PDB-4rb3: Crystal structure of Magnetospirillum gryphiswaldense MSR-1 Fur-M...

ID or keywords:

Entry

Database: PDB / ID: 4rb3

Title

Crystal structure of Magnetospirillum gryphiswaldense MSR-1 Fur-Mn2+-feoAB1 operator

Components

(DNA (25-MER)) x 2
DNA-binding transcriptional dual regulator of siderophore biosynthesis and transport(Fur family)

Keywords

METAL BINDING PROTEIN/DNA / ferric uptake regulator (FUR) / metal ion activation / operator recognition / cooperativity / broad substrate recognition / DNA shape readout / METAL BINDING PROTEIN-DNA complex

Function / homology

Function and homology information

negative regulation of siderophore biosynthetic process / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / zinc ion binding / cytosol
Similarity search - Function

Biological species

Magnetospirillum gryphiswaldense (magnetotactic)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Deng, Z. / Chen, Z.

Citation

Journal: Nat Commun
Title: Mechanistic insights into metal ion activation and operator recognition by the ferric uptake regulator.
Authors: Deng, Z. / Wang, Q. / Liu, Z. / Zhang, M. / Machado, A.C. / Chiu, T.P. / Feng, C. / Zhang, Q. / Yu, L. / Qi, L. / Zheng, J. / Wang, X. / Huo, X. / Qi, X. / Li, X. / Wu, W. / Rohs, R. / Li, Y. / Chen, Z.

History

Deposition	Sep 12, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 15, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_label_asym_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_ref_seq_dif.details / _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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Download

PDBx/mmCIF format	4rb3.cif.gz	177 KB	Display	PDBx/mmCIF format
PDB format	pdb4rb3.ent.gz	137.9 KB	Display	PDB format
PDBx/mmJSON format	4rb3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4rb3_validation.pdf.gz	460.1 KB	Display	wwPDB validaton report
Full document	4rb3_full_validation.pdf.gz	466.4 KB	Display
Data in XML	4rb3_validation.xml.gz	13.8 KB	Display
Data in CIF	4rb3_validation.cif.gz	18 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rb/4rb3 ftp://data.pdbj.org/pub/pdb/validation_reports/rb/4rb3	HTTPS FTP

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Related structure data

Related structure data	4rayC 4razC 4rb0C 4rb1C 4rb2SC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4rb2-d 3lmm-1 6ii0-4 5m4y-2 2ghj-d 4nl2-d 3cqg-d 6n3l-d 4nch-d 7bxf-d 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
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PDB pages

PDBj /

wwPDB /

NCBI

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Deposited unit

A: DNA (25-MER)

B: DNA (25-MER)

C: DNA-binding transcriptional dual regulator of siderophore biosynthesis and transport(Fur family)

D: DNA-binding transcriptional dual regulator of siderophore biosynthesis and transport(Fur family)

hetero molecules

48.9 kDa, 4 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)	93.995, 68.642, 83.995
Angle α, β, γ (deg.)	90.00, 108.70, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	D-307- HOH

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DNA chain , 2 types, 2 molecules AB

#1: DNA chain	DNA (25-MER) / feoAB1 operator Mass: 7646.970 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain	DNA (25-MER) / feoAB1 operator Mass: 7705.022 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 1 types, 2 molecules CD

#3: Protein	DNA-binding transcriptional dual regulator of siderophore biosynthesis and transport(Fur family) Mass: 16626.541 Da / Num. of mol.: 2 / Mutation: C9L, M14V, M16V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Magnetospirillum gryphiswaldense (magnetotactic) Strain: MSR-1 v2 / Gene: Fur, MGMSRv2_3137 / Production host: Escherichia coli (E. coli) / References: UniProt: V6F4Q0

#3: Protein

DNA-binding transcriptional dual regulator of siderophore biosynthesis and transport(Fur family)

Mass: 16626.541 Da / Num. of mol.: 2 / Mutation: C9L, M14V, M16V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Magnetospirillum gryphiswaldense (magnetotactic)
Strain: MSR-1 v2 / Gene: Fur, MGMSRv2_3137 / Production host:

Escherichia coli (E. coli) / References: UniProt: V6F4Q0

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Non-polymers , 3 types, 20 molecules

#4: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#5: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

Crystal	Density Matthews: 2.64 Å³/Da / Density % sol: 53.41 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 130 K
Diffraction source	Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 26, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.6→50 Å / Num. all: 15797 / Num. obs: 15330 / % possible obs: 97.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shell	Resolution: 2.6→2.64 Å / % possible all: 85.4

