PDB-6tsx: Crystal structure of horse L ferritin (HoLf) Fe(III)-loaded for 3...

ID or keywords:

Entry

Database: PDB / ID: 6tsx

Title

Crystal structure of horse L ferritin (HoLf) Fe(III)-loaded for 30 minutes

Components

Ferritin light chain

Keywords

METAL BINDING PROTEIN / horse L ferritin / HoLf / Fe(III) / trinuclear Fe(III) cluster

Function / homology

Function and homology information

ferritin complex / autolysosome / ferric iron binding / autophagosome / iron ion transport / ferrous iron binding / cytoplasmic vesicle / intracellular iron ion homeostasis / iron ion binding / cytoplasm
Similarity search - Function

Biological species

Equus caballus (horse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.021 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 21, 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 / struct_conn_type 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.3	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6tsx.cif.gz	81.7 KB	Display	PDBx/mmCIF format
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Validation report

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Full document	6tsx_full_validation.pdf.gz	6.7 MB	Display
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Data in CIF	6tsx_validation.cif.gz	13.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ts/6tsx ftp://data.pdbj.org/pub/pdb/validation_reports/ts/6tsx	HTTPS FTP

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Related structure data

Related structure data	6tr9C 6trzC 6ts0C 6ts1C 6tsaC 6tsfC 6tsjC 6tssC 5lg2S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3o7s-1 6ts1-1 3f36-1 6iaj-1 3f38-1 4lyx-1 2zg8-1 7bon-1 7bom-1 5e1u-1 2v2o-1 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 (10) #111 - Mar 2009 Hydrogenase similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #114 - Jun 2009 Vaults similarity (1) #57 - Sep 2004 Catalase similarity (1)

Deposited unit

AAA: Ferritin light chain

hetero molecules

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

1

AAA: Ferritin light chain

hetero molecules

x 24

defined by author&software
Evidence: gel filtration
507 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)	181.242, 181.242, 181.242
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	209
Space group name H-M	F432

Components on special symmetry positions

ID	Model	Components
1	1	AAA-215- CD
2	1	AAA-216- FE
3	1	AAA-304- HOH

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Protein , 1 types, 1 molecules AAA

#1: Protein	Ferritin light chain / Ferritin L subunit Mass: 20079.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P02791

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Non-polymers , 5 types, 119 molecules

#2: Chemical	ChemComp-O / OXYGEN ATOM Mass: 15.999 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O
#3: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-CD / CADMIUM ION Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: 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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Details

Has ligand of interest	Y
Has protein modification	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: 3.09 Å³/Da / Density % sol: 60.17 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 30 mM cadmium nitrate, 1 M ammonium sulfate, 200 mM sodium acetate, pH 5.5

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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	I04	1	0.9795
SYNCHROTRON	Diamond	I04	2	1.73894
SYNCHROTRON	Diamond	I04	3	1.7512

Detector

Type	ID	Detector	Date
DECTRIS EIGER2 X 16M	1	PIXEL	Jul 26, 2019
DECTRIS EIGER2 X 16M	2	PIXEL	Jul 26, 2019
DECTRIS EIGER2 X 16M	3	PIXEL	Jul 26, 2019

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	0.9795	1
2	1.73894	1
3	1.7512	1

Reflection

Entry-ID: 6TSX / 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)
2.02-104.64	17298	21.7	38.7	1	0.056	0.013	0.06	1	30.4
2.3-104.64	11874	17.9	52.8	0.999	0.068	0.019	0.084	2	23.8
2.3-90.47	11830	17.7	54.9	0.999	0.079	0.02	0.085	3	17.9

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
2.02-2.13	22.2	0.901	3.9	2442	0.915	0.199	0.941	1
2.3-2.42	12	1.149	2.1	1670	0.685	0.354	1.243	2
2.3-2.42	11.3	0.957	2.3	1695	0.749	0.305	1.041	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: 5LG2

5lg2

Resolution: 2.021→54.706 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.946 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.136

