PDB-6ro6: Crystal structure of the C-terminal dimerization domain of the es...

ID or keywords:

Entry

Database: PDB / ID: 6ro6

Title

Crystal structure of the C-terminal dimerization domain of the essential repressor DdrO from radiation-resistant Deinococcus bacteria (Deinococcus deserti)

Components

HTH-type transcriptional regulator DdrOC

Keywords

DNA BINDING PROTEIN

Function / homology

Function and homology information

DNA-binding transcription factor activity / DNA binding / cytosol
Similarity search - Function

Biological species

Deinococcus deserti (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.41 Å

Authors

Pignol, D. / Arnoux, P. / Siponen, M.I. / Brandelet, G. / De Groot, A. / Blanchard, L.

Citation

Journal: Nucleic Acids Res. / Year: 2019
Title: Crystal structure of the transcriptional repressor DdrO: insight into the metalloprotease/repressor-controlled radiation response in Deinococcus.
Authors: de Groot, A. / Siponen, M.I. / Magerand, R. / Eugenie, N. / Martin-Arevalillo, R. / Doloy, J. / Lemaire, D. / Brandelet, G. / Parcy, F. / Dumas, R. / Roche, P. / Servant, P. / Confalonieri, ...

History

Deposition	May 10, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 9, 2019	Provider: repository / Type: Initial release
Revision 1.1	Oct 23, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Dec 4, 2019	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Jan 24, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6ro6.cif.gz	340.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6ro6.ent.gz	237.6 KB	Display	PDB format
PDBx/mmJSON format	6ro6.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6ro6_validation.pdf.gz	492.3 KB	Display	wwPDB validaton report
Full document	6ro6_full_validation.pdf.gz	498.8 KB	Display
Data in XML	6ro6_validation.xml.gz	19.4 KB	Display
Data in CIF	6ro6_validation.cif.gz	27.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ro/6ro6 ftp://data.pdbj.org/pub/pdb/validation_reports/ro/6ro6	HTTPS FTP

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Related structure data

Related structure data	6rmqC 6rnxSC 6rnzC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3b0k-2 4flp-2 6p1g-1 3t3t-1 3f7x-d 5i5q-d 2p5p-3 2n93-d 3lrh-5 2a5w-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

6rmqC

6rnxSC

6rnzC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#144 - Dec 2011 Complex I similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (5)

Deposited unit

A: HTH-type transcriptional regulator DdrOC

B: HTH-type transcriptional regulator DdrOC

C: HTH-type transcriptional regulator DdrOC

D: HTH-type transcriptional regulator DdrOC

E: HTH-type transcriptional regulator DdrOC

F: HTH-type transcriptional regulator DdrOC

G: HTH-type transcriptional regulator DdrOC

H: HTH-type transcriptional regulator DdrOC

hetero molecules

55.1 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: HTH-type transcriptional regulator DdrOC

C: HTH-type transcriptional regulator DdrOC

hetero molecules

defined by author&software
Evidence: gel filtration, The protein appears as an equilibrium between dimers and tetramers
13.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: HTH-type transcriptional regulator DdrOC

D: HTH-type transcriptional regulator DdrOC

hetero molecules

defined by author&software
13.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: HTH-type transcriptional regulator DdrOC

hetero molecules

G: HTH-type transcriptional regulator DdrOC

hetero molecules

defined by author&software
13.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

F: HTH-type transcriptional regulator DdrOC

hetero molecules

H: HTH-type transcriptional regulator DdrOC

defined by author&software
13.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	51.910, 76.800, 102.320
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab

#1: Protein	HTH-type transcriptional regulator DdrOC Mass: 6768.865 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus deserti (bacteria) / Gene: ddrOC, Deide_20570 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: C1CYP4
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.88 Å³/Da / Density % sol: 34.69 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M Sodium Citrate Tribasic pH 4.5, 0.2 M Lithium sulfate, 46% w/v PEG 400

