PDB-4ejo: Crystal structure of padr family transcriptional regulator from E...

ID or keywords:

Entry

Database: PDB / ID: 4ejo

Title

Crystal structure of padr family transcriptional regulator from Eggerthella lenta DSM 2243

Components

Transcriptional regulator, PadR-like family

Keywords

TRANSCRIPTION REGULATOR / PSI-BIOLOGY / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG / TRANSCRIPTIONAL REGULATOR

Function / homology

Function and homology information

Transcription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology

Biological species

Eggerthella lenta (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.1 Å

Authors

Chang, C. / Li, H. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: TO BE PUBLISHED
Title: Crystal structure of padr family transcriptional regulator from Eggerthella lenta DSM 2243
Authors: Chang, C. / Li, H. / Bearden, J. / Joachimiak, A.

History

Deposition	Apr 6, 2012	Deposition site: RCSB / Processing site: RCSB
Supersession	Apr 25, 2012	ID: 3RI2
Revision 1.0	Apr 25, 2012	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ejo.cif.gz	104.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4ejo.ent.gz	88.2 KB	Display	PDB format
PDBx/mmJSON format	4ejo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4ejo_validation.pdf.gz	446.8 KB	Display	wwPDB validaton report
Full document	4ejo_full_validation.pdf.gz	450.4 KB	Display
Data in XML	4ejo_validation.xml.gz	10.9 KB	Display
Data in CIF	4ejo_validation.cif.gz	13.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ej/4ejo ftp://data.pdbj.org/pub/pdb/validation_reports/ej/4ejo	HTTPS FTP

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Related structure data

Similar structure data	2asb-d 5xbc-d 3w9g-2 2d2a-d 3jxi-2 3w9f-2 4nr4-d 6pvx-d 1o0o-d 3jxi-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) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: MCSG-APC100099

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#13 - Jan 2001 Alcohol Dehydrogenase similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1) #233 - May 2019 S-Nitrosylated Hemoglobin similarity (1) #44 - Aug 2003 Calmodulin similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

Deposited unit

A: Transcriptional regulator, PadR-like family

B: Transcriptional regulator, PadR-like family

hetero molecules

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

1

A: Transcriptional regulator, PadR-like family

hetero molecules

A: Transcriptional regulator, PadR-like family

hetero molecules

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

2

B: Transcriptional regulator, PadR-like family

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

Unit cell

Length a, b, c (Å)	55.783, 55.783, 132.425
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	80
Space group name H-M	I4₁

Components on special symmetry positions

ID	Model	Components
1	1	B-206- HOH

Details

unit A makes dimer with operator (x,y,z) (1-x,1-y,z) unit B makes dimer with operator (x,y,z) (-x,-y,z)

#1: Protein	Transcriptional regulator, PadR-like family Mass: 14110.361 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Eggerthella lenta (bacteria) Strain: ATCC 25559 / DSM 2243 / JCM 9979 / NCTC 11813 / VPI 0255 Gene: Elen_1533 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) MAGIC / References: UniProt: C8WHB0
#2: Chemical	ChemComp-EOH / ETHANOL Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 22 / 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: 1.83 Å³/Da / Density % sol: 32.61 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 0.1M PHOSPHATE-CITRATE PH 4.2, 40% ETHANOL, 5% PEG 1000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE, temperature 277 K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97948, 0.97959

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 11, 2010

Radiation

Monochromator: SI(111)DOUBLE CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97948	1
2	0.97959	1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.588
1	1	K, H, -L	2	0.412

Reflection

Resolution: 2.1→50 Å / Num. all: 11881 / Num. obs: 11880 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.6 % / R_merge(I) obs: 0.126 / Net I/σ(I): 33.9

Reflection shell

Resolution: 2.1→2.12 Å / Redundancy: 8.6 % / R_merge(I) obs: 0.542 / Mean I/σ(I) obs: 4 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.6.0117	refinement
PDB_EXTRACT	3.11	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
MLPHARE		phasing
DM		phasing
SHELXDE		phasing
RESOLVE		phasing
ARP/wARP		model building

Refinement

Method to determine structure:

MAD / Resolution: 2.1→50 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.929 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 13.543 / SU ML: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2353	532	4.5 %	RANDOM
R_work	0.181	-	-	-
obs	0.1833	11854	99.77 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso max: 174.83 Å² / B_iso mean: 44.9808 Å² / B_iso min: 6.08 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	15.51 Å²	0 Å²	0 Å²
2-	-	15.51 Å²	0 Å²
3-	-	-	-31.02 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1767	0	3	22	1792

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.02	1862
X-RAY DIFFRACTION	r_angle_refined_deg	1.667	1.99	2519
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.941	5	232
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.889	22.588	85
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.921	15	342
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.055	15	22
X-RAY DIFFRACTION	r_chiral_restr	0.104	0.2	281
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	1398
X-RAY DIFFRACTION	r_rigid_bond_restr	5.435	3	1862
X-RAY DIFFRACTION	r_sphericity_free	29.428	5	6
X-RAY DIFFRACTION	r_sphericity_bonded	28.29	5	1846

LS refinement shell

Resolution: 2.096→2.15 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.269	52	-
R_work	0.184	839	-
all	-	891	-
obs	-	893	98.34 %

