operation	13_555	y,x,-z	1
crystal symmetry operation	14_555	-y,-x,-z	1
crystal symmetry operation	15_555	y,-x,z	1
crystal symmetry operation	16_555	-y,x,z	1
crystal symmetry operation	17_555	x,z,-y	1
crystal symmetry operation	18_555	-x,z,y	1
crystal symmetry operation	19_555	-x,-z,-y	1
crystal symmetry operation	20_555	x,-z,y	1
crystal symmetry operation	21_555	z,y,-x	1
crystal symmetry operation	22_555	z,-y,x	1
crystal symmetry operation	23_555	-z,y,x	1
crystal symmetry operation	24_555	-z,-y,-x	1

Unit cell

Length a, b, c (Å)	151.386, 151.386, 151.386
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	211
Space group name H-M	I432

Components on special symmetry positions

ID	Model	Components
1	1	AAA-204- FE
2	1	AAA-205- FE
3	1	AAA-207- FE
4	1	AAA-209- FE
5	1	AAA-211- CD
6	1	AAA-318- HOH
7	1	AAA-415- HOH
8	1	AAA-444- HOH
9	1	AAA-449- HOH

#1: Protein	Ferritin light chain / Ferritin L subunit Mass: 19874.572 Da / Num. of mol.: 1 / Mutation: E60A,E61A,E64A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FTL / Plasmid: pET-21c / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -pLysS / References: UniProt: P02792
#2: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-O / OXYGEN ATOM Mass: 15.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O
#4: Chemical	ChemComp-CD / CADMIUM ION Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.73 Å³/Da / Density % sol: 66.98 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 80 mM cadmium nitrate, 80 mM ammonium sulfate, 200 mM sodium acetate, pH 4.6

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID	Serial crystal experiment
1	100	1	N
2	100	1	N
3	100	1	N

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	Diamond	I03	1	0.97622
SYNCHROTRON	Diamond	I03	2	1.73888
SYNCHROTRON	Diamond	I03	3	1.74478

Detector

Type	ID	Detector	Date
DECTRIS PILATUS3 6M	1	PIXEL	Feb 19, 2018
DECTRIS PILATUS3 6M	2	PIXEL	Feb 19, 2018
DECTRIS PILATUS3 6M	3	PIXEL	Feb 19, 2018

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	Si(111)	MAD	M	x-ray	1
2	Si(111)	MAD	M	x-ray	2
3	Si(111)	MAD	M	x-ray	3

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97622	1
2	1.73888	1
3	1.74478	1

Reflection

Entry-ID: 6TS0 / Observed criterion σ(I): 2 / % possible obs: 100 %

Resolution (Å)	Num. obs	Redundancy (%)	B_iso Wilson estimate (Å²)	CC_1/2	R_merge(I) obs	R_pim(I) all	R_rim(I) all	Diffraction-ID	Net I/σ(I)
2.2-107.05	15371	21	45.3	1	0.067	0.015	0.071	1	31.7
2.18-107.34	15908	20.1	55.9	1	0.088	0.022	0.101	2	21.2
2.5-107.45	10702	20	70.3	0.999	0.095	0.023	0.102	3	18.5

Reflection shell

% possible all: 100

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Diffraction-ID
2.2-2.32	21.6	0.834	4.2	2205	0.935	0.187	0.872	1
2.18-2.3	20	1.513	2.2	2272	0.744	0.351	1.585	2
2.5-2.64	20.2	1.564	2	1533	0.767	0.363	1.642	3

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0257	refinement
XDS		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5LG8

5lg8

Resolution: 2.2→47.918 Å / Cor.coef. F_o:F_c: 0.946 / Cor.coef. F_o:F_c free: 0.916 / Cross valid method: THROUGHOUT / ESU R: 0.197 / ESU R Free: 0.182

	R_factor	Num. reflection	% reflection
R_free	0.2481	755	4.961 %
R_work	0.2035	-	-
all	0.206	-	-
obs	-	15218	98.985 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 44.069 Å²

