PDB-3hhh: Crystal structure of transcriptional regulator, a member of PadR ...

ID or keywords:

Entry

Database: PDB / ID: 3hhh

Title

Crystal structure of transcriptional regulator, a member of PadR family, from Enterococcus faecalis V583

Components

Transcriptional regulator, PadR family

Keywords

TRANSCRIPTION REGULATOR / transcriptional regulator / PadR family / PF03551 / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

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

Enterococcus faecalis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.7 Å

Authors

Nocek, B. / Zhou, M. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal structure of transcriptional regulator, a membar of PadR family, from Enterococcus faecalis V583
Authors: Nocek, B. / Zhou, M. / Moy, S. / Joachimiak, A.

History

Deposition	May 15, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 2, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2	Nov 27, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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

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Download

PDBx/mmCIF format	3hhh.cif.gz	56.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3hhh.ent.gz	42.3 KB	Display	PDB format
PDBx/mmJSON format	3hhh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

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

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Related structure data

Similar structure data	3lif-2 3kwg-3 3lib-7 6py3-2 3lib-5 6d8v-d 4i0c-1 2ec2-2 3soh-2 3lib-8 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: APC29037

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Transcriptional regulator, PadR family

B: Transcriptional regulator, PadR family

hetero molecules

27.5 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)	86.766, 86.766, 84.731
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	146
Space group name H-M	H3

#1: Protein	Transcriptional regulator, PadR family Mass: 13595.331 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: EF_1297 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q835S6
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.26 Å³/Da / Density % sol: 45.51 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.05 M Ammonium Sulfate, 50mM Bis-Tris 6.5, 30% Pentaerythritol Ethoxylate (15/4 EO/OH), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 20, 2007 / Details: mirrors
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 2.7→40 Å / Num. all: 6530 / Num. obs: 6515 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.7 % / B_iso Wilson estimate: 62 Å² / R_merge(I) obs: 0.064 / Net I/σ(I): 33
Reflection shell	Resolution: 2.7→2.75 Å / Redundancy: 4.4 % / R_merge(I) obs: 0.144 / Mean I/σ(I) obs: 12 / % possible all: 100

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
SHELX		model building
Coot		model building
ARP/wARP		model building
REFMAC	5.5.0054	refinement
HKL-3000		data reduction
HKL-3000		data scaling
SHELX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.7→20 Å / Cor.coef. F_o:F_c: 0.93 / Cor.coef. F_o:F_c free: 0.898 / SU B: 33.968 / SU ML: 0.312 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R Free: 0.379 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26269	302	4.6 %	RANDOM
R_work	0.22088	-	-	-
all	0.23	6510	-	-
obs	0.223	6207	99.3 %	-

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 mean: 22.086 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.97 Å²	-1.99 Å²	0 Å²
2-	-	-3.97 Å²	0 Å²
3-	-	-	5.96 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1689	0	16	9	1714

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.022	1729
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1229
X-RAY DIFFRACTION	r_angle_refined_deg	0.929	1.982	2320
X-RAY DIFFRACTION	r_angle_other_deg	0.74	3	3008
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.626	5	202
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.665	24.667	75
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.294	15	355
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.594	15	10
X-RAY DIFFRACTION	r_chiral_restr	0.052	0.2	260
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	1813
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	331
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.237	1.5	1013
X-RAY DIFFRACTION	r_mcbond_other	0.023	1.5	417
X-RAY DIFFRACTION	r_mcangle_it	0.444	2	1636
X-RAY DIFFRACTION	r_scbond_it	0.486	3	716
X-RAY DIFFRACTION	r_scangle_it	0.835	4.5	684
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.7→2.768 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.433	25	-
R_work	0.32	462	-
obs	-	-	98.38 %

