PDB-6ez1: Structure of h. salinarum RosR (vng0258) grown from NaBr

ID or keywords:

Entry

Database: PDB / ID: 6ez1

Title

Structure of h. salinarum RosR (vng0258) grown from NaBr

Components

DNA binding protein

Keywords

DNA BINDING PROTEIN / Halophiles / wHTH DNA binding protein / RosR / High salt medium

Function / homology

Transcription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / metal ion binding / BROMIDE ION / PadR family transcription regulator RosR

Function and homology information

Biological species

Halobacterium salinarum (Halophile)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.75004310292 Å

Authors

Shaanan, B. / Kutnowski, N.

Funding support

Israel, 1items

Citation

Journal: J. Struct. Biol. / Year: 2018
Title: The 3-D structure of VNG0258H/RosR - A haloarchaeal DNA-binding protein in its ionic shell.
Authors: Kutnowski, N. / Shmuely, H. / Dahan, I. / Shmulevich, F. / Davidov, G. / Shahar, A. / Eichler, J. / Zarivach, R. / Shaanan, B.

History

Deposition	Nov 13, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 22, 2018	Provider: repository / Type: Initial release
Revision 1.1	Aug 29, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Oct 10, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3	May 1, 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6ez1.cif.gz	179.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6ez1.ent.gz	118.6 KB	Display	PDB format
PDBx/mmJSON format	6ez1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6ez1_validation.pdf.gz	10.4 MB	Display	wwPDB validaton report
Full document	6ez1_full_validation.pdf.gz	10.4 MB	Display
Data in XML	6ez1_validation.xml.gz	14 KB	Display
Data in CIF	6ez1_validation.cif.gz	20.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ez/6ez1 ftp://data.pdbj.org/pub/pdb/validation_reports/ez/6ez1	HTTPS FTP

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Related structure data

Related structure data	6f5cC 6faqC 6fdhC C: citing same article (ref.)
Similar structure data	2132 1nq2-d 4fbb-3 3m4u-1 1y0x-d 4fbb-2 3imy-d 3u5p-8 6s4t-d 4ngu-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	#122 - Feb 2010 Enhanceosome similarity (1) #220 - Apr 2018 Dehalogenases similarity (1)

Deposited unit

A: DNA binding protein

B: DNA binding protein

hetero molecules

31.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, SAXS supports the dimer in solution

Unit cell

Length a, b, c (Å)	40.884, 71.139, 41.719
Angle α, β, γ (deg.)	90.000, 110.334, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	DNA binding protein Mass: 14554.919 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Halophilic winged-helix-turn-helix DNA binding protein from H. salinarum Source: (gene. exp.) Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) (Halophile) Gene: VNG_0258H / Variant: NRC-1 / Production host: Haloferax volcanii (archaea) / References: UniProt: Q9HSF4
#2: Chemical	... ChemComp-BR / BROMIDE ION Mass: 79.904 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: Br / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.05 Å³/Da / Density % sol: 37.06 % / Description: monoclinic
Crystal grow	Temperature: 298 K / Method: evaporation / pH: 6.8 / Details: NaBr, MES, Ammonium sulfate / PH range: 6-7.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.91908 Å
Detector	Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 15, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.91908 Å / Relative weight: 1
Reflection	Resolution: 1.75→39.12 Å / Num. obs: 43032 / % possible obs: 97.4 % / Observed criterion σ(I): 1.82 / Redundancy: 6.2 % / B_iso Wilson estimate: 17.4188078183 Å² / CC_1/2: 0.991 / R_merge(I) obs: 0.112 / R_pim(I) all: 0.05 / R_rim(I) all: 0.123 / Net I/σ(I): 18.5
Reflection shell	Resolution: 1.75→1.79 Å / Redundancy: 4.1 % / R_merge(I) obs: 0.577 / Mean I/σ(I) obs: 1.45 / R_pim(I) all: 0.327 / R_rim(I) all: 0.669 / % possible all: 80

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Processing

Software

Name	Version	Classification
REFMAC	refmac5 version 5.8.0158	refinement
PHENIX	dev-2947	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: SAD derived model in NaCl

