PDB-2yjk: Structure of Dps from MICROBACTERIUM ARBORESCENS in the high iron form

ID or keywords:

Entry

Database: PDB / ID: 2yjk

Title

Structure of Dps from MICROBACTERIUM ARBORESCENS in the high iron form

Components

AFP

Keywords

METAL BINDING PROTEIN / METAL-BINDING PROTEIN / IRON UPTAKE / FERRITIN FOLD

Function / homology

Function and homology information

ferric iron binding
Similarity search - Function

Biological species

MICROBACTERIUM ARBORESCENS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Zeth, K. / Buecheler, R. / Boland, W.

Citation

Journal: J.Biol.Chem. / Year: 2011
Title: Structure and Mechanism of Iron Translocation by a Dps Protein from Microbacterium Arborescens.
Authors: Pesek, J. / Buecheler, R. / Albrecht, R. / Boland, W. / Zeth, K.

History

Deposition	May 19, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 1, 2011	Provider: repository / Type: Initial release
Revision 1.1	Oct 12, 2011	Group: Database references / Version format compliance
Revision 1.2	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2yjk.cif.gz	684.1 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	2yjk_validation.pdf.gz	534 KB	Display	wwPDB validaton report
Full document	2yjk_full_validation.pdf.gz	565.3 KB	Display
Data in XML	2yjk_validation.xml.gz	71.4 KB	Display
Data in CIF	2yjk_validation.cif.gz	99.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yj/2yjk ftp://data.pdbj.org/pub/pdb/validation_reports/yj/2yjk	HTTPS FTP

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Related structure data

Related structure data	2yjjC 1o9rS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1veq-d 1uvh-1 2yjj-d 3ge4-d 1o9r-1 2d5k-1 1vel-1 10161 6gcm-1 1jig-1 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 (3) #114 - Jun 2009 Vaults similarity (1) #57 - Sep 2004 Catalase similarity (1)

Deposited unit

A: AFP

B: AFP

C: AFP

D: AFP

E: AFP

F: AFP

G: AFP

H: AFP

I: AFP

J: AFP

K: AFP

L: AFP

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	87.580, 92.050, 128.580
Angle α, β, γ (deg.)	90.00, 96.04, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	G
8	1	H
9	1	I
10	1	J
11	1	K
12	1	L

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	4	A	10 - 160
2	1	1	4	B	10 - 160
3	1	1	4	C	10 - 160
4	1	1	4	D	10 - 160
5	1	1	4	E	10 - 160
6	1	1	4	F	10 - 160
7	1	1	4	G	10 - 160
8	1	1	4	H	10 - 160
9	1	1	4	I	10 - 160
10	1	1	4	J	10 - 160
11	1	1	4	K	10 - 160
12	1	1	4	L	10 - 160

#1: Protein	AFP / DPS Mass: 17284.432 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) MICROBACTERIUM ARBORESCENS (bacteria) / References: UniProt: Q1X6M4
#2: Chemical	ChemComp-OFE / Iron(II) oxide / ferrous oxide Mass: 71.844 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: FeO
#3: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 705 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.54 Å³/Da / Density % sol: 51.2 % / Description: NONE
Crystal grow	pH: 7.5 Details: 18% PEG 8000, 2% ISO-PROPANOL, 0.1 M NA-ACETATE, PH 7.5.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2→30 Å / Num. obs: 129605 / % possible obs: 98 % / Observed criterion σ(I): 1.5 / Redundancy: 2.05 % / R_merge(I) obs: 0.1 / Net I/σ(I): 7.3
Reflection shell	Resolution: 2→2.05 Å / Redundancy: 2 % / R_merge(I) obs: 0.88 / Mean I/σ(I) obs: 1.5 / % possible all: 96.8

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0109	refinement
XDS		data reduction
XDS		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O9R

1o9r

Resolution: 2→28.98 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.935 / SU B: 8.706 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2165	6821	5 %	RANDOM
R_work	0.16992	-	-	-
obs	0.17227	129604	100 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 31.239 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.95 Å²	0 Å²	-0.8 Å²
2-	-	0.89 Å²	0 Å²
3-	-	-	-0.11 Å²

Refinement step

Cycle: LAST / Resolution: 2→28.98 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13726	0	28	705	14459

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.025	0.022	13994
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.821	1.936	19111
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.557	5	1821
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.545	25.605	628
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.151	15	2228
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.309	15	60
X-RAY DIFFRACTION	r_chiral_restr	0.138	0.2	2308
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	10548
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	1.168	1.5	9080
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.159	2	14533
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	3.721	3	4914
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	6.166	4.5	4571
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Number: 1100 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	medium positional	0.36	0.5
2	B	medium positional	0.22	0.5
3	C	medium positional	0.23	0.5
4	D	medium positional	0.19	0.5
5	E	medium positional	0.33	0.5
6	F	medium positional	0.36	0.5
7	G	medium positional	0.3	0.5
8	H	medium positional	0.24	0.5
9	I	medium positional	0.18	0.5
10	J	medium positional	0.27	0.5
11	K	medium positional	0.29	0.5
12	L	medium positional	0.27	0.5
1	A	medium thermal	1.26	2
2	B	medium thermal	1.23	2
3	C	medium thermal	1.35	2
4	D	medium thermal	1.29	2
5	E	medium thermal	1.23	2
6	F	medium thermal	1.67	2
7	G	medium thermal	1.56	2
8	H	medium thermal	1.68	2
9	I	medium thermal	1.32	2
10	J	medium thermal	1.36	2
11	K	medium thermal	1.17	2
12	L	medium thermal	1.19	2

