PDB-1s3q: Crystal structures of a novel open pore ferritin from the hyperth...

ID or keywords:

Entry

Database: PDB / ID: 1s3q

Title

Crystal structures of a novel open pore ferritin from the hyperthermophilic Archaeon Archaeoglobus fulgidus

Components

ferritin

Keywords

METAL BINDING PROTEIN / Ferroxidase / four helix bundle / iron storage

Function / homology

Function and homology information

intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / identical protein binding / cytosol
Similarity search - Function

Biological species

Archaeoglobus fulgidus (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.1 Å

Authors

Johnson, E. / Cascio, D. / Sawaya, M. / Schroeder, I.

Citation

Journal: Structure / Year: 2005
Title: Crystal structures of a tetrahedral open pore ferritin from the hyperthermophilic archaeon Archaeoglobus fulgidus.
Authors: Johnson, E. / Cascio, D. / Sawaya, M.R. / Gingery, M. / Schroder, I.

History

Deposition	Jan 13, 2004	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 12, 2005	Provider: repository / Type: Initial release
Revision 1.1	Apr 29, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	1s3q.cif.gz	420.1 KB	Display	PDBx/mmCIF format
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Others	Other downloads

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Validation report

Summary document	1s3q_validation.pdf.gz	486 KB	Display	wwPDB validaton report
Full document	1s3q_full_validation.pdf.gz	524.7 KB	Display
Data in XML	1s3q_validation.xml.gz	40.3 KB	Display
Data in CIF	1s3q_validation.cif.gz	64.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s3/1s3q ftp://data.pdbj.org/pub/pdb/validation_reports/s3/1s3q	HTTPS FTP

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Related structure data

Related structure data	1sq3C C: citing same article (ref.)
Similar structure data	1sq3-1 5ls9-1 6qkm-1 2yav-1 2yaw-1 6m35-1 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 (6) #114 - Jun 2009 Vaults similarity (1) #57 - Sep 2004 Catalase similarity (1)

