PDB-5tpm: 2.8 Angstrom Crystal Structure of the C-terminal Dimerization Dom...

ID or keywords:

Entry

Database: PDB / ID: 5tpm

Title

2.8 Angstrom Crystal Structure of the C-terminal Dimerization Domain of Transcriptional Regulator PdhR from Escherichia coli.

Components

Pyruvate dehydrogenase complex repressor

Keywords

HYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding
Similarity search - Function

Biological species

Escherichia coli O6:H1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.8 Å

Authors

Minasov, G. / Wawrzak, Z. / Sandoval, J. / Skarina, T. / Grimshaw, S. / Kwon, K. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: 2.8 Angstrom Crystal Structure of the C-terminal Dimerization Domain of Transcriptional Regulator PdhR from Escherichia coli.
Authors: Minasov, G. / Wawrzak, Z. / Sandoval, J. / Skarina, T. / Grimshaw, S. / Kwon, K. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Oct 20, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 2, 2016	Provider: repository / Type: Initial release
Revision 1.1	Oct 23, 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 / pdbx_prerelease_seq / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5tpm.cif.gz	245.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5tpm.ent.gz	203.9 KB	Display	PDB format
PDBx/mmJSON format	5tpm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5tpm_validation.pdf.gz	440.2 KB	Display	wwPDB validaton report
Full document	5tpm_full_validation.pdf.gz	443.3 KB	Display
Data in XML	5tpm_validation.xml.gz	24.7 KB	Display
Data in CIF	5tpm_validation.cif.gz	32 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tp/5tpm ftp://data.pdbj.org/pub/pdb/validation_reports/tp/5tpm	HTTPS FTP

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Related structure data

Similar structure data	1af7-d 5chs-1 4zi2-1 5k25-d 1qvj-d 6hym-d 4lg0-d 2o0j-d 2aus-4 2aus-2 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
Other databases	TargetTrack: CSGID-IDP95705

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Pyruvate dehydrogenase complex repressor

B: Pyruvate dehydrogenase complex repressor

C: Pyruvate dehydrogenase complex repressor

D: Pyruvate dehydrogenase complex repressor

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

1

A: Pyruvate dehydrogenase complex repressor

B: Pyruvate dehydrogenase complex repressor

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

2

C: Pyruvate dehydrogenase complex repressor

D: Pyruvate dehydrogenase complex repressor

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

Unit cell

Length a, b, c (Å)	64.397, 95.347, 70.001
Angle α, β, γ (deg.)	90.00, 114.09, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	B
2	4	C
1	5	B
2	5	D
1	6	C
2	6	D

NCS domain segments:

Dom-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	A	96 - 235
2	1	B	96 - 235
1	2	A	96 - 246
2	2	C	96 - 246
1	3	A	96 - 234
2	3	D	96 - 234
1	4	B	96 - 235
2	4	C	96 - 235
1	5	B	96 - 234
2	5	D	96 - 234
1	6	C	96 - 234
2	6	D	96 - 234

NCS ensembles :

ID
6
1
2
3
4
5

#1: Protein	Pyruvate dehydrogenase complex repressor Mass: 18712.539 Da / Num. of mol.: 4 / Fragment: UNP residues 99-254 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O6:H1 (bacteria) / Strain: CFT073 / ATCC 700928 / UPEC / Gene: pdhR, c0140 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Magic / References: UniProt: P0ACM0, UniProt: P0ACL9*PLUS
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.72 Å³/Da / Density % sol: 54.9 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Protein: 15.0 mg/ml, 0.3M Sodium chloride, 0.01M HEPES pH 7.5; Screen: 0.2M NH4Formate, 20% (w/v) PEG3350;Cryo: paratone.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 14, 2016
Radiation	Monochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97856 Å / Relative weight: 1
Reflection	Resolution: 2.8→30 Å / Num. obs: 19376 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.6 % / B_iso Wilson estimate: 75.8 Å² / R_merge(I) obs: 0.094 / R_sym value: 0.094 / Net I/σ(I): 32.6
Reflection shell	Resolution: 2.8→2.85 Å / Redundancy: 8.4 % / R_merge(I) obs: 0.75 / Mean I/σ(I) obs: 2.7 / CC_1/2: 0.913 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0155	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.8→29.39 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.94 / SU B: 47.746 / SU ML: 0.395 / Cross valid method: THROUGHOUT / ESU R Free: 0.377 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25674	919	4.8 %	RANDOM
R_work	0.22211	-	-	-
obs	0.22377	18146	99.83 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 72.794 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	5.86 Å²	0 Å²	-7.14 Å²
2-	-	-2.67 Å²	0 Å²
3-	-	-	2.28 Å²

