PDB-4l9n: Crystal structure of MepR A103V mutant from multidrug resistant S...

ID or keywords:

Entry

Database: PDB / ID: 4l9n

Title

Crystal structure of MepR A103V mutant from multidrug resistant S. aureus clinical isolate

Components

MepR

Keywords

TRANSCRIPTION / wing-helix-turn-helix / wHTH / transcription repression

Function / homology

Function and homology information

response to stress / DNA-binding transcription factor activity
Similarity search - Function

Biological species

Staphylococcus aureus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Birukou, I. / Brennan, R.G.

Citation

Journal: MBio / Year: 2013
Title: The molecular mechanisms of allosteric mutations impairing MepR repressor function in multidrug-resistant strains of Staphylococcus aureus.
Authors: Birukou, I. / Tonthat, N.K. / Seo, S.M. / Schindler, B.D. / Kaatz, G.W. / Brennan, R.G.

History

Deposition	Jun 18, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 11, 2013	Provider: repository / Type: Initial release
Revision 1.1	Oct 30, 2013	Group: Database references
Revision 1.2	Nov 15, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

-
Download

PDBx/mmCIF format	4l9n.cif.gz	138 KB	Display	PDBx/mmCIF format
PDB format	pdb4l9n.ent.gz	110.8 KB	Display	PDB format
PDBx/mmJSON format	4l9n.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4l9n_validation.pdf.gz	443.1 KB	Display	wwPDB validaton report
Full document	4l9n_full_validation.pdf.gz	444.3 KB	Display
Data in XML	4l9n_validation.xml.gz	14.7 KB	Display
Data in CIF	4l9n_validation.cif.gz	21.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/l9/4l9n ftp://data.pdbj.org/pub/pdb/validation_reports/l9/4l9n	HTTPS FTP

-
Related structure data

Related structure data	4l9jC 4l9tC 4l9vC 4ld5C C: citing same article (ref.)
Similar structure data	2an7-d 6esx-d 4q57-d 6l8f-1 6l8f-2 3oei-3 1qn2-d 2eak-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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: MepR

B: MepR

hetero molecules

34.2 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)	31.793, 95.125, 105.614
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	MepR / MarR family transcription repressor MepR Mass: 17049.236 Da / Num. of mol.: 2 / Mutation: A103V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: mepR / Production host: Escherichia coli (E. coli) / References: UniProt: Q5Y812
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.34 Å³/Da / Density % sol: 47.48 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.2 M (NH4)2SO4, 0.1 M Na acetate pH 4.6 and 30% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 28, 2012
Radiation	Monochromator: Si 111. Rosenbaum-Rock double-crystal monochromator: Water cooled, sagittal focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.6→50 Å / Num. all: 43266 / Num. obs: 41385 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2

-
Processing

Software

Name	Version	Classification
PHENIX	1.8.1_1168	refinement
PDB_EXTRACT	3.11	data extraction
SERGUI	control program	data collection
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX	(Phaser)	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.6→25.641 Å / Occupancy max: 1 / Occupancy min: 0.26 / SU ML: 0.15 / σ(F): 0 / Phase error: 23.52 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2174	1895	4.83 %	random
R_work	0.1895	-	-	-
obs	0.1909	39266	90.77 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 110.14 Å² / B_iso mean: 29.3971 Å² / B_iso min: 10.35 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→25.641 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2175	0	5	239	2419

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	2500
X-RAY DIFFRACTION	f_angle_d	0.908	3410
X-RAY DIFFRACTION	f_chiral_restr	0.059	382
X-RAY DIFFRACTION	f_plane_restr	0.004	458
X-RAY DIFFRACTION	f_dihedral_angle_d	15.057	954

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.6-1.6402	0.28	87	0.2615	1769	1856	62
1.6402-1.6846	0.3087	110	0.246	2022	2132	70
1.6846-1.7341	0.2659	116	0.2352	2221	2337	77
1.7341-1.7901	0.2591	116	0.218	2444	2560	84
1.7901-1.854	0.2734	137	0.2087	2671	2808	92
1.854-1.9283	0.2004	140	0.1961	2734	2874	95
1.9283-2.016	0.2449	144	0.1895	2847	2991	97
2.016-2.1222	0.2546	146	0.1717	2869	3015	98
2.1222-2.2551	0.19	144	0.1751	2864	3008	99
2.2551-2.4291	0.2068	145	0.1852	2902	3047	99
2.4291-2.6733	0.2257	149	0.1853	2930	3079	99
2.6733-3.0596	0.2202	147	0.1886	2936	3083	99
3.0596-3.8527	0.2063	154	0.1786	3010	3164	100
3.8527-25.641	0.1982	160	0.1916	3152	3312	100