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
MOLREP		phasing
REFMAC	5.7.0029	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 4RB2

4rb2

Resolution: 2.6→44.56 Å / Cor.coef. F_o:F_c: 0.933 / Cor.coef. F_o:F_c free: 0.927 / SU B: 25.186 / SU ML: 0.262 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.798 / ESU R Free: 0.33 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26485	786	5.1 %	RANDOM
R_work	0.23243	-	-	-
obs	0.23411	14488	96.98 %	-
all	-	15330	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 74.257 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.16 Å²	0 Å²	4.25 Å²
2-	-	2.28 Å²	-0 Å²
3-	-	-	0.36 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→44.56 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2101	1019	9	15	3144

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.016	3286
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	0.944	1.663	4665
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.183	5	267
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.273	22.523	107
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.146	15	351
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.556	15	27
X-RAY DIFFRACTION	r_chiral_restr	0.066	0.2	481
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	2170
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
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

LS refinement shell

Resolution: 2.6→2.667 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.499	62	-
R_work	0.413	920	-
obs	-	-	85.99 %

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	9.3462	-4.7339	-3.0415	2.659	2.2307	2.9034	0.3122	1.0658	0.4545	-0.1169	-0.3862	-0.1282	-0.1273	0.071	0.074	0.2787	0.0525	-0.0175	0.227	0.0587	0.2938	-15.2107	12.9002	19.6028
2	4.0114	-0.8999	-2.3078	0.2035	0.5145	1.3419	0.0683	0.4658	0.0204	-0.0071	-0.0994	-0.0235	-0.0611	-0.2042	0.0311	0.214	0.0387	0.0099	0.6507	0.076	0.2668	13.4926	6.8949	10.8384
3	0.6162	-1.0425	-0.3891	2.1695	-1.0411	7.6792	0.3353	0.1238	0.2898	-0.4706	-0.2646	-0.5251	-0.7302	0.5015	-0.0707	0.2343	-0.0383	0.141	0.5606	0.1142	0.2249	34.767	6.8867	-0.3227
4	1.0274	0.4269	-1.8315	0.6277	-0.4425	3.5757	0.1214	0.1895	0.0355	-0.0117	-0.0087	-0.0886	-0.1487	-0.2211	-0.1127	0.2085	0.099	-0.0286	0.5987	0.0701	0.1436	30.9662	5.4959	1.8808
5	11.5487	-3.6569	-1.1076	6.3968	-3.3058	2.6605	0.1373	-0.3609	-0.1322	-0.2094	0.2171	0.5932	0.0868	-0.039	-0.3544	0.1893	0.0434	-0.0745	0.6282	-0.0422	0.1481	9.3802	3.447	9.6511
6	1.8265	-1.0844	1.8594	3.5816	-0.2197	2.3735	0.0943	0.6051	0.0492	-0.0557	-0.3662	0.2258	-0.074	0.3564	0.272	0.1813	0.1417	-0.1135	0.571	-0.0646	0.1675	-11.7935	11.3808	17.6943
7	7.5923	-0.1355	-2.5221	0.0327	-0.3561	7.4818	0.2905	0.87	0.261	-0.0057	-0.0646	-0.0342	0.3621	0.8284	-0.2259	0.2143	0.0644	-0.1145	0.3287	-0.0526	0.3205	40.4634	1.3858	16.9305
8	8.6222	-1.9282	-1.0809	0.7264	-1.1447	6.6534	0.0029	0.0786	0.3448	0.2013	-0.0295	-0.088	-0.9394	-0.0023	0.0266	0.3156	-0.0222	-0.0402	0.0169	-0.0041	0.3007	30.9822	7.9603	24.1298