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	2.7789	-1.5421	0.1268	1.5482	-0.7298	0.665	-0.2187	-0.404	-0.2703	0.0752	0.2846	0.2378	0.1197	-0.1356	-0.0659	0.3213	-0.0735	-0.0209	0.3778	0.0107	0.3664	16.6105	32.1133	21.3557
2	3.2708	1.4752	-0.5023	0.9949	-1.0895	2.3624	-0.2155	-0.2243	0.3016	0.1035	-0.1044	-0.0058	-0.5652	0.0218	0.3199	0.3695	0.0064	-0.0852	0.2323	-0.0906	0.3567	32.5436	39.4223	27.1469
3	7.8096	-1.3258	0.0139	1.5638	-0.6409	4.7787	-0.0575	-0.4143	0.0941	0.3165	0.0223	0.067	-0.2059	-0.2729	0.0352	0.302	-0.0068	-0.0053	0.2775	-0.0406	0.2868	26.2189	37.3896	35.2697
4	0.1501	-1.2964	0.7382	12.2068	-8.1691	6.8496	0.0244	0.0175	-0.0602	-0.1626	-0.0212	0.3384	-0.0152	-0.2558	-0.0032	0.3549	0.0052	-0.0081	0.3646	-0.0399	0.3672	17.2761	37.2769	30.2824
5	8.8184	4.367	4.6681	2.9889	0.3478	7.277	0.5154	-0.8567	-0.2341	0.4676	-0.5069	-0.11	-0.0685	-0.1535	-0.0085	0.3249	0.0641	0.0635	0.3107	0.0267	0.2918	24.9194	27.5782	31.6202
6	3.6835	-0.7863	-0.6006	7.6293	-0.4231	0.3377	-0.0563	0.1111	-0.4775	-0.1768	-0.0381	-0.0438	0.1973	-0.1322	0.0944	0.1944	-0.0297	-0.0027	0.237	-0.0028	0.1829	33.9408	26.0865	24.401
7	2.7181	-0.8018	0.7604	5.3106	-4.265	3.4331	-0.0568	-0.8129	0.1993	0.8388	0.1074	0.0885	-0.6662	-0.0884	-0.0506	0.3677	0.0166	-0.021	0.4665	-0.0398	0.2908	38.2623	33.9012	40.3556
8	5.0994	-1.2865	1.9013	3.3681	-1.0143	1.7901	0.0121	-0.0555	0.0821	0.0861	-0.002	-0.0217	-0.0235	-0.0352	-0.0101	0.1209	-0.0222	0.0066	0.0919	-0.0225	0.2166	35.0282	34.8604	24.1426
9	3.7165	-1.7646	1.8061	6.3011	2.4862	2.9274	-0.1089	0.4065	0.5034	0.0828	-0.2209	-0.1305	-0.0246	0.1982	0.3298	0.159	-0.0209	-0.0175	0.2624	0.0854	0.3126	20.6818	40.8024	10.0301
10	11.6889	-0.4214	-3.8679	5.8266	-1.5451	3.3343	0.1916	0.4864	0.2826	-0.1019	-0.1036	0.6588	-0.0715	-0.5506	-0.0881	0.3194	-0.0153	-0.0236	0.3129	0.0083	0.3352	10.015	44.8873	5.7545
11	4.2455	-1.8229	4.6682	5.7847	-0.9718	5.3475	0.176	0.0412	-0.3228	-0.1153	0.1765	0.0723	0.188	0.0979	-0.3526	0.2488	0.0462	-0.0301	0.2154	0.0368	0.334	17.7116	30.2713	13.43
12	0.018	0.1044	0.0153	1.5746	0.2002	0.0263	-0.0041	0.0433	0.0495	-0.4459	-0.0411	0.4246	-0.0543	0.0104	0.0452	0.3099	0.0336	-0.0893	0.3244	0.0639	0.3304	5.4829	34.7117	6.9721
13	0.7126	-0.9927	-0.9903	5.6899	1.6777	3.5778	0.0515	0.3242	0.1945	-0.6432	0.1143	0.0458	-0.2624	0.0267	-0.1658	0.3355	-0.0389	-0.0438	0.3863	0.0088	0.349	2.812	32.9459	-0.6213
14	7.3394	3.3074	-4.702	4.6798	1.0634	6.3948	-0.3098	0.3251	-0.1639	-0.5808	0.3899	-0.2494	-0.2233	0.2929	-0.0801	0.2731	-0.0303	-0.0154	0.3644	0.0156	0.2524	13.9753	32.9723	0.1082
15	8.2637	-2.4175	-2.0272	2.3159	-1.1537	8.1396	0.0303	0.1742	-0.2267	-0.3927	0.0292	0.0689	0.1914	-0.0754	-0.0596	0.2884	0.0129	-0.0199	0.2465	-0.0107	0.308	10.9017	23.9229	4.8942
16	7.9227	0.7467	-0.7481	5.0892	6.178	7.8599	0.0197	-0.3589	-0.2582	0.4398	-0.2298	0.1492	0.5538	-0.257	0.2101	0.2163	-0.0489	-0.0378	0.253	0.091	0.3712	-0.8359	25.735	10.8909
17	2.1463	0.3885	-2.0178	0.9082	-2.4259	7.2942	0.1109	0.4667	0.3042	-0.2852	-0.2722	-0.2177	0.3475	0.5621	0.1612	0.5672	0.0201	0.1137	0.4128	0.0177	0.5577	-2.6921	24.7738	-8.5409
18	2.0753	-1.3501	-2.4738	3.5842	0.8481	3.2654	-0.2427	0.0337	-0.2486	0.1024	0.0093	0.7253	0.2814	-0.171	0.2333	0.1142	-0.0366	-0.0592	0.2551	-0.0105	0.3267	-0.6322	33.6176	10.1628
19	6.4919	1.2876	6.3602	6.409	2.5087	6.5236	0.2375	-0.4955	0.1334	0.1862	-0.3113	0.1276	0.2684	-0.4539	0.0738	0.2034	-0.0054	0.0001	0.2964	-0.0223	0.2845	10.9206	41.9883	18.1054
20	9.3581	-0.6862	-9.1399	4.6924	2.8139	9.9407	0.5778	-0.4965	0.2761	0.2661	-0.2638	-0.4045	-0.3923	0.3002	-0.3141	0.3206	0.0021	-0.086	0.1946	-0.0898	0.5907	22.5912	46.193	20.663

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 13
2	X-RAY DIFFRACTION	2	A	14 - 23
3	X-RAY DIFFRACTION	3	A	24 - 35
4	X-RAY DIFFRACTION	4	A	36 - 42
5	X-RAY DIFFRACTION	5	A	43 - 49
6	X-RAY DIFFRACTION	6	A	50 - 59
7	X-RAY DIFFRACTION	7	A	60 - 70
8	X-RAY DIFFRACTION	8	A	71 - 90
9	X-RAY DIFFRACTION	9	A	91 - 100
10	X-RAY DIFFRACTION	10	A	101 - 105
11	X-RAY DIFFRACTION	11	B	1 - 13
12	X-RAY DIFFRACTION	12	B	14 - 19
13	X-RAY DIFFRACTION	13	B	20 - 27
14	X-RAY DIFFRACTION	14	B	28 - 40
15	X-RAY DIFFRACTION	15	B	41 - 49
16	X-RAY DIFFRACTION	16	B	50 - 62
17	X-RAY DIFFRACTION	17	B	63 - 72
18	X-RAY DIFFRACTION	18	B	73 - 88
19	X-RAY DIFFRACTION	19	B	89 - 95
20	X-RAY DIFFRACTION	20	B	96 - 104

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