	R_factor	Num. reflection	% reflection
R_free	0.2211	900	5.204 %
R_work	0.1844	-	-
all	0.186	-	-
obs	-	17294	99.971 %

Solvent computation

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

Displacement parameters

B_iso mean: 41.696 Å²

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

Refine analyze

Luzzati coordinate error obs: 0.24 Å

Refinement step

Cycle: LAST / Resolution: 2.021→54.706 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1348	0	21	98	1467

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.013	1379
X-RAY DIFFRACTION	r_bond_other_d	0.036	0.017	1275
X-RAY DIFFRACTION	r_angle_refined_deg	1.907	1.636	1859
X-RAY DIFFRACTION	r_angle_other_deg	2.4	1.575	2943
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.16	5	170
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.853	22.381	84
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.599	15	241
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.835	15	11
X-RAY DIFFRACTION	r_chiral_restr	0.132	0.2	169
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	1563
X-RAY DIFFRACTION	r_gen_planes_other	0.014	0.02	302
X-RAY DIFFRACTION	r_nbd_refined	0.246	0.2	315
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.207	0.2	1035
X-RAY DIFFRACTION	r_nbtor_refined	0.187	0.2	682
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	605
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.184	0.2	52
X-RAY DIFFRACTION	r_metal_ion_refined	0.15	0.2	7
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.146	0.2	10
X-RAY DIFFRACTION	r_nbd_other	0.184	0.2	36
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.154	0.2	13
X-RAY DIFFRACTION	r_mcbond_it	3.474	4.185	677
X-RAY DIFFRACTION	r_mcbond_other	3.477	4.184	676
X-RAY DIFFRACTION	r_mcangle_it	4.211	6.245	845
X-RAY DIFFRACTION	r_mcangle_other	4.208	6.247	846
X-RAY DIFFRACTION	r_scbond_it	6.466	4.757	701
X-RAY DIFFRACTION	r_scbond_other	6.462	4.755	702
X-RAY DIFFRACTION	r_scangle_it	9.189	6.867	1012
X-RAY DIFFRACTION	r_scangle_other	9.184	6.865	1013
X-RAY DIFFRACTION	r_lrange_it	10.183	50.951	1594
X-RAY DIFFRACTION	r_lrange_other	9.866	50.641	1577

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 (%)
2.021-2.073	0.234	67	0.223	1182	X-RAY DIFFRACTION	100
2.073-2.13	0.177	68	0.209	1146	X-RAY DIFFRACTION	100
2.13-2.192	0.213	67	0.193	1101	X-RAY DIFFRACTION	100
2.192-2.259	0.194	54	0.187	1108	X-RAY DIFFRACTION	100
2.259-2.333	0.211	53	0.184	1068	X-RAY DIFFRACTION	100
2.333-2.415	0.213	50	0.164	1029	X-RAY DIFFRACTION	100
2.415-2.506	0.197	47	0.175	985	X-RAY DIFFRACTION	100
2.506-2.609	0.199	46	0.167	968	X-RAY DIFFRACTION	100
2.609-2.724	0.21	57	0.168	917	X-RAY DIFFRACTION	100
2.724-2.857	0.286	54	0.161	878	X-RAY DIFFRACTION	100
2.857-3.012	0.203	51	0.152	834	X-RAY DIFFRACTION	100
3.012-3.194	0.188	49	0.157	799	X-RAY DIFFRACTION	100
3.194-3.415	0.156	40	0.164	770	X-RAY DIFFRACTION	100
3.415-3.688	0.202	37	0.151	706	X-RAY DIFFRACTION	100
3.688-4.039	0.209	49	0.153	652	X-RAY DIFFRACTION	100
4.039-4.515	0.22	32	0.157	598	X-RAY DIFFRACTION	100
4.515-5.212	0.265	24	0.158	552	X-RAY DIFFRACTION	100
5.212-6.38	0.391	22	0.255	474	X-RAY DIFFRACTION	100
6.38-9.005	0.208	21	0.25	379	X-RAY DIFFRACTION	100

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Protein , 1 types, 1 molecules AAA

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