	B_aniso -1	B_aniso -2
1-	0 Å²	0 Å²
2-	-	0 Å²
3-	-	-

Refine analyze

Luzzati coordinate error obs: 0.3 Å

Refinement step

Cycle: LAST / Resolution: 2.2→47.918 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1352	0	11	162	1525

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.013	1394
X-RAY DIFFRACTION	r_bond_other_d	0.036	0.017	1290
X-RAY DIFFRACTION	r_angle_refined_deg	1.875	1.64	1882
X-RAY DIFFRACTION	r_angle_other_deg	2.471	1.579	2981
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.909	5	174
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.928	21.951	82
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.076	15	245
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	24.618	15	11
X-RAY DIFFRACTION	r_chiral_restr	0.174	0.2	171
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	1584
X-RAY DIFFRACTION	r_gen_planes_other	0.009	0.02	309
X-RAY DIFFRACTION	r_nbd_refined	0.241	0.2	327
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.215	0.2	1086
X-RAY DIFFRACTION	r_nbtor_refined	0.189	0.2	673
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.076	0.2	636
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.164	0.2	99
X-RAY DIFFRACTION	r_metal_ion_refined	0.139	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.14	0.2	22
X-RAY DIFFRACTION	r_nbd_other	0.258	0.2	57
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.158	0.2	19
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.122	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	4.392	4.546	687
X-RAY DIFFRACTION	r_mcbond_other	4.371	4.538	686
X-RAY DIFFRACTION	r_mcangle_it	5.703	6.774	858
X-RAY DIFFRACTION	r_mcangle_other	5.703	6.782	859
X-RAY DIFFRACTION	r_scbond_it	6.478	4.947	705
X-RAY DIFFRACTION	r_scbond_other	6.473	4.953	706
X-RAY DIFFRACTION	r_scangle_it	8.915	7.192	1021
X-RAY DIFFRACTION	r_scangle_other	8.915	7.192	1021
X-RAY DIFFRACTION	r_lrange_it	11.418	54.199	1668
X-RAY DIFFRACTION	r_lrange_other	11.424	53.586	1633

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.2-2.257	0.319	51	0.308	1066	X-RAY DIFFRACTION	99.6432
2.257-2.319	0.317	61	0.298	1016	X-RAY DIFFRACTION	99.63
2.319-2.386	0.292	58	0.279	984	X-RAY DIFFRACTION	99.4275
2.386-2.46	0.376	43	0.272	967	X-RAY DIFFRACTION	98.4405
2.46-2.54	0.316	44	0.259	947	X-RAY DIFFRACTION	99.1992
2.54-2.63	0.256	53	0.26	881	X-RAY DIFFRACTION	98.2124
2.63-2.729	0.296	51	0.251	890	X-RAY DIFFRACTION	98.431
2.729-2.84	0.253	39	0.23	835	X-RAY DIFFRACTION	99.2054
2.84-2.966	0.234	39	0.2	825	X-RAY DIFFRACTION	98.7429
2.966-3.111	0.227	38	0.187	775	X-RAY DIFFRACTION	98.4261
3.111-3.279	0.272	32	0.18	749	X-RAY DIFFRACTION	98.4868
3.279-3.478	0.237	45	0.172	690	X-RAY DIFFRACTION	98.262
3.478-3.718	0.214	34	0.181	664	X-RAY DIFFRACTION	99.2888
3.718-4.015	0.229	22	0.171	639	X-RAY DIFFRACTION	97.9259
4.015-4.398	0.214	36	0.145	579	X-RAY DIFFRACTION	99.1936
4.398-4.916	0.155	32	0.131	529	X-RAY DIFFRACTION	99.8221
4.916-5.674	0.215	29	0.157	473	X-RAY DIFFRACTION	100
5.674-6.945	0.278	18	0.207	415	X-RAY DIFFRACTION	100
6.945-9.801	0.168	20	0.204	330	X-RAY DIFFRACTION	100

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