Deposited unit

A: ferritin

B: ferritin

C: ferritin

D: ferritin

E: ferritin

F: ferritin

G: ferritin

H: ferritin

I: ferritin

J: ferritin

K: ferritin

L: ferritin

hetero molecules

251 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ferritin

B: ferritin

C: ferritin

D: ferritin

E: ferritin

F: ferritin

G: ferritin

H: ferritin

I: ferritin

J: ferritin

K: ferritin

L: ferritin

hetero molecules

A: ferritin

B: ferritin

C: ferritin

D: ferritin

E: ferritin

F: ferritin

G: ferritin

H: ferritin

I: ferritin

J: ferritin

K: ferritin

L: ferritin

hetero molecules

defined by author
501 kDa, 24 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	183.437, 187.831, 178.089
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg label comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	ILE	LEU	4	A	A	4 - 162	4 - 162
2	1	1	ILE	LEU	4	D	D	4 - 162	4 - 162
3	1	1	ILE	LEU	4	E	E	4 - 162	4 - 162
4	1	1	ILE	LEU	4	G	G	4 - 162	4 - 162
5	1	1	ILE	LEU	4	J	J	4 - 162	4 - 162
6	1	1	ILE	LEU	4	K	K	4 - 162	4 - 162
1	1	2	ILE	GLN	4	B	B	4 - 164	4 - 164
2	1	2	ILE	GLN	4	C	C	4 - 164	4 - 164
3	1	2	ILE	GLN	4	F	F	4 - 164	4 - 164
4	1	2	ILE	GLN	4	H	H	4 - 164	4 - 164
5	1	2	ILE	GLN	4	I	I	4 - 164	4 - 164
6	1	2	ILE	GLN	4	L	L	4 - 164	4 - 164
1	1	3	ALA	ILE	1	C	C	18 - 20	18 - 20
2	1	3	ALA	ILE	1	A	A	18 - 20	18 - 20
3	1	3	ALA	ILE	1	B	B	18 - 20	18 - 20
4	1	3	ALA	ILE	1	D	D	18 - 20	18 - 20
5	1	3	ALA	ILE	1	E	E	18 - 20	18 - 20
6	1	3	ALA	ILE	1	F	F	18 - 20	18 - 20
7	1	3	ALA	ILE	1	G	G	18 - 20	18 - 20
8	1	3	ALA	ILE	1	H	H	18 - 20	18 - 20
9	1	3	ALA	ILE	1	I	I	18 - 20	18 - 20
10	1	3	ALA	ILE	1	J	J	18 - 20	18 - 20
11	1	3	ALA	ILE	1	K	K	18 - 20	18 - 20
12	1	3	ALA	ILE	1	L	L	18 - 20	18 - 20
13	2	3	GLU	ALA	4	C	C	51 - 56	51 - 56
14	2	3	GLU	ALA	4	A	A	51 - 56	51 - 56
15	2	3	GLU	ALA	4	B	B	51 - 56	51 - 56
16	2	3	GLU	ALA	4	D	D	51 - 56	51 - 56
17	2	3	GLU	ALA	4	E	E	51 - 56	51 - 56
18	2	3	GLU	ALA	4	F	F	51 - 56	51 - 56
19	2	3	GLU	ALA	4	G	G	51 - 56	51 - 56
20	2	3	GLU	ALA	4	H	H	51 - 56	51 - 56
21	2	3	GLU	ALA	4	I	I	51 - 56	51 - 56
22	2	3	GLU	ALA	4	J	J	51 - 56	51 - 56
23	2	3	GLU	ALA	4	K	K	51 - 56	51 - 56
24	2	3	GLU	ALA	4	L	L	51 - 56	51 - 56
25	3	3	HIS	VAL	4	C	C	95 - 97	95 - 97
26	3	3	HIS	VAL	4	A	A	95 - 97	95 - 97
27	3	3	HIS	VAL	4	B	B	95 - 97	95 - 97
28	3	3	HIS	VAL	4	D	D	95 - 97	95 - 97
29	3	3	HIS	VAL	4	E	E	95 - 97	95 - 97
30	3	3	HIS	VAL	4	F	F	95 - 97	95 - 97
31	3	3	HIS	VAL	4	G	G	95 - 97	95 - 97
32	3	3	HIS	VAL	4	H	H	95 - 97	95 - 97
33	3	3	HIS	VAL	4	I	I	95 - 97	95 - 97
34	3	3	HIS	VAL	4	J	J	95 - 97	95 - 97
35	3	3	HIS	VAL	4	K	K	95 - 97	95 - 97
36	3	3	HIS	VAL	4	L	L	95 - 97	95 - 97
37	4	3	ALA	GLU	4	C	C	127 - 133	127 - 133
38	4	3	ALA	GLU	4	A	A	127 - 133	127 - 133
39	4	3	ALA	GLU	4	B	B	127 - 133	127 - 133
40	4	3	ALA	GLU	4	D	D	127 - 133	127 - 133
41	4	3	ALA	GLU	4	E	E	127 - 133	127 - 133
42	4	3	ALA	GLU	4	F	F	127 - 133	127 - 133
43	4	3	ALA	GLU	4	G	G	127 - 133	127 - 133
44	4	3	ALA	GLU	4	H	H	127 - 133	127 - 133
45	4	3	ALA	GLU	4	I	I	127 - 133	127 - 133
46	4	3	ALA	GLU	4	J	J	127 - 133	127 - 133
47	4	3	ALA	GLU	4	K	K	127 - 133	127 - 133
48	4	3	ALA	GLU	4	L	L	127 - 133	127 - 133

NCS ensembles :

ID
1
2
3

#1: Protein	ferritin Mass: 20760.139 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: Ftn / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 codon plus / References: UniProt: O29424
#2: Chemical	... ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Zn
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 866 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal	Density Matthews: 3.39 Å³/Da / Density % sol: 63.44 %
Crystal grow	Temperature: 293 K / Method: microbatch under oil / pH: 7.5 Details: PEG 400, HEPES, MgCl2, pH 7.5, microbatch under oil, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 8.2.2 / Wavelength: 0.9720, 0.9800, 0.9797

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 27, 2003

Radiation

Monochromator: Double-crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.972	1
2	0.98	1
3	0.9797	1

Reflection

Resolution: 2.1→90 Å / Num. obs: 174236 / % possible obs: 97.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / R_merge(I) obs: 0.069 / R_sym value: 0.069 / Net I/σ(I): 13.32

Reflection shell

Resolution: 2.1→2.18 Å / Mean I/σ(I) obs: 5.16 / R_sym value: 0.242 / % possible all: 99.6

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Processing

Software

Name	Version	Classification
REFMAC	5.1.24	refinement
DENZO		data reduction
SCALEPACK		data scaling
MLPHARE		phasing

Refinement

Method to determine structure:

MAD / Resolution: 2.1→15.01 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.921 / SU B: 3.486 / SU ML: 0.096 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21771	8714	5 %	RANDOM
R_work	0.17858	-	-	-
obs	0.18055	164841	98.39 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 25.332 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.06 Å²	0 Å²	0 Å²
2-	-	-0.11 Å²	0 Å²
3-	-	-	0.05 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→15.01 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16133	0	24	866	17023