Refinement step

Cycle: 1 / Resolution: 2.8→29.39 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4750	0	0	60	4810

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	4827
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	4686
X-RAY DIFFRACTION	r_angle_refined_deg	1.469	1.971	6508
X-RAY DIFFRACTION	r_angle_other_deg	0.942	3	10697
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	1.412	5	586
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	19.233	22.959	267
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.007	15	839
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.147	15	64
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	732
X-RAY DIFFRACTION	r_gen_planes_refined	0.024	0.02	5491
X-RAY DIFFRACTION	r_gen_planes_other	0.019	0.02	1169
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	2.916	6.034	2350
X-RAY DIFFRACTION	r_mcbond_other	2.912	6.033	2349
X-RAY DIFFRACTION	r_mcangle_it	4.734	9.047	2931
X-RAY DIFFRACTION	r_mcangle_other	4.733	9.048	2932
X-RAY DIFFRACTION	r_scbond_it	3.496	6.637	2477
X-RAY DIFFRACTION	r_scbond_other	3.496	6.639	2478
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	5.883	9.749	3577
X-RAY DIFFRACTION	r_long_range_B_refined	8.613	73.909	5554
X-RAY DIFFRACTION	r_long_range_B_other	8.572	73.914	5551
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	9018	0.12
1	2	B	9018	0.12
2	1	A	9750	0.11
2	2	C	9750	0.11
3	1	A	8884	0.13
3	2	D	8884	0.13
4	1	B	9036	0.12
4	2	C	9036	0.12
5	1	B	9252	0.09
5	2	D	9252	0.09
6	1	C	8912	0.13
6	2	D	8912	0.13