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
Detector	Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 18, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.966 Å / Relative weight: 1
Reflection	Resolution: 1.41→61.42 Å / Num. obs: 73609 / % possible obs: 92.4 % / Redundancy: 4.9 % / B_iso Wilson estimate: 20.95 Å² / R_merge(I) obs: 0.037 / Net I/σ(I): 17.5
Reflection shell	Resolution: 1.41→1.43 Å / Num. unique obs: 3911 / CC_1/2: 0.49

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Processing

Software

Name	Version	Classification
PHENIX	1.16_3549	refinement
PHENIX	1.16_3549	refinement
XDS		data reduction
autoPROC		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6RNX

6rnx

Resolution: 1.41→60 Å / SU ML: 0.1754 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.7956

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2237	4002	5.44 %	RANDOM
R_work	0.1947	-	-	-
obs	0.1962	73601	92.38 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 35.99 Å²

Refinement step

Cycle: LAST / Resolution: 1.41→60 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3667	0	50	110	3827

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.018	3870
X-RAY DIFFRACTION	f_angle_d	1.533	5274
X-RAY DIFFRACTION	f_chiral_restr	0.0982	573
X-RAY DIFFRACTION	f_plane_restr	0.0094	663
X-RAY DIFFRACTION	f_dihedral_angle_d	5.4147	2486

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.41-1.43	0.3622	151	0.3486	2530	X-RAY DIFFRACTION	99.7
1.43-1.44	0.3533	155	0.3301	2560	X-RAY DIFFRACTION	99.96
1.44-1.46	0.3146	157	0.3134	2528	X-RAY DIFFRACTION	99.78
1.46-1.48	0.3186	164	0.2942	2549	X-RAY DIFFRACTION	99.49
1.48-1.5	0.3103	176	0.2858	2549	X-RAY DIFFRACTION	99.82
1.5-1.52	0.3048	156	0.2794	2553	X-RAY DIFFRACTION	99.78
1.52-1.55	0.3163	154	0.2703	2532	X-RAY DIFFRACTION	99.63
1.55-1.57	0.2643	145	0.262	2612	X-RAY DIFFRACTION	99.75
1.57-1.59	0.2874	146	0.2553	2531	X-RAY DIFFRACTION	99.81
1.59-1.62	0.276	148	0.2416	2596	X-RAY DIFFRACTION	99.78
1.62-1.65	0.3183	129	0.2359	2552	X-RAY DIFFRACTION	99.52
1.65-1.68	0.2532	115	0.2377	2219	X-RAY DIFFRACTION	93.92
1.72-1.76	0.3306	14	0.2334	193	X-RAY DIFFRACTION	61.79
1.76-1.8	0.23	153	0.218	2572	X-RAY DIFFRACTION	99.45
1.8-1.84	0.2457	132	0.2284	2604	X-RAY DIFFRACTION	99.93
1.84-1.89	0.2251	131	0.2234	2604	X-RAY DIFFRACTION	99.89
1.89-1.95	0.2526	152	0.2186	2564	X-RAY DIFFRACTION	99.71
1.95-2.01	0.2295	121	0.2011	2603	X-RAY DIFFRACTION	99.23
2.01-2.08	0.2322	169	0.1964	2561	X-RAY DIFFRACTION	98.88
2.08-2.16	0.1991	160	0.1809	2550	X-RAY DIFFRACTION	98.76
2.16-2.26	0.2027	145	0.175	2586	X-RAY DIFFRACTION	99.24
2.26-2.38	0.2607	136	0.1851	2598	X-RAY DIFFRACTION	99.42
2.38-2.53	0.2444	142	0.1941	2599	X-RAY DIFFRACTION	99.49
2.53-2.73	0.2305	114	0.1879	2643	X-RAY DIFFRACTION	99.14
2.73-3	0.2173	165	0.2072	2609	X-RAY DIFFRACTION	99.28
3-3.44	0.2401	159	0.1989	2598	X-RAY DIFFRACTION	98.29
3.44-4.33	0.1924	155	0.154	2637	X-RAY DIFFRACTION	98.28
4.33-60	0.1755	158	0.1723	2767	X-RAY DIFFRACTION	98.35