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	0.1036	1.3764	0.1575	26.8957	-5.9769	8.4597	0.0371	0.0316	0.0701	0.236	0.3887	1.2135	0.3805	-0.2922	-0.4258	0.1531	0.0176	0.0234	0.2593	0.0804	0.3183	19.726	14.947	9.901
2	1.8825	-1.9299	-1.0358	4.9239	0.7224	0.6162	-0.0107	-0.0241	-0.0211	-0.1848	0.0411	0.1674	0.0608	0.0027	-0.0304	0.1909	-0.0053	-0.0576	0.1893	-0.0126	0.3055	21.517	35.611	5.737
3	11.6429	-4.707	8.4849	1.9074	-3.4322	6.1879	-0.3679	-0.2534	0.2208	0.1483	0.1219	-0.1031	-0.3024	-0.1813	0.246	0.2226	0.0366	0.0048	0.1953	-0.0471	0.4618	10.337	46.031	7.717
4	16.6783	14.5975	12.6634	13.6907	12.8182	12.9071	0.5655	-0.0861	-0.4577	0.3822	-0.1909	-0.4226	0.2045	-0.2718	-0.3746	0.1407	0.1153	-0.149	0.1163	-0.1355	0.4584	11.065	35.421	4.625
5	4.1164	2.5886	-1.3985	5.5687	-0.7174	0.4843	-0.1806	-0.4418	-0.2434	-0.3043	0.0575	0.1539	0.0616	0.1462	0.1231	0.2061	0.0449	-0.0254	0.2282	0.0213	0.3193	17.649	37.71	15.314
6	5.5255	-0.1955	2.6152	0.8955	0.0702	1.2719	0.0246	-0.5635	0.1817	0.0892	-0.1182	0.0881	0.0411	-0.2657	0.0935	0.203	0.0033	-0.006	0.2341	-0.0457	0.3217	14.608	50.305	13.229
7	0.2941	-1.3596	-0.3579	7.823	2.5926	1.1736	-0.0126	0.0101	0.0668	0.0208	0.153	-0.1179	-0.0335	-0.0475	-0.1403	0.1588	0.0101	-0.0003	0.279	0.081	0.3507	29.393	44.831	1.803
8	3.4566	-7.2655	-2.6939	19.7981	4.4248	2.5235	-0.2599	-0.216	-0.1314	0.0229	0.1279	0.1879	0.1983	0.2855	0.132	0.2403	-0.0102	0.0225	0.1744	0.0224	0.2732	34.006	26.105	-3.575
9	2.7235	1.5614	-1.0205	16.568	7.7037	5.2088	0.0631	0.0253	-0.4232	0.3994	-0.2387	-0.3971	0.2929	-0.3055	0.1757	0.1716	0.0067	0.0499	0.2364	-0.0412	0.3454	7.617	-13.813	-7.288
10	1.6882	3.1803	-0.2124	7.0947	1.889	4.8675	-0.3268	-0.1479	0.1706	-0.5899	-0.3191	0.5972	0.3836	-0.1644	0.6459	0.278	0.026	-0.0237	0.2058	0.0084	0.4322	6.257	7.598	-3.3
11	23.7477	-1.5017	9.1805	0.096	-0.5818	3.5507	-0.1267	0.5956	-0.0538	0.022	0.0395	-0.0121	-0.0922	0.2379	0.0872	0.2247	-0.0698	0.0003	0.1394	0.0652	0.4241	17.599	18.087	-5.242
12	12.1787	-2.1947	1.892	17.5995	-22.9482	30.0033	-0.0967	-0.8	-0.1279	0.1192	0.4087	0.2829	-0.1371	-0.4325	-0.312	0.1262	-0.019	0.0197	0.1731	0.0003	0.3881	16.729	7.632	-2.138
13	4.4744	-17.7931	-0.986	70.7913	3.9213	0.2173	-0.0759	0.0911	-0.351	0.7808	-0.135	1.2918	0.0423	-0.0153	0.2109	0.5704	-0.6714	0.191	0.818	-0.2911	0.345	9.191	10.658	-12.521
14	1.9469	-0.4945	-1.41	2.4418	-1.7932	3.0197	0.082	0.1095	0.0875	-0.1203	-0.0018	-0.0006	0.0256	-0.1075	-0.0801	0.1717	-0.0172	-0.0214	0.2112	0.0187	0.3068	13.269	22.456	-10.855
15	5.2432	-0.9421	-2.9476	9.3223	-4.3598	4.2702	0.1171	-0.041	-0.268	0.1215	-0.2683	0.0862	-0.144	0.1852	0.1512	0.1413	0.0007	0.0138	0.2317	0.0826	0.3837	-1.449	16.864	0.743
16	3.7298	-0.2526	-1.503	14.6798	-1.495	0.7809	-0.0893	0.3386	0.067	0.7579	0.1471	0.0608	-0.0409	-0.1605	-0.0578	0.1489	-0.0205	-0.0166	0.2091	0.0281	0.2957	-6.492	-2.794	6.393

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 12
2	X-RAY DIFFRACTION	2	A	13 - 28
3	X-RAY DIFFRACTION	3	A	29 - 34
4	X-RAY DIFFRACTION	4	A	35 - 45
5	X-RAY DIFFRACTION	5	A	46 - 59
6	X-RAY DIFFRACTION	6	A	60 - 83
7	X-RAY DIFFRACTION	7	A	84 - 95
8	X-RAY DIFFRACTION	8	A	96 - 111
9	X-RAY DIFFRACTION	9	B	0 - 12
10	X-RAY DIFFRACTION	10	B	13 - 28
11	X-RAY DIFFRACTION	11	B	29 - 34
12	X-RAY DIFFRACTION	12	B	35 - 45
13	X-RAY DIFFRACTION	13	B	46 - 59
14	X-RAY DIFFRACTION	14	B	60 - 83
15	X-RAY DIFFRACTION	15	B	84 - 95
16	X-RAY DIFFRACTION	16	B	96 - 115

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