Resolution: 1.75004310292→34.2783354663 Å / SU ML: 0.169322950602 / Cross valid method: FREE R-VALUE / σ(F): 1.93612010501 / Phase error: 21.071803648
Details: Residues 1-10 in both chains are predicted to be natively disrodered residues 70-76 in both chains belong to the wing domain which is notoriously flexible

	R_factor	Num. reflection	% reflection
R_free	0.209013814378	2186	5.07994050939 %
R_work	0.170094126367	-	-
obs	0.172098550035	43032	96.8600175569 %

Solvent computation

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

Displacement parameters

B_iso mean: 25.8986593944 Å²

Refinement step

Cycle: LAST / Resolution: 1.75004310292→34.2783354663 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1764	0	38	267	2069

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.00308713472184	1805
X-RAY DIFFRACTION	f_angle_d	0.589561088126	2446
X-RAY DIFFRACTION	f_chiral_restr	0.0371181548246	274
X-RAY DIFFRACTION	f_plane_restr	0.00278601810263	327
X-RAY DIFFRACTION	f_dihedral_angle_d	11.5634602151	1094

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 (%)
1.75-1.7881	0.293531574222	89	0.249112478466	2073	X-RAY DIFFRACTION	78.4470246734
1.7881-1.8297	0.293115674381	87	0.231677462849	2321	X-RAY DIFFRACTION	85.9386152748
1.8297-1.8754	0.280699341552	138	0.227793022589	2415	X-RAY DIFFRACTION	92.2659920492
1.8754-1.9261	0.208168689123	128	0.204402202336	2563	X-RAY DIFFRACTION	97.8901418698
1.9261-1.9828	0.233189847	141	0.186875075129	2653	X-RAY DIFFRACTION	99.8927422238
1.9828-2.0468	0.195697401136	152	0.170268104224	2647	X-RAY DIFFRACTION	99.6794871795
2.0468-2.12	0.205428168567	155	0.164763633026	2574	X-RAY DIFFRACTION	100
2.12-2.2048	0.182638382286	135	0.163742947999	2645	X-RAY DIFFRACTION	99.892202659
2.2048-2.3051	0.219968189287	149	0.163318736401	2636	X-RAY DIFFRACTION	99.7850232891
2.3051-2.4266	0.219685202153	132	0.159811394443	2636	X-RAY DIFFRACTION	99.711815562
2.4266-2.5786	0.199427631281	141	0.172066472805	2644	X-RAY DIFFRACTION	99.7492836676
2.5786-2.7776	0.218287985737	124	0.168784609785	2635	X-RAY DIFFRACTION	99.7108782074
2.7776-3.057	0.218480313592	185	0.169142828955	2563	X-RAY DIFFRACTION	99.4931209269
3.057-3.499	0.20629975468	144	0.156194899358	2618	X-RAY DIFFRACTION	99.3167925207
3.499-4.4069	0.172311539079	152	0.141622963637	2602	X-RAY DIFFRACTION	99.2074927954
4.4069-34.2849	0.208532962489	134	0.182403373445	2621	X-RAY DIFFRACTION	98.7809250627