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	2.81130747341	0.403554325161	-0.050374600163	3.89531664513	0.812929657926	2.64068296391	-0.220443872588	0.532265464484	-0.11926947309	-0.536437291196	0.178259971217	-0.23107207916	-0.0746040869347	-0.0494173936956	0.05688664474	0.18479675914	-0.0560890829789	0.0644126495046	0.207419411482	-0.0534624266871	0.15140707641	17.9041230765	-10.2195891098	-8.87604390433
2	4.02137396325	0.00669333941248	-0.083386752271	2.73593410067	0.161130818325	3.28625311357	-0.135672875668	-0.272802564342	0.209662367072	0.470875504413	0.0787777625729	0.0109000246981	0.0614630226043	0.0578646694311	0.0703848286821	0.173594393529	0.014206730498	-0.0196589279898	0.110803368613	-0.0115936710584	0.110384003908	16.9251802103	9.89736932078	8.65823951515
3	2.05344266212	0.024964344413	0.326747740798	4.5025360291	-0.788394829881	4.06198609105	-0.0957933893538	-0.137922957889	-0.0635613019855	0.728670957859	-0.0690515858198	-0.550210214708	-0.044055701815	0.0398842075334	0.102422332308	0.219032444383	-0.0238917175818	-0.0618830324313	0.0994591982627	0.0182940568529	0.185730818286	19.7730688749	-10.5105424102	7.90190450116
4	2.20160248477	-0.261402673882	1.39940616161	4.01997488798	-0.363298593026	4.72624851811	-0.00970781489691	0.471556103264	0.159006202055	-0.408311940384	-0.07098047008	-0.269729970789	0.00492418788334	0.293995396702	0.0468527645999	0.170298042999	-8.49194653196E-5	0.0278114419902	0.215211630414	0.0515530341771	0.153439135723	18.7649285577	10.9969562862	-8.10860871239
5	2.79121039468	0.126563747982	0.117562507022	5.84121397978	-0.95690021965	1.82888773116	-0.00452818546952	-0.283493394761	-0.219635148022	0.00650355524266	0.0895246923338	0.0302392051534	0.219849610015	0.244658762699	-0.0984028442397	0.207201876	0.0352449762341	-0.00375016229557	0.333911618675	0.0430352169673	0.126527594018	15.1349632424	28.4446341642	-16.0816282394
6	3.42610217405	-1.01686972809	-1.1412875429	6.33144249807	1.74575303774	3.7753058224	-0.0291343471868	0.0906307886405	-0.0810013512411	-0.182102480241	0.0895631119187	0.0107903138615	0.460389707702	-0.172867386143	-0.0536336937091	0.276682084403	-0.0226067804148	-0.0607805500639	0.168482653423	-0.0183448628383	0.131542461366	9.2922625133	30.5306148042	-35.5111991369
7	0.720534907083	0.488925734871	-0.187637774163	6.78380255204	-0.627402917256	0.464167400327	0.0478813742999	0.351012165722	0.163839463054	0.0265413477376	0.0817960579866	0.397652869982	-0.0251368716296	-0.246069284228	-0.0839559614419	0.173358497678	0.0493867474681	0.0328752723325	0.369370161197	0.0647138294241	0.143492563294	33.3077713617	7.1252264086	-35.2037943707
8	1.47007379251	0.339649167587	0.220869533516	7.01333989052	-0.0328545212798	5.27787128155	0.263875504861	-0.0672817864372	0.343529427565	0.186259685433	0.165501642164	-0.0440752555364	-0.541786976396	0.324725418054	-0.321640388048	0.213163605322	-0.0368851436392	0.0845297073762	0.184427741461	-0.0203283550211	0.22937243656	42.9347468303	9.18615799532	-17.6469262308

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 73:129)
2	X-RAY DIFFRACTION	2	(chain B and resid 73:129)
3	X-RAY DIFFRACTION	3	(chain C and resid 74:129)
4	X-RAY DIFFRACTION	4	(chain D and resid 74:129)
5	X-RAY DIFFRACTION	5	(chain E and resid 74:128)
6	X-RAY DIFFRACTION	6	(chain F and resid 76:128)
7	X-RAY DIFFRACTION	7	(chain G and resid 75:129)
8	X-RAY DIFFRACTION	8	(chain H and resid 75:129)

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