PDB-6tsf: Crystal structure of human L ferritin (HuLf) Fe(III)-loaded for 6...

ID or keywords:

Entry

Database: PDB / ID: 6tsf

Title

Crystal structure of human L ferritin (HuLf) Fe(III)-loaded for 60 minutes

Components

Ferritin light chain

Keywords

METAL BINDING PROTEIN / human L ferritin / HuLf / 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 uptake and transport / ferrous iron binding / azurophil granule lumen / iron ion transport ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.09 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 20, 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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_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	6tsf.cif.gz	83.6 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ts/6tsf ftp://data.pdbj.org/pub/pdb/validation_reports/ts/6tsf	HTTPS FTP

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Related structure data

Related structure data	6tr9C 6trzC 6ts0C 6ts1C 6tsaC 6tsjC 6tssC 6tsxC 5lg8S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6tsa-1 6ts0-1 6tsj-1 6u8j-d 5wab-d 2900 3a6p-d 3p8c-d 4n78-d 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

20.9 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
502 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)	151.140, 151.140, 151.140
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-202- FE
2	1	AAA-206- FE
3	1	AAA-214- CD
4	1	AAA-394- HOH
5	1	AAA-428- HOH
6	1	AAA-432- HOH
7	1	AAA-435- HOH

#1: Protein	Ferritin light chain / Ferritin L subunit Mass: 20048.682 Da / Num. of mol.: 1 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.: 13 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CD / CADMIUM ION Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#4: Chemical	ChemComp-O / OXYGEN ATOM Mass: 15.999 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: O
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 145 / 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: 3.59 Å³/Da / Density % sol: 65.72 %
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	1.73891
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	1.73891	1
3	1.74478	1

Reflection

Entry-ID: 6TSF / Observed criterion σ(I): 2

Resolution (Å)	Num. obs	% possible 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)
2.09-106.87	16631	93.5	20.3	42.6	1	0.065	0.015	0.069	1	26.8
2.15-107.16	16493	100	20.4	48.7	1	0.088	0.023	0.106	2	22
2.3-107.84	13798	100	19.4	58	0.999	0.1	0.024	0.107	3	15.4

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
2.09-2.2	21.5	0.849	3.7	2531	0.925	0.19	0.887	1
2.15-2.27	20.1	1.305	2.5	2362	0.794	0.303	1.37	2
2.3-2.42	19.3	1.583	2.1	1969	0.823	0.375	1.657	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: 2.09→47.84 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.945 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.173

	R_factor	Num. reflection	% reflection
R_free	0.252	823	4.988 %
R_work	0.2087	-	-
all	0.211	-	-
obs	-	16500	92.848 %

Solvent computation

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

Displacement parameters

B_iso mean: 44.84 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: 2.09→47.84 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1382	0	17	145	1544

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.013	1415
X-RAY DIFFRACTION	r_bond_other_d	0.036	0.017	1298
X-RAY DIFFRACTION	r_angle_refined_deg	1.858	1.64	1907
X-RAY DIFFRACTION	r_angle_other_deg	2.439	1.58	3009
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.857	5	173
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.38	22.588	85
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.642	15	254
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	25.739	15	10
X-RAY DIFFRACTION	r_chiral_restr	0.17	0.2	171
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	1600
X-RAY DIFFRACTION	r_gen_planes_other	0.01	0.02	306
X-RAY DIFFRACTION	r_nbd_refined	0.252	0.2	330
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.215	0.2	1100
X-RAY DIFFRACTION	r_nbtor_refined	0.191	0.2	679
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	649
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.171	0.2	92
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.009	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.104	0.2	5
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.254	0.2	27
X-RAY DIFFRACTION	r_nbd_other	0.262	0.2	60
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.137	0.2	13
X-RAY DIFFRACTION	r_mcbond_it	4.231	4.557	689
X-RAY DIFFRACTION	r_mcbond_other	4.187	4.547	688
X-RAY DIFFRACTION	r_mcangle_it	5.556	6.8	860
X-RAY DIFFRACTION	r_mcangle_other	5.552	6.812	861
X-RAY DIFFRACTION	r_scbond_it	6.323	5.041	723
X-RAY DIFFRACTION	r_scbond_other	6.319	5.046	724
X-RAY DIFFRACTION	r_scangle_it	8.946	7.332	1044
X-RAY DIFFRACTION	r_scangle_other	8.945	7.338	1045
X-RAY DIFFRACTION	r_lrange_it	11.001	54.795	1675
X-RAY DIFFRACTION	r_lrange_other	10.848	54.194	1641

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 (%)
2.09-2.145	0.392	64	0.321	1219	X-RAY DIFFRACTION	99.9221
2.145-2.203	0.335	64	0.31	1197	X-RAY DIFFRACTION	99.6838
2.203-2.267	0.331	39	0.297	557	X-RAY DIFFRACTION	49.0535
2.267-2.337	0.333	60	0.284	1119	X-RAY DIFFRACTION	99.8307
2.337-2.414	0.358	49	0.291	1087	X-RAY DIFFRACTION	98.355
2.414-2.498	0.358	45	0.293	1032	X-RAY DIFFRACTION	97.29
2.498-2.592	0.338	51	0.287	989	X-RAY DIFFRACTION	96.6543
2.592-2.698	0.392	43	0.293	798	X-RAY DIFFRACTION	79.7913
2.698-2.818	0.321	41	0.236	951	X-RAY DIFFRACTION	99.3988
2.818-2.956	0.258	52	0.197	895	X-RAY DIFFRACTION	99.4748
2.956-3.115	0.245	42	0.197	881	X-RAY DIFFRACTION	99.5685
3.115-3.304	0.295	46	0.195	812	X-RAY DIFFRACTION	99.6516
3.304-3.532	0.267	41	0.195	661	X-RAY DIFFRACTION	84.9879
3.532-3.815	0.216	41	0.186	601	X-RAY DIFFRACTION	83.3766
3.815-4.178	0.205	37	0.165	605	X-RAY DIFFRACTION	90.1685
4.178-4.671	0.256	26	0.141	616	X-RAY DIFFRACTION	99.6894
4.671-5.391	0.164	37	0.149	549	X-RAY DIFFRACTION	99.8296
5.391-6.599	0.216	20	0.193	479	X-RAY DIFFRACTION	100
6.599-9.314	0.166	18	0.182	386	X-RAY DIFFRACTION	100

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