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	1.5529	1.3734	2.4083	4.7655	6.4618	8.7109	0.2081	-0.1723	-0.1436	0.3767	-0.4223	0.0572	0.3615	-0.8193	0.2782	0.1885	-0.049	0.023	0.1683	-0.0093	0.1627	-7.2009	16.0992	25.3627
2	8.2072	0.1936	0.0813	1.7451	0.3839	2.7469	-0.1657	-0.5901	0.1117	0.0385	0.1148	-0.1749	-0.2305	0.1535	0.066	0.1086	-0.0152	-0.0181	0.1563	-0.0548	0.1598	2.3044	5.2052	14.0247
3	6.9109	4.165	-5.4669	4.832	-3.6909	5.9319	0.3339	-0.3822	-0.2021	0.6571	-0.2213	-0.0933	-0.4702	0.331	-0.1735	0.2575	-0.0027	-0.0435	0.269	-0.008	0.2097	8.3542	-1.3007	16.7117
4	3.9448	0.2508	0.7133	3.7731	-0.8374	4.5597	-0.1462	-0.0877	-0.4202	0.1579	-0.012	0.0817	0.3551	-0.0356	0.0356	0.1233	0.0202	0.0305	0.0906	-0.0057	0.1387	0.5605	-4.1336	8.296
5	0.6532	-1.0111	-0.3433	1.5605	0.5268	0.1781	-0.3033	-0.4878	0.2744	0.4655	0.3276	-0.29	-0.153	0.0685	0.1582	0.6798	0.8441	-0.6115	0.4095	0.0819	0.982	16.2766	-12.2077	9.4209
6	7.0736	3.6101	2.3997	2.1092	2.5797	7.6915	0.0492	0.0808	-0.7372	0.3868	-0.2915	-0.6534	0.381	0.7343	0.0422	0.0797	0.031	0.033	0.1321	-0.0113	0.1866	8.2729	-2.7399	6.8726
7	0.4367	-2.2017	-2.565	4.9256	6.3201	7.5549	-0.1273	0.0344	-0.0433	0.1374	-0.0918	0.1654	-0.1109	0.0153	0.1821	0.1383	-0.0153	-0.0085	0.1095	-0.0144	0.1785	0.2566	18.0117	10.9816
8	6.5241	-2.1827	2.1078	2.6795	-3.6007	8.1383	0.2244	-0.1965	-0.1866	0.1094	-0.2845	-0.288	-0.3134	0.6079	0.1944	0.242	-0.0654	-0.0126	0.2041	-0.0023	0.1702	5.3989	29.287	30.3368
9	0.3983	-1.5755	1.7207	8.2824	-6.5596	6.2453	0.323	0.0837	-0.0144	-0.4963	-0.4176	0.0382	0.1629	0.6889	0.1984	0.2379	0.0378	0.0374	0.2577	0.0174	0.2434	7.0649	14.1824	34.796
10	2.2757	-0.7442	-1.2999	1.7671	0.2247	1.9639	0.0819	0.4582	-0.3298	-0.2034	-0.018	0.1801	-0.0257	-0.262	-0.0911	0.1417	0.0141	-0.0467	0.2219	0.0441	0.149	-2.1221	-0.631	44.5938
11	8.1374	-3.2591	-7.5308	2.5413	3.0377	6.7148	0.0724	0.1127	-0.0913	-0.3563	-0.1211	0.1594	-0.0481	-0.2548	0.0037	0.2279	0.0168	-0.0491	0.2867	-0.0004	0.2078	-10.0758	-6.6265	42.3235
12	1.1044	-0.189	1.0653	4.2538	3.3403	5.1213	0.1398	-0.0344	-0.2202	0.0074	-0.0326	-0.1757	0.3503	-0.107	-0.1488	0.1102	0.0036	-0.0009	0.134	0.0119	0.1695	-0.5059	-10.1004	49.3228
13	0.5052	0.3389	0.0143	0.3741	-0.3039	1.8759	-0.4833	0.5516	0.4242	-0.7884	0.0908	0.7416	-0.8678	0.3634	0.3685	1.4863	-0.4869	-0.2998	0.5976	-0.0627	0.9863	-14.9749	-19.3601	49.0053
14	1.4952	2.9662	-1.27	9.3939	-4.8584	2.1837	-0.1449	0.113	-0.0486	-0.1996	0.1091	-0.0012	-0.1389	-0.0997	0.0233	0.1742	0.0082	0.0008	0.14	-0.0039	0.1605	-0.8013	10.37	49.3323
15	3.0434	1.8924	2.3987	6.3856	3.5475	8.3666	0.0413	0.0036	-0.0086	-0.2622	-0.0948	0.2479	-0.0793	-0.4527	0.0845	0.211	0.0031	0.0146	0.1954	0.016	0.1952	-5.3445	29.2996	32.7089

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 27 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 28 through 43 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 44 through 61 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 62 through 81 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 82 through 88 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 89 through 94 )	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 95 through 118 )	A
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 119 through 139 )	A
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 2 through 27 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 28 through 43 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 44 through 60 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 61 through 81 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 82 through 88 )	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 89 through 118 )	B
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 119 through 140 )	B

-
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://pdbjlvh1.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