PDB-4oqq: Structure of the effector-binding domain of deoxyribonucleoside r...

ID or keywords:

Entry

Database: PDB / ID: 4oqq

Title

Structure of the effector-binding domain of deoxyribonucleoside regulator DeoR from Bacillus subtilis

Components

Deoxyribonucleoside regulator

Keywords

TRANSCRIPTION / Rossmann Fold / Sugar-binding transcriptional regulator / Schiff base

Function / homology

Function and homology information

regulation of DNA-templated transcription initiation / cis-regulatory region sequence-specific DNA binding / carbohydrate binding / identical protein binding
Similarity search - Function

Biological species

Bacillus subtilis subsp. subtilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Rezacova, P. / Skerlova, J.

Citation

Journal: Febs J. / Year: 2014
Title: Structure of the effector-binding domain of deoxyribonucleoside regulator DeoR from Bacillus subtilis.
Authors: Skerlova, J. / Fabry, M. / Hubalek, M. / Otwinowski, Z. / Rezacova, P.

History

Deposition	Feb 10, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 4, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jun 18, 2014	Group: Database references
Revision 1.2	Oct 1, 2014	Group: Database references
Revision 1.3	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 / 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 / _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	4oqq.cif.gz	218.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4oqq.ent.gz	179.9 KB	Display	PDB format
PDBx/mmJSON format	4oqq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4oqq_validation.pdf.gz	444.4 KB	Display	wwPDB validaton report
Full document	4oqq_full_validation.pdf.gz	445.9 KB	Display
Data in XML	4oqq_validation.xml.gz	21.9 KB	Display
Data in CIF	4oqq_validation.cif.gz	31.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oq/4oqq ftp://data.pdbj.org/pub/pdb/validation_reports/oq/4oqq	HTTPS FTP

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Related structure data

Related structure data	4oqpSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1ogk-1 4xuk-d 1uh5-d 6ttv-d 4u0l-1 6p5w-d 2x9q-d 6jge-d 6tl1-d 6ttw-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
Related items in Molecule of the Month	#48 - Dec 2003 Catabolite Activator Protein similarity (1)

Deposited unit

A: Deoxyribonucleoside regulator

B: Deoxyribonucleoside regulator

hetero molecules

59.1 kDa, 2 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)	63.081, 63.081, 150.129
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	145
Space group name H-M	P3₂

#1: Protein	Deoxyribonucleoside regulator Mass: 29371.447 Da / Num. of mol.: 2 / Fragment: C-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria) Strain: 168 / Gene: deoR, yxxC, BSU39430 / Plasmid: pET151 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P39140
#2: Chemical	ChemComp-BCN / BICINE Mass: 163.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄ / Comment: pH buffer*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.94 Å³/Da / Density % sol: 58.1 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Bicine, 20% (w/v) PEG 6000; 12.5 mg/mL protein in 20 mM trisodium citrate pH 7.0, 150 mM NaCl, 0.02% (v/v) 2-mercaptoethanol; protein:reservoir 1:2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 15, 2012 Details: Double crystal monochromator with 2 sets of Rh-soated silicon and glass mirrors
Radiation	Monochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.8→50 Å / Num. all: 62177 / Num. obs: 57887 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / R_merge(I) obs: 0.048
Reflection shell	Resolution: 1.8→1.86 Å / Redundancy: 2.6 % / R_merge(I) obs: 0.179 / Mean I/σ(I) obs: 2.9 / % possible all: 53.3

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Processing

Software

Name	Version	Classification
MAR345dtb		data collection
PHASER		phasing
REFMAC	5.7.0032	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4OQP

4oqp

Resolution: 1.8→27.31 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.956 / SU B: 6.298 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22756	2921	5.1 %	RANDOM
R_work	0.19276	-	-	-
obs	0.19455	54842	92.87 %	-
all	-	62177	-	-

Solvent computation

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

Displacement parameters

B_iso mean: 52.488 Å²

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

Refinement step

Cycle: LAST / Resolution: 1.8→27.31 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3970	0	22	225	4217