9	5.659	2.0839	4.0673	1.359	0.2263	6.3746	0.1277	0.6815	-0.976	0.8195	0.6205	-0.7494	-1.2368	-1.5035	-0.7482	0.8507	0.6655	-0.5541	1.469	0.2614	1.0887	28.9874	10.8702	15.5639
10	6.7655	-3.8558	0.1687	2.24	0.4522	7.6647	-0.0251	0.306	-0.3922	0.0335	-0.2085	0.2146	0.153	-0.8235	0.2337	0.1915	-0.0747	0.0041	0.2039	-0.0849	0.2814	24.6839	-1.0827	22.8371
11	0.9893	0.903	-0.8496	1.8306	-0.1007	1.1874	0.0345	-0.0775	-0.0566	0.1975	-0.1167	0.0187	0.065	0.0641	0.0822	0.2292	0.0083	-0.0994	0.1297	-0.0158	0.3498	24.4704	1.2397	34.8685
12	4.3952	4.9795	0.2244	8.7788	0.6012	3.1407	0.2565	-0.3011	-0.3802	0.6331	-0.0397	-0.3887	0.1338	0.1951	-0.2168	0.2005	0.0392	-0.1197	0.0626	0.014	0.3047	21.4298	-11.9973	41.772
13	0.3688	0.0278	-0.4369	4.5599	1.5007	1.0616	-0.0501	-0.0262	0.02	-0.1683	0.104	-0.0389	-0.0473	0.0306	-0.054	0.2181	0.0272	-0.0978	0.079	0.0058	0.3395	16.0288	-9.5657	38.2953
14	3.1907	-0.7929	-0.5673	1.7297	-1.564	2.4315	0.2126	0.282	-0.4878	0.0371	-0.0852	0.3698	0.0829	-0.0513	-0.1274	0.2486	0.0217	-0.1189	0.0422	-0.0875	0.3099	-10.7633	-3.7006	27.1711
15	3.2427	-5.9256	-0.2842	13.6957	4.3426	5.3597	0.6933	0.9547	-0.7001	-0.729	-0.9566	1.1743	0.2961	0.5957	0.2633	0.4108	0.3924	-0.4201	0.7814	-0.4696	0.5052	-12.1121	-5.5692	16.0087
16	4.2349	-2.0138	1.4928	1.3439	0.0742	2.1692	0.1148	0.4003	-0.048	-0.0218	-0.0773	-0.0081	-0.0288	0.343	-0.0374	0.2896	0.0067	-0.0697	0.1429	-0.0452	0.2493	-4.1529	2.3745	26.4975
17	2.0806	-4.416	-3.2813	12.6142	0.0591	19.9619	0.1167	-0.0525	-0.1682	-0.3452	-0.4778	0.2513	-0.1755	1.4023	0.3611	0.2067	-0.09	-0.0085	0.2854	-0.1412	0.3488	7.8178	-5.7834	25.0144
18	5.4573	-0.5898	1.2853	0.0718	-0.3032	4.4168	0.3535	0.3341	-0.5884	-0.0255	-0.0392	0.0818	0.1671	0.1301	-0.3143	0.3241	0.0413	-0.0633	0.0346	-0.0156	0.3377	1.2976	-7.9919	34.3225
19	0.7977	1.101	1.9768	1.7689	2.5889	5.4541	0.0458	-0.0324	-0.0541	-0.0089	-0.0557	0.1223	0.2058	0.0866	0.0098	0.2746	-0.0007	-0.0389	0.0878	0.032	0.3588	10.5185	-14.6051	36.4374
20	0.7258	0.5454	-0.4708	3.5584	1.7341	1.9971	-0.0661	-0.0509	-0.0689	-0.0577	0.0102	0.0953	-0.0716	0.1574	0.0558	0.2358	0.0042	-0.0392	0.0518	0.0287	0.3092	15.6124	-6.2106	40.626

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 9
2	X-RAY DIFFRACTION	2	A	10 - 18
3	X-RAY DIFFRACTION	3	A	19 - 25
4	X-RAY DIFFRACTION	4	B	1 - 10
5	X-RAY DIFFRACTION	5	B	11 - 14
6	X-RAY DIFFRACTION	6	B	15 - 25
7	X-RAY DIFFRACTION	7	C	1 - 20
8	X-RAY DIFFRACTION	8	C	21 - 39
9	X-RAY DIFFRACTION	9	C	40 - 59
10	X-RAY DIFFRACTION	10	C	60 - 79
11	X-RAY DIFFRACTION	11	C	80 - 99
12	X-RAY DIFFRACTION	12	C	100 - 115
13	X-RAY DIFFRACTION	13	C	116 - 136
14	X-RAY DIFFRACTION	14	D	2 - 41
15	X-RAY DIFFRACTION	15	D	42 - 51
16	X-RAY DIFFRACTION	16	D	52 - 69
17	X-RAY DIFFRACTION	17	D	70 - 77
18	X-RAY DIFFRACTION	18	D	78 - 89
19	X-RAY DIFFRACTION	19	D	90 - 111
20	X-RAY DIFFRACTION	20	D	112 - 134

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