LS refinement shell

Resolution: 1.998→2.05 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.309	479	-
R_work	0.276	9110	-
obs	-	-	100 %

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	1.0688	0.1263	-0.2205	1.2374	0.165	0.4726	-0.0216	0.1919	0.0512	-0.0321	-0.0298	-0.0287	-0.0972	-0.0166	0.0514	0.0964	0.0092	-0.0201	0.1439	0.0257	0.0262	10.358	3.7507	2.9134
2	0.7098	0.0284	-0.0526	1.4764	-0.1184	0.7284	0.0036	0.1	0.0196	-0.0153	-0.0194	0.0872	-0.062	-0.0979	0.0158	0.032	0.0164	-0.0044	0.1106	-0.0266	0.043	-8.3684	-1.8379	15.0941
3	1.3063	0.0241	0.3021	0.5342	0.0703	1.1055	-0.0793	0.1365	0.1828	-0.0476	-0.0265	-0.0385	-0.1443	0.0522	0.1058	0.2059	0.0097	-0.0564	0.041	0.06	0.1393	17.2327	28.6702	21.5173
4	1.1654	-0.1886	0.2261	0.4016	0.0143	1.2178	0.0417	0.029	-0.1544	0.0216	-0.0312	0.0622	0.0391	-0.1055	-0.0105	0.0683	-0.0132	-0.0014	0.0347	-0.0377	0.1243	5.0697	-27.8019	26.2796
5	0.9102	-0.1711	0.4998	1.162	-0.1261	0.7771	-0.0276	0.2589	0.1138	-0.1136	-0.0202	0.0312	-0.0864	0.0668	0.0478	0.0813	-0.0248	0.0218	0.1512	0.0633	0.0713	39.6256	8.5351	14.1301
6	1.1184	0.0731	0.4864	1.0107	-0.1449	1.2012	0.01	0.0874	-0.0566	-0.0392	-0.0061	-0.0106	-0.0021	0.0635	-0.0039	0.032	0.0093	0.044	0.091	-0.0035	0.0709	41.7097	-13.1876	20.7625
7	0.8989	-0.1303	-0.0223	1.2479	0.2343	0.6666	-0.0212	-0.1294	0.049	-0.0044	-0.0544	0.0622	-0.0646	-0.0543	0.0756	0.0706	-0.0043	-0.0078	0.0629	-0.0211	0.0186	23.8831	3.4395	62.7274
8	1.0104	-0.2505	-0.0373	1.3737	0.3967	1.0117	0.0101	-0.052	-0.055	0.0163	-0.0137	-0.0282	0.0359	0.0638	0.0036	0.0169	-0.0009	-0.0089	0.0329	0.0202	0.0222	40.9379	-6.0671	51.0622
9	1.207	0.0076	0.1135	0.3978	-0.1582	1.341	-0.0761	-0.0323	0.2087	0.0098	-0.0321	0.0341	-0.1786	-0.0445	0.1082	0.1798	0.017	-0.0483	0.0066	-0.0197	0.1353	22.4593	28.3857	43.7271
10	1.441	0.0745	0.2087	0.2694	0.0227	1.0896	0.0308	0.0458	-0.1514	0.024	-0.0122	-0.0241	0.0868	0.0056	-0.0186	0.0835	-0.0034	-0.0059	0.0038	0.0088	0.1276	22.7924	-29.3318	40.5757
11	1.159	0.2536	0.6768	1.206	0.0788	1.0342	-0.067	-0.1941	0.1001	0.0715	0.0046	-0.0206	-0.1121	-0.1473	0.0624	0.0841	0.052	0.0258	0.1223	-0.0738	0.1057	-4.2276	12.7411	51.878
12	0.799	0.0616	0.6741	0.7574	0.1764	1.2367	-0.002	-0.0368	-0.0175	0.0586	-0.0076	-0.0008	-0.0093	-0.1286	0.0096	0.0304	-0.0073	0.0418	0.132	-0.0184	0.0721	-10.314	-8.316	45.3297

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	10 - 158
2	X-RAY DIFFRACTION	2	B	7 - 158
3	X-RAY DIFFRACTION	3	C	2 - 158
4	X-RAY DIFFRACTION	4	D	7 - 158
5	X-RAY DIFFRACTION	5	E	7 - 158
6	X-RAY DIFFRACTION	6	F	7 - 158
7	X-RAY DIFFRACTION	7	G	6 - 158
8	X-RAY DIFFRACTION	8	H	7 - 158
9	X-RAY DIFFRACTION	9	I	11 - 158
10	X-RAY DIFFRACTION	10	J	11 - 158
11	X-RAY DIFFRACTION	11	K	7 - 158
12	X-RAY DIFFRACTION	12	L	7 - 158

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