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.019	4103
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3989
X-RAY DIFFRACTION	r_angle_refined_deg	1.439	1.964	5547
X-RAY DIFFRACTION	r_angle_other_deg	0.79	3	9178
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.788	5	524
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.194	24.286	189
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.636	15	738
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.52	15	28
X-RAY DIFFRACTION	r_chiral_restr	0.086	0.2	631
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	4669
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	927
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	1.513	2.259	2054
X-RAY DIFFRACTION	r_mcbond_other	1.513	2.256	2053
X-RAY DIFFRACTION	r_mcangle_it	2.234	3.376	2571
X-RAY DIFFRACTION	r_mcangle_other	2.072	3.222	2572
X-RAY DIFFRACTION	r_scbond_it	2.014	2.576	2049
X-RAY DIFFRACTION	r_scbond_other	1.863	2.444	2049
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.851	3.571	2970
X-RAY DIFFRACTION	r_long_range_B_refined	6.277	18.448	4840
X-RAY DIFFRACTION	r_long_range_B_other	6.276	18.458	4841
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.797→1.844 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.344	110	-
R_work	0.319	2136	-
obs	-	-	49.24 %

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	2.1152	1.7292	1.2237	12.8229	1.1566	5.0145	-0.0063	-0.1651	0.2262	1.7581	-0.3456	-0.6415	-0.9684	1.3212	0.3519	0.7385	-0.4173	-0.1799	0.6524	0.0287	0.2666	57.293	35.699	181.095
2	5.5759	-1.614	-2.8934	6.7176	1.547	6.1648	0.1003	0.0951	0.562	0.4905	-0.3341	-0.4369	-1.4698	1.2031	0.2339	0.6503	-0.478	-0.1593	0.4197	0.1028	0.295	56.256	41.946	169.043
3	2.2435	0.2806	-0.0463	2.5901	-0.6408	5.4983	-0.0293	0.2327	0.2201	0.3202	-0.3387	-0.2155	-1.149	1.4555	0.3679	0.3242	-0.3733	-0.0845	0.5014	0.1282	0.2389	53.776	35.265	160.444
4	4.2126	-0.1525	0.8222	2.0249	-1.1063	5.2566	-0.1075	0.2455	0.5417	0.2364	-0.2492	-0.3456	-1.1511	0.9072	0.3566	0.3554	-0.262	-0.0298	0.2922	0.0789	0.2149	49.98	36.49	155.554
5	11.8167	2.5766	-1.441	2.2496	-1.0445	4.7417	-0.1473	0.3085	0.0303	-0.1318	0.0391	-0.2118	-0.3679	0.4345	0.1083	0.1176	-0.0606	0.0297	0.0628	0.0071	0.0911	44.657	29.207	152.907
6	1.6664	0.5476	1.1496	1.5042	-0.796	7.2276	0.0493	0.2279	-0.1031	-0.008	-0.0187	-0.0211	-0.0344	0.633	-0.0306	0.0439	-0.0047	0.003	0.0779	0.0026	0.1267	43.391	22.588	157.581
7	6.9415	2.3457	4.7382	0.8484	0.9337	11.8388	0.1012	0.2756	0.2135	0.098	0.1037	0.0887	-0.8543	0.1763	-0.2049	0.5691	0.1903	0.0926	0.125	0.0112	0.2734	31.143	36.213	165.37
8	11.8148	-0.359	1.0442	2.5616	0.2586	10.399	-0.006	-0.3898	0.2798	0.2688	0.1641	0.4283	-1.2157	-1.1967	-0.1582	0.3082	0.1587	0.0687	0.1579	0.0369	0.1776	30.376	28.711	171.647