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.021	16506
X-RAY DIFFRACTION	r_bond_other_d	0	0.02	14803
X-RAY DIFFRACTION	r_angle_refined_deg	1.571	1.948	22248
X-RAY DIFFRACTION	r_angle_other_deg	0.857	3	34411
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.069	5	1935
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.143	0.2	2355
X-RAY DIFFRACTION	r_gen_planes_refined	0.015	0.02	18237
X-RAY DIFFRACTION	r_gen_planes_other	0.007	0.02	3483
X-RAY DIFFRACTION	r_nbd_refined	0.239	0.3	4255
X-RAY DIFFRACTION	r_nbd_other	0.273	0.3	16509
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other	0.095	0.5	8603
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.201	0.5	1417
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined	0.079	0.5	16
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.313	0.3	17
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.214	0.3	51
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.415	0.5	17
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	2.273	2	9711
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	3.322	3	15562
X-RAY DIFFRACTION	r_scbond_it	3.274	2	6795
X-RAY DIFFRACTION	r_scangle_it	4.865	3	6686
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
3	1	C	44	tight positional	0.07	0.05
3	2	A	44	tight positional	0.06	0.05
3	3	B	44	tight positional	0.07	0.05
3	4	D	44	tight positional	0.06	0.05
3	5	E	44	tight positional	0.06	0.05
3	6	F	44	tight positional	0.06	0.05
3	7	G	44	tight positional	0.06	0.05
3	8	H	44	tight positional	0.05	0.05
3	9	I	44	tight positional	0.42	0.05
3	10	J	44	tight positional	0.06	0.05
3	11	K	44	tight positional	0.06	0.05
3	12	L	44	tight positional	0.06	0.05
1	1	A	2527	medium positional	0.42	0.5
1	2	D	2527	medium positional	0.43	0.5
1	3	E	2527	medium positional	0.39	0.5
1	4	G	2527	medium positional	0.35	0.5
1	5	J	2527	medium positional	0.42	0.5
1	6	K	2527	medium positional	0.42	0.5
2	1	B	2567	medium positional	0.38	0.5
2	2	C	2567	medium positional	0.39	0.5
2	3	F	2567	medium positional	0.41	0.5
2	4	H	2567	medium positional	0.56	0.5
2	5	I	2567	medium positional	0.51	0.5
2	6	L	2567	medium positional	0.4	0.5
3	1	C	240	medium positional	0.35	0.5
3	2	A	240	medium positional	0.36	0.5
3	3	B	240	medium positional	0.36	0.5
3	4	D	240	medium positional	0.36	0.5
3	5	E	240	medium positional	0.4	0.5
3	6	F	240	medium positional	0.34	0.5
3	7	G	240	medium positional	0.44	0.5
3	8	H	240	medium positional	0.37	0.5
3	9	I	240	medium positional	0.44	0.5
3	10	J	240	medium positional	0.33	0.5
3	11	K	240	medium positional	0.43	0.5
3	12	L	240	medium positional	0.31	0.5
3	1	C	44	tight thermal	0.42	0.5
3	2	A	44	tight thermal	0.44	0.5
3	3	B	44	tight thermal	0.41	0.5
3	4	D	44	tight thermal	0.42	0.5
3	5	E	44	tight thermal	0.46	0.5
3	6	F	44	tight thermal	0.47	0.5
3	7	G	44	tight thermal	0.34	0.5
3	8	H	44	tight thermal	0.48	0.5
3	9	I	44	tight thermal	0.38	0.5
3	10	J	44	tight thermal	0.55	0.5
3	11	K	44	tight thermal	0.54	0.5
3	12	L	44	tight thermal	0.4	0.5
1	1	A	2527	medium thermal	1.1	2
1	2	D	2527	medium thermal	1.21	2
1	3	E	2527	medium thermal	1.4	2
1	4	G	2527	medium thermal	1.23	2
1	5	J	2527	medium thermal	1.2	2
1	6	K	2527	medium thermal	1.35	2
2	1	B	2567	medium thermal	1.32	2
2	2	C	2567	medium thermal	1.35	2
2	3	F	2567	medium thermal	1.47	2
2	4	H	2567	medium thermal	1.37	2
2	5	I	2567	medium thermal	1.23	2
2	6	L	2567	medium thermal	1.7	2
3	1	C	240	medium thermal	1.9	2
3	2	A	240	medium thermal	1.9	2
3	3	B	240	medium thermal	1.33	2
3	4	D	240	medium thermal	1.55	2
3	5	E	240	medium thermal	1.33	2
3	6	F	240	medium thermal	2.24	2
3	7	G	240	medium thermal	2.07	2
3	8	H	240	medium thermal	1.76	2
3	9	I	240	medium thermal	1.53	2
3	10	J	240	medium thermal	1.6	2
3	11	K	240	medium thermal	1.93	2
3	12	L	240	medium thermal	1.39	2

LS refinement shell

Resolution: 2.101→2.154 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.235	624
R_work	0.179	12152

Refinement TLS params.

