PDB-3uki: Crystal structure of reduced OxyR from Porphyromonas gingivalis

ID or keywords:

Entry

Database: PDB / ID: 3uki

Title

Crystal structure of reduced OxyR from Porphyromonas gingivalis

Components

OxyR

Keywords

TRANSCRIPTION REGULATOR / beta-alpha-barrels / DNA-binding / transcription regulation / redox-sensitive transcription regulation

Function / homology

Function and homology information

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

Biological species

Porphyromonas gingivalis (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 4.15 Å

Authors

Svintradze, D.V. / Wright, H.T. / Collazo-Santiago, E.A. / Lewis, J.P.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structures of the Porphyromonas gingivalis OxyR regulatory domain explain differences in expression of the OxyR regulon in Escherichia coli and P. gingivalis.
Authors: Svintradze, D.V. / Peterson, D.L. / Collazo-Santiago, E.A. / Lewis, J.P. / Wright, H.T.

History

Deposition	Nov 9, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 31, 2013	Provider: repository / Type: Initial release
Revision 1.1	Oct 2, 2013	Group: Database references
Revision 1.2	Nov 27, 2013	Group: Database references
Revision 1.3	Sep 13, 2023	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 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3uki.cif.gz	438.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3uki.ent.gz	365.9 KB	Display	PDB format
PDBx/mmJSON format	3uki.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uk/3uki ftp://data.pdbj.org/pub/pdb/validation_reports/uk/3uki	HTTPS FTP

-
Related structure data

Related structure data	3ho7SC 3t22C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2xfs-2 5t3e-1 4pza-d 4kt6-2 5dwv-d 6daa-d 4rpo-2 4znw-d 2epj-d 5o0i-d 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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: OxyR

B: OxyR

C: OxyR

D: OxyR

102 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: OxyR

B: OxyR

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

2

C: OxyR

D: OxyR

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

Unit cell

Length a, b, c (Å)	63.236, 82.814, 170.484
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	OxyR Mass: 25621.574 Da / Num. of mol.: 4 / Fragment: Regulatory domain (UNP residues 90-308) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Gene: oxyR / Production host: Escherichia coli (E. coli) / References: UniProt: Q20K61

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.18 Å³/Da / Density % sol: 43.52 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.2M LiSO4, 20% PEG3350, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 28, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 3.5→33.948 Å / Num. all: 11495 / Num. obs: 10378 / % possible obs: 87.85 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 2.91 % / R_merge(I) obs: 0.289 / Net I/σ(I): 2.4
Reflection shell	Resolution: 3.5→3.63 Å / Redundancy: 2.97 % / R_merge(I) obs: 0.676 / Mean I/σ(I) obs: 0.8 / % possible all: 87.85

-
Processing

Software

Name	Version	Classification
CrystalClear		data collection
PHENIX		model building
PHENIX	(phenix.refine: 1.6.4_486)	refinement
CrystalClear		data reduction
d*TREK		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3HO7

3ho7

Resolution: 4.15→21.647 Å / SU ML: 0.78 / σ(F): 1.36 / Phase error: 44.73 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.405	687	10 %
R_work	0.3088	-	-
obs	0.3186	6873	96.37 %
all	-	11495	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.5328 Å²	0 Å²	0 Å²
2-	-	-0.1286 Å²	0 Å²
3-	-	-	1.6614 Å²

Refinement step

Cycle: LAST / Resolution: 4.15→21.647 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6106	0	0	0	6106

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	6223
X-RAY DIFFRACTION	f_angle_d	1.329	8473
X-RAY DIFFRACTION	f_dihedral_angle_d	16.268	2215
X-RAY DIFFRACTION	f_chiral_restr	0.061	996
X-RAY DIFFRACTION	f_plane_restr	0.005	1104

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 (%)
4.15-4.4679	0.3848	134	0.2825	1211	X-RAY DIFFRACTION	98
4.4679-4.9127	0.4362	138	0.2845	1246	X-RAY DIFFRACTION	98
4.9127-5.6128	0.4116	137	0.3142	1230	X-RAY DIFFRACTION	97
5.6128-7.031	0.4374	141	0.3642	1268	X-RAY DIFFRACTION	98
7.031-21.6473	0.3774	137	0.3039	1231	X-RAY DIFFRACTION	91