9	0.9922	0.643	-0.3215	1.3993	-1.5567	6.7178	0.0673	0.0254	-0.0213	0.2134	-0.0313	-0.0608	-0.271	0.4679	-0.0361	0.1053	-0.0267	0.0035	0.0433	-0.0113	0.0947	42.069	22.36	168.223
10	2.3779	0.9781	0.151	3.0912	-1.4146	5.1125	0.0764	-0.1829	0.1563	0.8897	-0.2983	-0.054	-1.1392	0.8427	0.222	0.5204	-0.288	-0.0726	0.2277	0.0127	0.1569	49.728	33.635	177.708
11	6.9938	2.8831	-0.0075	2.7857	0.3078	3.0522	-0.9913	0.9259	0.8477	-0.6414	0.6808	0.2522	-0.8715	0.3436	0.3106	0.7428	-0.2336	-0.1599	0.4398	0.1232	0.2868	31.227	48.923	118.348
12	10.6697	-8.103	-8.4574	19.4402	-0.9001	10.7735	1.1671	-0.5613	0.4162	0.0314	-1.1064	-0.9539	-1.3678	1.3047	-0.0607	0.8621	-0.6339	-0.0944	0.7038	0.0765	0.5241	47.298	49.374	124.603
13	6.3171	-0.2485	-0.3634	3.3674	-0.4714	0.4787	-0.4087	0.3867	0.6302	0.0806	0.243	-0.1378	-0.5641	-0.0941	0.1657	0.9171	0.0209	-0.2654	0.3394	0.0113	0.2683	34.101	48.444	136.818
14	4.0554	-0.132	1.1085	3.1949	-0.6374	2.1818	-0.5753	0.0475	0.6951	0.1054	0.3168	-0.1643	-0.777	0.1691	0.2586	0.466	-0.0791	-0.1089	0.2231	-0.0427	0.1902	37.726	44.277	142.681
15	1.6594	-0.7754	0.9947	6.3616	-0.3112	3.6791	-0.3025	0.0237	0.5215	0.5137	0.0599	-0.2988	-0.9269	0.0536	0.2426	0.3382	-0.0554	-0.0675	0.1529	-0.0242	0.2113	37.345	41.504	146.755
16	1.4811	0.3058	0.9693	2.299	-0.5686	4.5386	-0.1013	0.0363	-0.0377	0.083	0.1306	0.095	-0.3393	-0.2444	-0.0294	0.0716	0.0165	-0.0119	0.0599	-0.0104	0.1087	30.164	29.535	142.218
17	1.3786	-3.3194	2.4085	12.0652	-0.7964	10.3762	-0.159	-0.0429	0.0071	0.027	0.5399	-0.2805	-0.7289	0.4354	-0.381	0.1984	-0.2234	0.0469	0.7977	-0.0924	0.2903	47.357	26.869	134.387
18	5.8249	-4.3419	0.0398	9.1133	0.3744	7.2631	0.1084	0.3086	-0.1797	-0.2612	0.1724	-0.5313	0.5209	1.2481	-0.2809	0.1324	-0.0003	0.021	0.3342	-0.0979	0.1663	41.24	22.467	128.116
19	0.7492	0.6774	0.8762	1.0398	0.7066	5.2541	-0.1426	0.1028	0.0563	-0.0481	0.188	0.0231	-0.4809	-0.1483	-0.0453	0.0903	-0.0071	0.0076	0.0712	0.0048	0.0976	29.83	29.641	131.54
20	2.7629	0.8573	1.1219	2.7519	0.5196	3.0904	-0.5394	0.5218	0.1653	-0.4688	0.3438	-0.1674	-0.8514	0.4008	0.1957	0.4221	-0.2694	-0.0426	0.2565	0.057	0.1676	35.972	41.667	121.877

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	59 - 86
2	X-RAY DIFFRACTION	2	A	87 - 104
3	X-RAY DIFFRACTION	3	A	105 - 126
4	X-RAY DIFFRACTION	4	A	127 - 162
5	X-RAY DIFFRACTION	5	A	163 - 179
6	X-RAY DIFFRACTION	6	A	180 - 213
7	X-RAY DIFFRACTION	7	A	214 - 223
8	X-RAY DIFFRACTION	8	A	224 - 242
9	X-RAY DIFFRACTION	9	A	243 - 273
10	X-RAY DIFFRACTION	10	A	274 - 311
11	X-RAY DIFFRACTION	11	B	59 - 81
12	X-RAY DIFFRACTION	12	B	82 - 93
13	X-RAY DIFFRACTION	13	B	94 - 121
14	X-RAY DIFFRACTION	14	B	122 - 149
15	X-RAY DIFFRACTION	15	B	150 - 175
16	X-RAY DIFFRACTION	16	B	176 - 213
17	X-RAY DIFFRACTION	17	B	214 - 223
18	X-RAY DIFFRACTION	18	B	224 - 242
19	X-RAY DIFFRACTION	19	B	243 - 274
20	X-RAY DIFFRACTION	20	B	275 - 311

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