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

ID	L11 (°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)
1	0.3203	0.3082	-0.0772	1.3013	-0.2813	0.1887	0.0096	0.0886	-0.0393	-0.1192	-0.0152	-0.1484	0.035	0.018	0.0056	0.099	0.0248	0.0484	0.1748	-0.0322	0.0793	58.513	76.713	129.104
2	0.4763	0.0337	0.0156	1.4464	-0.3794	0.1588	-0.0191	0.1209	0.0434	-0.0927	0.0083	0.0162	0.0358	0.0091	0.0108	0.1168	0.0252	-0.0122	0.1649	-0.0297	0.021	33.139	81.306	126.54
3	1.122	-0.6647	0.255	0.6672	0.061	0.4061	0.0285	0.0489	0.23	-0.0022	0.0491	-0.3232	-0.0372	-0.0413	-0.0775	0.104	-0.0237	0.0229	0.0706	0.0448	0.2221	64.21	130.313	150.067
4	1.0823	-0.6764	0.3403	0.7307	0.0632	0.2549	0.0247	0.1223	0.0563	-0.1423	-0.0264	-0.1509	-0.0549	0.0124	0.0018	0.1207	-0.0008	0.0817	0.1432	0.0789	0.0993	59.019	113.886	130.674
5	0.5562	0.2515	0.5328	0.4712	0.4977	1.0126	0.0208	0.0776	-0.0195	-0.0195	0.027	-0.1857	-0.0538	0.0856	-0.0479	0.0409	0.015	0.0501	0.1363	0.0104	0.2357	85.18	94.196	148.331
6	0.5925	0.3158	0.6187	0.3509	0.3265	1.1784	0.0971	0.0089	-0.0173	0.0082	0.0076	-0.0447	0.153	0.0689	-0.1047	0.0759	0.0432	-0.0195	0.1116	0.0147	0.2293	83.974	72.271	162.091
7	0.3102	-0.0489	-0.3281	0.391	-0.5352	1.4249	0.0089	0.0828	-0.1124	-0.0345	-0.0011	0.015	0.1123	-0.0329	-0.0079	0.115	-0.0126	-0.036	0.0848	-0.0471	0.1224	17.343	45.854	157.882
8	0.6325	0.0145	-0.3084	0.2065	-0.3319	1.2047	-0.0639	-0.1059	-0.1287	-0.0205	0.039	-0.0335	0.0623	0.1371	0.0249	0.1184	0.0548	-0.0145	0.1223	-0.0413	0.1103	42.753	42.899	162.53
9	1.4636	-0.3565	0.7995	0.1609	-0.1482	0.8405	-0.0053	-0.1369	0.0562	0.0149	-0.0619	-0.0322	-0.0507	-0.0942	0.0671	0.1345	-0.016	-0.0072	0.1419	0.0086	0.0391	11.866	63.746	212.414
10	1.1888	-0.2214	0.6336	0.1484	0.0282	0.4593	0.0317	-0.0037	-0.0964	0.0313	0.0086	0.0377	0.1167	0.0374	-0.0403	0.1489	-0.0054	-0.0249	0.1059	0.0385	0.083	16.79	45.121	195.061
11	0.2705	-0.4172	-0.2357	0.886	0.3637	0.3872	-0.0102	0.0073	-0.0474	0.0666	0.0277	0.065	0.0079	-0.0399	-0.0175	0.0957	-0.0282	-0.0371	0.1148	0.001	0.1041	-9.27	64.252	176.382
12	0.5009	-0.2453	-0.4681	0.5257	0.2939	0.5738	0.0238	0.0091	-0.0678	-0.0122	-0.0451	0.0621	-0.023	0.0112	0.0214	0.0908	0.0092	-0.0606	0.1208	-0.0119	0.0673	-7.711	79.357	155.379

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	3 - 164	3 - 164
2	X-RAY DIFFRACTION	2	B	B	3 - 164	3 - 164
3	X-RAY DIFFRACTION	3	C	C	3 - 164	3 - 164
4	X-RAY DIFFRACTION	4	D	D	3 - 164	3 - 164
5	X-RAY DIFFRACTION	5	E	E	3 - 164	3 - 164
6	X-RAY DIFFRACTION	6	F	F	3 - 164	3 - 164
7	X-RAY DIFFRACTION	7	G	G	3 - 164	3 - 164
8	X-RAY DIFFRACTION	8	H	H	3 - 164	3 - 164
9	X-RAY DIFFRACTION	9	I	I	3 - 164	3 - 164
10	X-RAY DIFFRACTION	10	J	J	3 - 164	3 - 164
11	X-RAY DIFFRACTION	11	K	K	3 - 164	3 - 164
12	X-RAY DIFFRACTION	12	L	L	3 - 164	3 - 164

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