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	1.5522	0.0608	-0.7424	2.3962	-0.7742	1.4896	0.1901	0.0336	0.8516	-0.3832	-0.4385	-0.3984	-0.1581	0.0152	-1.5243	0.1103	0.1589	0.0172	0.7828	0.1139	0.8733	11.1585	9.4622	56.2851
2	1.1128	-0.2629	0.3411	2.2196	-2.7142	3.3312	0.0071	0.3905	0.3682	-0.201	0.1264	-0.7541	-0.0526	0.0904	-0.2201	0.8694	0.0855	0.0893	0.9748	-0.0908	1.0042	6.5871	-0.2989	47.1808
3	6.376	-5.7194	0.695	7.4651	-0.3228	1.4188	-0.3094	1.1216	0.4013	0.8857	0.3651	-0.7421	1.5587	1.4173	-0.4925	1.1403	-0.2234	0.1696	0.7126	0.061	0.3329	-7.916	-3.2559	53.2719
4	8.1025	-2.0471	-3.8392	7.5498	0.7315	1.953	1.2312	0.0272	1.4213	1.6994	-0.1421	-1.04	-1.2058	0.1377	2.2991	1.2183	0.1418	0.1168	0.5277	0.0858	0.5711	3.0255	-5.4838	55.5846
5	7.8917	-7.5059	-7.9119	9.3709	7.0871	8.0078	1.1143	-0.9567	0.6073	-0.674	0.3983	-1.4661	-1.7603	0.7459	0.5549	0.9445	-0.1092	-0.3537	0.8999	-0.1213	0.7257	2.0586	-12.6019	57.1895
6	0.8286	0.0331	-0.8752	6.2382	-0.6119	4.3644	-1.0027	0.229	-0.9377	1.5755	0.4507	-1.4076	-0.1457	0.537	-0.2678	0.8034	0.0089	-0.1191	0.9128	0.1245	1.2916	20.4275	2.0522	52.5037
7	4.5283	-0.6559	-0.3017	1.4906	-2.9018	6.206	-0.907	-0.1794	-1.2722	0.2123	-0.1634	0.3024	-0.2266	0.4399	-1.3623	0.5759	-0.2919	0.2197	0.6148	-0.1689	0.701	-17.0125	2.4339	47.429
8	4.6837	0.2924	-0.1381	0.1884	-0.0257	3.4105	-1.2143	0.6089	-0.681	-0.8914	0.9791	-0.272	-0.2742	1.2765	0.2156	1.1466	-0.3005	0.3704	0.847	-0.2659	0.6632	-17.1007	1.2425	40.8249
9	3.0744	-0.1061	2.5956	0.5755	-0.0118	2.601	0.075	-0.5157	0.2462	0.2892	-0.068	0.1011	-0.6318	0.0537	0.1475	0.9663	0.0747	0.0648	0.8264	-0.0413	0.9127	-13.2864	14.1	55.9785
10	0.7339	0.7787	-0.703	2.1307	0.64	2.2241	-0.9655	-0.4051	-0.6362	0.9022	0.7041	0.6245	0.9267	0.3304	0.0108	0.9035	0.1111	0.1725	1.0465	-0.0155	0.8057	20.9074	-1.0471	-1.064
11	4.528	-3.3104	-2.1902	9.4565	6.7567	6.0884	-0.0053	0.0868	-1.3982	0.6579	-0.9411	1.2598	-0.0359	-1.0983	-1.278	0.654	0.219	-0.3548	1.1817	0.0606	1.1962	23.05	-9.3331	9.2897
12	1.2415	1.391	-1.1552	1.5582	-1.293	1.0756	0.6134	-0.0366	1.8404	0.1965	0.5684	-0.3294	-0.9983	0.3101	2.1925	1.3789	0.3307	0.5983	0.8685	-0.221	1.4533	30.6978	-7.1887	15.4441
13	0.5961	-1.0779	-0.5537	5.1683	0.2053	3.0062	0.047	0.3063	0.2308	0.7107	0.2866	0.2129	0.0195	0.195	-0.1467	0.9177	0.0668	0.0635	0.8647	0.0015	0.5303	16.8446	15.3326	15.306
14	4.2298	0.6911	0.6368	1.3207	2.4548	4.6667	-0.456	0.6946	-0.7095	0.7921	0.0854	0.5062	1.3783	0.068	4.7598	1.5656	0.4186	1.0528	1.2242	0.2953	1.5114	31.8696	-10.3006	6.395
15	5.3973	-4.5648	-1.0461	5.7611	1.644	2.1318	-0.13	0.3825	-2.1614	0.0265	-1.0672	2.3749	0.6146	-0.5082	-0.1512	1.0332	-0.2815	0.0654	1.8241	-0.2179	1.1045	32.9432	5.6256	4.2508
16	5.2542	1.6179	0.84	1.5175	-0.0857	3.5332	-0.4784	-0.9283	0.5591	-0.2229	-0.2909	-0.7304	0.6483	-1.8867	-1.5081	0.9869	0.0696	-0.102	1.0248	0.195	0.7844	-3.6938	10.9952	17.3663
17	1.9996	3.829	1.0609	1.391	0.3781	1.1256	1.6589	-1.7372	-1.1471	-0.023	-0.9875	1.804	-0.6746	0.2897	-0.2221	1.7546	0.123	0.1167	0.7517	0.33	1.1349	-6.1949	-2.9431	18.7718
18	4.4685	0.8082	-4.7973	1.8508	-2.1743	6.1798	0.2842	1.0017	0.5636	0.2139	1.3623	-0.4824	-0.5833	-2.1547	0.1133	0.7439	-0.3207	-0.0014	1.7958	0.3057	0.9627	-10.1	2.5659	5.9325
19	6.9613	-2.2634	-1.4035	1.3343	1.8451	4.5452	0.5591	1.2445	-0.121	-0.624	-0.8995	0.6248	0.8027	-0.4109	-0.2793	1.0831	0.7132	-0.1099	1.5595	-0.6055	0.9178	4.4198	5.4154	-15.0857
20	1.9031	-1.508	0.0198	1.7289	0.2728	1.5752	-0.9846	-0.1077	-2.7576	3.3978	-0.6298	0.4587	-0.3268	-0.3782	-0.4571	2.4836	0.5651	-0.5162	1.8927	-0.0835	1.8071	-0.0902	-4.0259	1.2655
21	2.074	0.7587	-2.4009	0.7689	-0.9093	2.7007	0.4491	-0.8215	-0.6548	-0.492	-0.4914	0.1843	0.1807	0.212	-0.5047	0.8996	0.0096	-0.0282	1.2068	0.0982	0.9536	-4.6231	7.6852	2.5677

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 91 through 113 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 114 through 224 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 225 through 237 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 238 through 248 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 249 through 265 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 266 through 307 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 92 through 115 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 116 through 128 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 129 through 307 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 92 through 128 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 129 through 146 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 147 through 156 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 157 through 269 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 270 through 279 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 280 through 308 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 93 through 128 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 129 through 146 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 147 through 169 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 170 through 192 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 193 through 205 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 206 through 307 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi