PDB-8k3f: Crystal structure of the recombination mediator protein RecR from...

ID or keywords:

Entry

Database: PDB / ID: 8k3f

Title

Crystal structure of the recombination mediator protein RecR from Campylobacter jejuni

Components

Recombination protein RecR

Keywords

RECOMBINATION / Recombination mediator protein

Function / homology

Function and homology information

DNA recombination / DNA repair / DNA binding / metal ion binding
Similarity search - Function

Biological species

Campylobacter jejuni (Campylobacter)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.603 Å

Authors

Lee, S.J. / Yoon, S.I.

Funding support

Korea, Republic Of, 1items

Citation

Journal: Int J Mol Sci / Year: 2023
Title: Structural and Biochemical Analysis of the Recombination Mediator Protein RecR from Campylobacter jejuni.
Authors: Lee, S.J. / Ahn, S.Y. / Oh, H.B. / Kim, S.Y. / Song, W.S. / Yoon, S.I.

History

Deposition	Jul 15, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 1, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8k3f.cif.gz	301.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8k3f.ent.gz	244.9 KB	Display	PDB format
PDBx/mmJSON format	8k3f.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8k3f_validation.pdf.gz	1.9 MB	Display	wwPDB validaton report
Full document	8k3f_full_validation.pdf.gz	1.9 MB	Display
Data in XML	8k3f_validation.xml.gz	26.6 KB	Display
Data in CIF	8k3f_validation.cif.gz	35.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k3/8k3f ftp://data.pdbj.org/pub/pdb/validation_reports/k3/8k3f	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#73 - Jan 2006 Topoisomerase similarity (2) #168 - Dec 2013 DNA Helicase similarity (2)

Deposited unit

A: Recombination protein RecR

B: Recombination protein RecR

C: Recombination protein RecR

D: Recombination protein RecR

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	231.427, 64.186, 74.621
Angle α, β, γ (deg.)	90.00, 100.60, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Recombination protein RecR Mass: 22091.568 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: recR / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2U0QSA2
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.18 Å³/Da / Density % sol: 61.36 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: ethanol, Hepes, magnesium chloride

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 30, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 2.6→30 Å / Num. obs: 32226 / % possible obs: 97 % / Redundancy: 2.8 % / CC_1/2: 0.992 / Net I/σ(I): 19.5
Reflection shell	Resolution: 2.6→2.64 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1614 / CC_1/2: 0.666 / % possible all: 97.2

-
Processing

Software

Name	Version	Classification
PHENIX	(1.15.2_3472: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.603→29.178 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.69 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2462	1616	5.02 %
R_work	0.2066	-	-
obs	0.2086	32221	96.76 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.603→29.178 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5659	0	4	32	5695

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	5742
X-RAY DIFFRACTION	f_angle_d	0.63	7791
X-RAY DIFFRACTION	f_dihedral_angle_d	21.795	2042
X-RAY DIFFRACTION	f_chiral_restr	0.043	954
X-RAY DIFFRACTION	f_plane_restr	0.004	1004

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 (%)
2.6031-2.6797	0.3795	133	0.3336	2448	X-RAY DIFFRACTION	94
2.6797-2.7661	0.3109	169	0.2963	2549	X-RAY DIFFRACTION	98
2.7661-2.8649	0.3001	146	0.262	2569	X-RAY DIFFRACTION	99
2.8649-2.9795	0.2942	118	0.2559	2584	X-RAY DIFFRACTION	99
2.9795-3.1149	0.2918	113	0.248	2594	X-RAY DIFFRACTION	98
3.1149-3.2789	0.2903	141	0.2552	2579	X-RAY DIFFRACTION	98
3.2789-3.4841	0.2696	131	0.2225	2554	X-RAY DIFFRACTION	98
3.4841-3.7525	0.2484	143	0.201	2582	X-RAY DIFFRACTION	98
3.7525-4.1292	0.2431	128	0.1769	2561	X-RAY DIFFRACTION	97
4.1292-4.7246	0.1885	141	0.175	2529	X-RAY DIFFRACTION	96
4.7246-5.9442	0.2223	124	0.1866	2543	X-RAY DIFFRACTION	95
5.9442-29.178	0.2118	129	0.1729	2513	X-RAY DIFFRACTION	92