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	8.37765479671	-1.66241495953	5.915984031	5.13185021699	-0.906757175043	4.65276885746	-0.129295036896	0.818635117433	0.963576860664	-0.00916141704138	-0.312233494698	-0.249368319714	-1.59264915351	0.849266663846	0.613177809706	0.227879146587	-0.0128842889448	-0.00371927808051	0.198474538788	0.0684549735362	0.186527429058	8.26056768344	28.2506174205	5.02838919821
2	2.70001847158	-3.36159303844	1.35227629294	6.5048372001	0.931204929159	5.41822519289	-0.0368159645139	0.148445949243	0.189912199414	0.159433964854	-0.0350047376949	0.0724894858978	-0.309062746098	0.0309991254897	0.10225562712	0.103742650109	-0.0173310589197	-0.0117976464595	0.0686185450693	0.00228612793915	0.0475601540679	1.34935955734	25.536862714	14.3038708497
3	1.54804215512	-2.08697723048	-0.924743687987	5.20702957716	2.47494731018	5.73218500792	0.0379864790297	0.0889960137663	0.0205670668427	-0.0228177635036	0.0822925798645	0.410624949709	-0.17030250776	-0.283458395447	-0.0811493586496	0.0984659408511	0.00405472465011	0.0332324344808	0.111080509355	0.027836267112	0.109665234483	-1.1420398665	23.4708394496	22.6938032005
4	2.1544023402	0.77834014058	0.143014444332	3.0271425039	-3.95305534197	5.89262817263	-0.100639296511	-0.0407075221511	0.0850616720265	0.445126857851	-0.267200899129	-0.564853682984	-0.584930555654	0.599021815853	0.2782738854	0.145492122717	-0.05298191473	-0.048613080555	0.185185645904	-0.0097383904771	0.150966435987	8.66454981029	27.6931686893	21.6219354401
5	5.8141230771	0.266698638748	-2.93801794922	1.58462478023	1.81517737791	4.94471009784	-0.0408920413614	-0.911993392577	0.661050189228	1.11529998088	-0.252461275872	0.0831357079657	-0.285745895946	0.167680023069	-0.0853073922364	0.684088382575	0.0015898313777	-0.0476453798951	0.158803014964	-0.0839157692983	0.242014644207	1.0790019614	37.822488128	23.8856616881
6	0.503084391005	1.04089967432	0.707506333574	6.55386552956	5.48957824702	5.19972081297	0.000789105455787	0.0534603236586	0.0180572743526	-0.147569167149	-0.0341102856021	0.0683141854161	-0.318632647682	0.036168713599	-0.0123154007271	0.0866449992793	0.0405291152739	-0.0391301860196	0.0873360216295	-0.00431790692417	0.152242826413	-1.5541066576	27.2590102972	5.57107895157
7	3.21534609184	-0.371549079897	0.0229203370068	2.83728559374	0.77991201105	2.85536062421	0.0407031924459	-0.0939007144341	-0.319433762223	0.470004003073	-0.0600468811698	0.208678742652	0.0378758735559	-0.747104685598	0.0146956573966	-0.117910834745	-0.0627819501273	-0.0612619876965	0.1630966387	1.31923899407E-5	0.178750402791	-12.1322167484	12.7510897359	3.05840281645
8	4.64281729041	-0.448500680966	-5.83328794395	3.23792754612	1.15129816438	7.45292731812	-0.41442771389	-1.20806050415	-1.20729556052	0.6766890112	-0.440229886525	-0.264439784259	0.644620100948	0.519546806371	0.495266970777	0.13544544901	-0.0300600746589	0.0401038294464	0.272733400194	0.066428485718	0.2041774253	7.3320912359	12.8438279587	13.4009199113
9	4.77551635387	1.275343214	-0.0908968585273	4.35540924989	2.0219421368	2.83269880122	0.137504300866	-0.147299290581	-0.174537245737	0.170663017605	-0.0728913640319	0.262711768535	0.290836462419	-0.0494467593327	0.0239785319307	0.0222255967998	0.0258594375611	0.0204030477939	0.109662036901	0.0266559831532	0.0940420850209	7.58950205451	14.5338487681	1.50539447828
10	4.19695509164	1.49774625328	-1.79705133952	6.76300346809	0.433983080329	3.48825641985	-0.0156040345159	0.111089887872	-0.133087608768	-0.515682527808	0.0959233633663	0.0742459449818	-0.138236289151	-0.0832741574928	-0.0722259878465	0.050500303486	-0.00666618452984	-0.0214634884209	0.123968878725	0.011590710877	0.0753854344027	10.5007534325	16.6875461682	-6.7434417249
11	6.92375527919	-4.490145682	5.41461108255	7.52541443591	-2.16874731507	7.7269590804	-0.142926503187	-0.507744156491	0.730113313643	0.4846849775	0.13467058714	-0.94351822707	-0.952798737413	0.360230645501	0.127361348462	0.136275304899	-0.0774736332164	-0.00926618742794	0.240848146118	-0.041173966078	0.184066631386	17.4068878908	24.6635660877	-3.76162243372
12	3.27785826424	1.07826535699	-0.942929146214	1.45459818946	0.294545492396	0.583249317471	-0.0513457397792	-0.0690068970105	-0.334813045524	0.365169969325	0.0169065979946	-0.0242555418384	0.088521298516	0.508183381759	0.203711934292	-0.100302173435	-0.0445522524332	-0.0661867615525	0.21674451709	0.0103392204987	0.188432719257	18.0772515545	11.2427072772	2.16573123436
13	8.12332451882	-1.65403302643	-3.23237511324	5.87259824201	1.17828047343	1.93742533669	0.094465131412	0.547742068757	-0.589051133871	-0.899888134438	-0.405249344093	-0.747201487483	0.165784428421	0.120880245632	0.240991986457	0.229828528268	0.0507545331192	0.0805993602839	0.132353052573	0.0303562992437	0.301798660133	12.9230338673	2.93655392608	0.388554640322
14	5.3080478158	1.41818006927	-1.5491977349	6.29807391076	-1.22829162458	2.06117945905	-0.237973590181	1.9138760018	1.30658091022	-2.04488497392	0.383484099905	-0.032119431645	-0.908391277495	-0.0911235634004	-0.0670394504724	1.15996631787	-0.144482575769	-0.134851418903	0.987572526051	-0.20755523957	0.994498392243	15.9176737276	3.60745327775	-15.055189116
15	8.9739680391	4.23320041423	0.616748428328	7.0719537731	-2.16758203505	8.5454495757	-0.261489063603	0.661650219784	-0.509118337388	-0.488918081346	0.102611737148	-0.466259621212	0.668405988196	0.249204595938	0.281512874484	0.0837613642824	0.0514127728656	0.0258640012492	0.0843514633927	-0.0011516412375	0.190900812682	10.7797633861	5.04255542849	-3.53923078007
16	6.19797027284	-6.15339328061	-3.42474244929	7.43823382085	3.31627961351	2.74019854523	-0.135789514699	-0.215127164251	0.0697200876518	0.0544049339751	0.174907471552	-0.0762683922094	0.0609412034309	0.0389156105941	-0.0308334443379	0.0428430533047	-0.0109289245235	-0.0292330998105	0.102298632295	-0.0136722733392	0.148923881698	-2.20271970225	13.2120456301	8.82707428459
17	2.49304462294	0.128750924276	-1.40400796133	1.79830578859	0.14074368456	2.71411896482	-0.448662061024	0.182624394961	0.236732025511	-0.283771587648	-0.049991886087	0.428623712707	-0.336313507467	-0.780579226357	-0.0424335517438	0.0423663083475	0.140683645154	-0.0861910040478	0.192510913834	-0.0389529987419	0.226823371117	-12.6742696671	22.7750584578	0.448135748227

