PDB-2yjj: Structure of Dps from MICROBACTERIUM ARBORESCENS in the low iron form

ID or keywords:

Entry

Database: PDB / ID: 2yjj

Title

Structure of Dps from MICROBACTERIUM ARBORESCENS in the low 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: 2.05 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 29, 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_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_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_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.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	2yjj.cif.gz	678.6 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	2yjj.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	2yjj_validation.pdf.gz	531.1 KB	Display	wwPDB validaton report
Full document	2yjj_full_validation.pdf.gz	557.4 KB	Display
Data in XML	2yjj_validation.xml.gz	72.5 KB	Display
Data in CIF	2yjj_validation.cif.gz	102.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yj/2yjj ftp://data.pdbj.org/pub/pdb/validation_reports/yj/2yjj	HTTPS FTP

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Related structure data

Related structure data	2yjkC 1o9rS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2yjk-d 1veq-d 1o9r-1 1uvh-1 3ge4-d 2d5k-1 10161 6b0d-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

208 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)	87.530, 91.920, 128.450
Angle α, β, γ (deg.)	90.00, 96.10, 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-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical	ChemComp-OFE / Iron(II) oxide / ferrous oxide Mass: 71.844 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: FeO
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 920 / 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: 2.48 Å³/Da / Density % sol: 50.35 % / Description: NONE
Crystal grow	pH: 7.5 Details: 18% PEG8000, 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: 2.05→2.1 Å / Num. obs: 120300 / % possible obs: 99.4 % / Observed criterion σ(I): 1.8 / Redundancy: 3.5 % / R_merge(I) obs: 0.08 / Net I/σ(I): 7.3
Reflection shell	Resolution: 2.05→2.1 Å / Redundancy: 3.3 % / R_merge(I) obs: 0.79 / Mean I/σ(I) obs: 1.8 / % possible all: 97.9

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0071	refinement
XDS		data reduction
XDS		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O9R

1o9r

Resolution: 2.05→29.01 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.931 / SU B: 9.618 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22574	6332	5 %	RANDOM
R_work	0.17114	-	-	-
obs	0.17382	120298	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: 31.046 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.07 Å²	0 Å²	-0.08 Å²
2-	-	0.08 Å²	0 Å²
3-	-	-	-0.03 Å²

Refinement step

Cycle: LAST / Resolution: 2.05→29.01 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13589	0	22	920	14531

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.024	0.022	13822
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.774	1.935	18863
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.221	5	1786
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	42.593	25.57	623
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.794	15	2204
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.261	15	60
X-RAY DIFFRACTION	r_chiral_restr	0.124	0.2	2271
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	10412
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	1.081	1.5	8948
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.993	2	14330
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	3.515	3	4874
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	5.783	4.5	4532
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: 1103 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	medium positional	0.34	0.5
2	B	medium positional	0.2	0.5
3	C	medium positional	0.24	0.5
4	D	medium positional	0.22	0.5
5	E	medium positional	0.23	0.5
6	F	medium positional	0.23	0.5
7	G	medium positional	0.33	0.5
8	H	medium positional	0.32	0.5
9	I	medium positional	0.32	0.5
10	J	medium positional	0.2	0.5
11	K	medium positional	0.22	0.5
12	L	medium positional	0.29	0.5
1	A	medium thermal	1.42	2
2	B	medium thermal	1.3	2
3	C	medium thermal	1.28	2
4	D	medium thermal	1.21	2
5	E	medium thermal	1.31	2
6	F	medium thermal	1.61	2
7	G	medium thermal	1.35	2
8	H	medium thermal	1.26	2
9	I	medium thermal	1.42	2
10	J	medium thermal	1.29	2
11	K	medium thermal	1.15	2
12	L	medium thermal	1.33	2

LS refinement shell

Resolution: 2.05→2.103 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.29	466	-
R_work	0.261	8840	-
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	0.7075	0.046	-0.2001	1.0164	0.0046	0.3646	-0.0171	0.2038	0.0522	-0.0351	-0.048	-0.0181	-0.086	-0.0002	0.0651	0.0931	0.0069	-0.0167	0.1421	0.0291	0.0317	10.3489	3.9352	2.8709
2	0.7886	0.1436	-0.0612	1.1041	-0.1836	0.7833	0.0101	0.1051	0.0305	-0.0168	-0.0469	0.0747	-0.0691	-0.0734	0.0369	0.0269	0.0202	-0.0045	0.1038	-0.0333	0.0334	-8.3837	-1.6832	14.9336
3	1.5898	-0.0053	0.2367	0.2964	0.1234	1.4269	-0.0979	0.1851	0.215	-0.0537	-0.0247	-0.0003	-0.1931	0.0076	0.1226	0.2102	0.0121	-0.0517	0.0362	0.0556	0.1465	15.9616	28.9568	22.0721
4	1.2372	-0.2408	0.4117	0.3562	-0.0313	1.2875	0.0177	0.1117	-0.1729	0.0048	-0.0152	0.0538	0.0869	-0.1363	-0.0025	0.0502	-0.0168	0.0148	0.0405	-0.0404	0.1167	5.4431	-27.8514	25.7324
5	0.8396	-0.1861	0.3475	1.2177	-0.1829	0.3411	-0.038	0.2468	0.1449	-0.0993	-0.0017	0.0013	-0.1045	0.0677	0.0397	0.0951	-0.0276	0.0184	0.1305	0.0594	0.0661	39.8139	8.7451	14.2562
6	0.8758	0.0063	0.4204	0.8974	-0.129	1.1452	0.0145	0.1554	-0.0605	-0.072	-0.0001	-0.0129	-0.0081	0.0743	-0.0144	0.0288	0.0007	0.0343	0.0782	-0.0076	0.0597	41.4355	-13.3329	20.546
7	0.619	0.1547	-0.0728	1.5513	0.1461	0.4498	-0.0235	-0.1548	0.0222	-0.0345	-0.0429	0.0685	-0.0379	-0.0646	0.0664	0.0552	0.0024	-0.0017	0.0572	-0.0199	0.0165	24.2006	4.2205	62.3391
8	0.5577	0.0864	0.0047	1.5365	0.1733	0.5308	0.0248	-0.0559	0.004	-0.0309	-0.0283	-0.0492	-0.0282	0.0665	0.0034	0.0096	-0.003	0.0027	0.0202	0.0121	0.0263	41.1962	-5.3266	50.7643
9	1.0661	0.1052	0.3599	0.3781	-0.1738	1.3955	-0.0759	-0.0033	0.2175	0.0028	-0.0508	0.0345	-0.2029	-0.0858	0.1267	0.1817	0.0189	-0.0439	0.0176	-0.0126	0.132	22.3959	28.3489	43.8921
10	1.7715	0.0996	0.248	0.2578	-0.0751	1.2476	0.0491	0.0416	-0.1917	0.0297	-0.0149	-0.0209	0.1013	-0.0004	-0.0342	0.0618	-0.0058	0.0045	0.0027	-0.0011	0.1247	22.7087	-29.4014	40.4864
11	1.2328	0.191	0.6821	1.1469	-0.0656	1.1121	-0.0381	-0.1376	0.1117	0.0439	-0.0367	0.0095	-0.1289	-0.1428	0.0748	0.0838	0.0418	0.02	0.0933	-0.0692	0.0959	-4.6471	12.8804	51.4821
12	1.1027	-0.1065	0.9125	0.9224	0.0658	1.77	0.0208	-0.0588	-0.0203	0.0658	-0.0372	0.0206	-0.0113	-0.1382	0.0164	0.0327	-0.0095	0.0424	0.0956	-0.0241	0.073	-10.1287	-8.5548	45.8377

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	13 - 161
2	X-RAY DIFFRACTION	2	B	10 - 160
3	X-RAY DIFFRACTION	3	C	13 - 161
4	X-RAY DIFFRACTION	4	D	14 - 161
5	X-RAY DIFFRACTION	5	E	12 - 161
6	X-RAY DIFFRACTION	6	F	12 - 161
7	X-RAY DIFFRACTION	7	G	5 - 161
8	X-RAY DIFFRACTION	8	H	15 - 161
9	X-RAY DIFFRACTION	9	I	14 - 161
10	X-RAY DIFFRACTION	10	J	14 - 161
11	X-RAY DIFFRACTION	11	K	13 - 161
12	X-RAY DIFFRACTION	12	L	12 - 161

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