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	5.2038	-0.844	2.777	6.9824	-0.3274	7.4103	0.3895	1.405	-0.7832	0.386	-1.7057	-2.5522	0.9536	1.6194	1.0974	0.4278	-0.0068	0.0087	0.7564	0.3156	0.9566	-41.5673	-40.1436	41.6866
2	3.8699	-0.2083	-3.3022	5.1555	-3.6405	9.9228	0.6387	-0.622	0.9867	0.4547	-0.4641	-0.4702	-0.5482	1.1482	-0.1228	0.395	-0.1127	-0.0242	0.5139	0.0068	0.5711	-50.2435	-32.2136	45.5979
3	2.9931	-1.8016	5.1831	3.6686	-1.6858	3.6298	0.1931	-1.5556	-0.1768	0.4417	0.0856	0.1634	0.2393	-1.6772	-0.195	0.4783	-0.0456	0.1032	0.7117	0.0566	0.4449	-79.5246	-32.1582	40.2134
4	9.7019	2.1165	0.8354	6.6612	-0.3725	8.4953	0.1711	0.0564	-0.7434	-0.3468	-0.0213	0.287	1.0937	-1.0128	-0.0983	0.4699	-0.0524	0.006	0.3911	0.0147	0.2888	-82.5672	-35.2262	28.4306
5	6.9816	-2.5249	-1.4283	0.6614	-1.7861	6.3944	0.0925	-0.1348	-0.6821	0.3439	0.1066	0.3371	0.6533	-0.0374	-0.2536	0.5457	-0.0626	-0.0573	0.2276	0.0666	0.55	-71.1438	-22.9772	10.4055
6	9.2447	1.2037	-2.061	6.2671	-2.5553	4.0529	0.1907	-1.061	-0.4809	0.1182	-0.1956	-0.5763	-0.0169	0.761	0.0148	0.378	-0.0177	-0.1034	0.4505	0.0809	0.4496	-37.1426	-12.1467	3.0684
7	2.3899	-1.5343	2.7334	5.2014	0.0292	2.9768	0.9192	1.763	-0.0507	-0.6982	-0.6395	0.323	0.3068	0.4633	-0.2399	0.6767	-0.0507	0.001	0.423	0.0996	0.3393	-45.5357	-11.8066	-11.1898
8	9.7862	1.2192	-2.6275	4.1122	-0.7486	6.1895	-0.2049	0.9129	-0.0067	-0.4378	0.2288	0.1477	0.1446	-0.1204	-0.0025	0.5123	-0.0103	-0.1164	0.2201	0.0339	0.2933	-69.3091	-14.7767	-6.6953
9	7.2129	0.0926	1.3367	6.1595	-0.2301	7.8213	-0.1883	-0.0406	0.8435	-0.387	0.0651	0.5078	-0.3121	-0.6928	0.0766	0.3897	0.0316	-0.0905	0.2469	0.0269	0.4814	-77.0185	-10.7472	-1.7584
10	5.5386	2.7053	1.9101	2.5102	1.7576	9.6845	-0.0196	-0.486	1.3554	-0.0209	-0.5198	1.2052	-1.4504	-1.7984	0.28	0.6684	0.2835	0.071	0.625	-0.0506	0.7192	-83.0849	-8.2493	6.4758
11	7.0595	4.5899	0.6123	3.504	-1.1133	7.0413	-0.0756	0.3632	0.1865	-0.2447	-0.1024	-0.8031	0.1119	0.4006	0.1239	0.4062	0.0735	0.0926	0.3387	0.1221	0.5552	-73.2982	-23.3337	21.8388
12	7.4401	0.9679	-1.6151	6.8983	0.3486	7.3891	0.3096	-0.3955	2.1226	0.0276	-0.4244	-0.1534	-1.3519	-0.7799	0.1143	0.5635	0.0812	-0.0558	0.449	-0.1429	0.7942	-62.8458	-26.6325	44.7276
13	5.1864	0.0451	1.4461	1.8592	-0.0573	9.9124	0.2539	0.1666	0.6573	0.037	-0.2185	-0.1986	-0.0867	0.1815	-0.0956	0.3043	-0.0206	0.0688	0.2786	0.0846	0.5607	-55.3088	-35.2377	41.9892
14	8.5142	1.7431	-5.2764	4.1562	-3.9293	10.3395	0.1167	-1.2621	-0.4251	0.2761	0.0243	0.1649	0.3736	-0.1906	-0.1964	0.4575	-0.1238	-0.1	0.9325	0.1991	0.4	-25.9394	-34.1251	45.6701
15	5.3103	1.119	1.3234	4.0696	-2.7868	8.0324	0.311	-0.4616	0.1744	0.4035	-0.2539	0.0248	-0.9662	1.0694	-0.0487	0.4407	-0.1004	0.0501	0.6882	0.028	0.3361	-18.2039	-22.341	36.2155
16	6.7459	-4.7045	-3.4166	6.8475	-0.2844	4.9819	0.5368	1.5874	-2.2355	-0.499	-0.1827	-0.7933	1.6174	-1.0289	-0.3351	0.6535	-0.1279	-0.0832	0.3999	-0.0502	0.6556	-53.296	-18.9916	-7.9174
17	4.2796	-0.2126	0.2315	1.3905	-2.8864	6.6334	-0.1119	-0.4244	-0.0813	-0.1376	-0.0362	-0.2707	-0.1354	0.374	0.118	0.4976	-0.033	-0.0345	0.2277	0.0571	0.4922	-45.8872	-10.6064	-2.1773
18	2.7024	-4.4583	2.9893	9.6045	-1.9148	9.2917	-0.2227	0.2289	0.4882	-1.326	0.476	0.3569	-0.8903	1.408	-0.1504	0.573	-0.1642	0.0114	0.8275	0.2258	0.6337	-19.2501	-12.094	-1.977
19	5.5072	-1.4649	0.4855	9.557	0.5393	8.2645	-0.06	0.5249	0.579	-0.0555	0.3194	-0.3687	-0.6535	1.0596	-0.2283	0.4964	-0.0495	0.0583	0.8164	0.185	0.4322	-16.9199	-16.1491	8.8008
20	5.1047	-0.0692	-2.4641	7.1711	-3.5531	9.8888	0.0084	0.5131	0.0026	-0.7576	0.0396	-0.1224	0.8607	1.3512	0.0031	0.4849	0.0113	-0.0532	0.8672	0.0385	0.3808	-16.1405	-26.5435	6.2497
21	5.9141	2.2609	-4.0187	2.2098	-0.851	8.906	0.1259	1.0627	-0.5258	-1.1438	-0.195	-0.6473	1.3728	1.3553	0.2528	0.9443	0.3367	0.0256	1.2712	-0.0487	0.661	-8.3585	-30.9897	9.5079
22	4.8253	-0.1006	0.3276	6.9068	-5.4079	9.1413	-0.0364	0.7734	-0.3118	-0.6364	0.7694	0.9292	0.741	-0.9813	-0.7023	0.4783	-0.0852	-0.074	0.7419	0.0743	0.3818	-24.588	-28.2446	28.8255

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 16 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 17 through 54 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 55 through 89 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 90 through 161 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 162 through 189 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 5 through 37 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 38 through 54 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 55 through 97 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 98 through 138 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 139 through 161 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 162 through 189 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 0 through 16 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 17 through 52 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 53 through 112 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 113 through 189 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 0 through 16 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 17 through 54 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 55 through 74 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 75 through 97 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 98 through 151 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 152 through 161 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 162 through 189 )

-
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