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A and (resid 11 through 16 )
2	X-RAY DIFFRACTION	2	chain A and (resid 17 through 28 )
3	X-RAY DIFFRACTION	3	chain A and (resid 29 through 44 )
4	X-RAY DIFFRACTION	4	chain A and (resid 45 through 62 )
5	X-RAY DIFFRACTION	5	chain A and (resid 63 through 76 )
6	X-RAY DIFFRACTION	6	chain A and (resid 77 through 99 )
7	X-RAY DIFFRACTION	7	chain A and (resid 100 through 120 )
8	X-RAY DIFFRACTION	8	chain B and (resid 11 through 16 )
9	X-RAY DIFFRACTION	9	chain B and (resid 17 through 28 )
10	X-RAY DIFFRACTION	10	chain B and (resid 29 through 44 )
11	X-RAY DIFFRACTION	11	chain B and (resid 45 through 49 )
12	X-RAY DIFFRACTION	12	chain B and (resid 50 through 62 )
13	X-RAY DIFFRACTION	13	chain B and (resid 63 through 70 )
14	X-RAY DIFFRACTION	14	chain B and (resid 71 through 75 )
15	X-RAY DIFFRACTION	15	chain B and (resid 76 through 81 )
16	X-RAY DIFFRACTION	16	chain B and (resid 82 through 99 )
17	X-RAY DIFFRACTION	17	chain B and (resid 100 through 120 )

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