LS refinement shell

Resolution: 2.8→2.872 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.436	78	-
R_work	0.401	1280	-
obs	-	-	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	1.5732	-0.3682	-0.0366	0.279	0.1616	0.2602	0.0595	0.0886	0.0521	0.0156	-0.0242	0.0217	-0.0135	-0.0522	-0.0352	0.0596	-0.0049	0.0086	0.0517	0.006	0.0671	9.8726	59.034	47.2555
2	0.9337	0.174	0.7084	6.2033	3.0584	4.3943	0.0048	-0.2511	-0.0675	0.4974	0.0294	0.2088	0.3022	0.0169	-0.0342	0.0442	-0.002	0.0184	0.1349	0.0023	0.0197	11.696	60.1295	55.1463
3	0.4834	0.1701	0.0206	3.5743	0.7059	0.1896	-0.0455	-0.0111	0.0124	-0.0224	0.0648	-0.0327	-0.0101	0.0743	-0.0193	0.0692	0	-0.0147	0.0838	-0.0011	0.0554	22.0313	61.9876	54.8156
4	1.3623	2.0051	0.6776	3.1696	0.8045	0.5436	-0.0898	0.0121	0.2436	-0.0906	-0.0418	0.2967	-0.0957	0.0191	0.1317	0.0229	0.0087	-0.0023	0.0741	0.0429	0.1198	10.5923	70.2916	47.0261
5	4.4109	2.7021	0.9943	1.9561	0.4056	0.3625	0.0162	0.0451	0.041	0.0216	0.0411	0.1221	-0.0068	0.0085	-0.0573	0.059	-0.0125	0.0056	0.0922	-0.0107	0.0423	34.6928	81.4863	48.5114
6	0.1413	-0.0861	0.6307	0.0656	-0.4909	3.6833	0.0621	0.1033	0.0214	-0.011	0.0146	0.015	0.0764	-0.0177	-0.0767	0.0363	0.0587	0.0843	0.4146	-0.0173	0.3036	17.7766	51.7602	34.2975
7	0.8529	0.9398	0.488	2.492	0.879	0.6343	-0.019	0.0272	-0.034	0.0432	0.055	-0.092	0.0544	0.0586	-0.036	0.0296	0.0093	0.0171	0.0687	-0.0154	0.059	31.8271	44.8065	26.1968
8	0.7118	0.5373	0.0119	4.0771	2.2466	4.2267	-0.0682	0.0086	-0.2043	0.2099	0.0729	-0.0994	0.1216	0.0709	-0.0047	0.0275	0.0138	0.0257	0.0529	0.0081	0.0617	23.0709	44.648	34.3221
9	3.9867	1.6544	2.5273	3.616	2.8423	3.4601	0.1113	0.1002	0.2341	-0.2317	-0.1536	0.029	0.0292	0.2014	0.0423	0.0921	0.0255	0.0289	0.1571	-0.0072	0.0771	24.2586	52.5379	21.7983
10	3.9148	1.394	0.1869	1.1279	0.4269	1.1653	0.0235	0.0691	0.0539	-0.0748	-0.0581	0.0089	0.0114	-0.0373	0.0345	0.0512	-0.0058	0.0055	0.0724	-0.0088	0.0457	11.6342	48.6736	24.1086
11	4.4452	-0.1062	-3.1793	1.8677	0.6107	2.9817	-0.1006	-0.174	-0.213	-0.0459	-0.1293	0.4043	0.0927	-0.0325	0.2298	0.0071	-0.0018	-0.0068	0.0439	-0.0136	0.0988	20.1268	35.8752	62.816
12	0.6391	-0.5953	0.6374	2.5721	0.5033	1.236	0.0915	-0.0296	-0.125	0.0239	-0.0648	0.3255	0.1507	-0.0829	-0.0267	0.0342	-0.043	0.0022	0.0858	-0.0102	0.1172	6.2434	26.7783	56.1634
13	0.3268	0.1946	0.1468	0.8887	0.3706	1.5046	0.0278	-0.0258	0.0181	-0.0317	0.006	0.0823	0.0024	-0.0544	-0.0338	0.0372	-0.0005	-0.0091	0.0541	0.0159	0.0777	17.5504	36.777	54.5159
14	0.3284	-0.2541	0.0287	3.0693	2.8489	3.1398	0.0355	-0.0599	-0.1709	0.2387	-0.1159	0.1977	0.3479	-0.0174	0.0804	0.0906	0.01	0.0195	0.105	0.0385	0.1085	19.6734	23.3637	60.4082
15	2.6218	0.4136	-0.3085	0.5113	1.1533	3.5736	-0.1239	0.0063	-0.1574	0.0351	-0.0455	0.0631	0.075	-0.173	0.1694	0.0729	-0.0077	0.0188	0.084	0.007	0.0701	30.2491	12.1981	39.2808
16	4.2021	-0.3875	-1.2759	1.9832	0.6548	0.5595	-0.1593	-0.0707	-0.1969	-0.0777	0.0721	0.0901	0.0495	0.0719	0.0872	0.0695	-0.0191	0.0396	0.1473	-0.0329	0.0387	39.077	41.3787	56.4071
17	3.0517	1.6282	1.2867	3.9011	0.5646	2.5866	-0.2056	0.2492	0.1988	-0.5825	0.3161	-0.0443	-0.3195	0.4174	-0.1104	0.1409	-0.0619	0.0767	0.1699	0.0113	0.1197	42.3387	50.0369	55.4359
18	2.8665	0.574	3.3078	0.9046	1.0143	4.1146	0.0188	-0.0215	0.076	0.0471	-0.0018	0.0687	0.0311	-0.0247	-0.0171	0.0524	-0.0057	0.0163	0.0534	0.0016	0.1235	36.868	54.8578	66.6539
19	0.5259	-0.1809	0.166	1.7193	1.5773	1.7951	0.0346	0.0317	-0.0118	0.0966	0.0086	-0.1077	0.0762	0.0859	-0.0432	0.0518	-0.009	-0.008	0.0839	0.0018	0.0804	47.6562	41.7054	63.9362
20	1.331	0.2499	-0.1798	0.1358	0.3446	1.9962	0.0375	-0.088	0.03	0.0228	-0.0065	-0.0377	-0.0139	0.0844	-0.031	0.0891	-0.0029	-0.0069	0.0895	-0.0032	0.108	39.3271	45.3415	73.2791

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-2 - 131
2	X-RAY DIFFRACTION	2	A	132 - 169
3	X-RAY DIFFRACTION	3	A	170 - 190
4	X-RAY DIFFRACTION	4	A	191 - 228
5	X-RAY DIFFRACTION	5	A	229 - 250
6	X-RAY DIFFRACTION	6	B	-2 - 113
7	X-RAY DIFFRACTION	7	B	114 - 151
8	X-RAY DIFFRACTION	8	B	152 - 191
9	X-RAY DIFFRACTION	9	B	192 - 222
10	X-RAY DIFFRACTION	10	B	223 - 236
11	X-RAY DIFFRACTION	11	C	-2 - 127
12	X-RAY DIFFRACTION	12	C	128 - 146
13	X-RAY DIFFRACTION	13	C	147 - 188
14	X-RAY DIFFRACTION	14	C	189 - 234
15	X-RAY DIFFRACTION	15	C	235 - 247
16	X-RAY DIFFRACTION	16	D	-2 - 126
17	X-RAY DIFFRACTION	17	D	127 - 173
18	X-RAY DIFFRACTION	18	D	174 - 191
19	X-RAY DIFFRACTION	19	D	192 - 222
20	X-RAY DIFFRACTION	20	D	223 - 235

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+
Jul 12, 2017. Major update of PDB

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Yorodumi