PDB-4aik: Crystal structure of RovA from Yersinia in complex with an invasi...

ID or keywords:

Entry

Database: PDB / ID: 4aik

Title

Crystal structure of RovA from Yersinia in complex with an invasin promoter fragment

Components

ROVA PROMOTER FRAGMENT, 5'-D(*AP*TP*GP*AP*TP*AP*TP*TP *AP*TP**TP*TP*AP*TP*AP*TP*GP*AP*TP*AP*A)-3'
ROVA PROMOTER FRAGMENT, 5'-D(*TP*TP*TP*AP*TP*CP*AP*TP *AP*TP*AP*AP*AP*TP*AP*AP*TP*AP*TP*CP*A)-3'
TRANSCRIPTIONAL REGULATOR SLYA

Keywords

TRANSCRIPTION /

TRANSCRIPTION FACTOR / GLOBAL REGULATOR / VIRULENCE REGULATION / THERMOSENSING

Function / homology

Function and homology information

DNA-binding transcription repressor activity / DNA-binding transcription activator activity /

protein-DNA complex / transcription cis-regulatory region binding / positive regulation of DNA-templated transcription
Similarity search - Function

Biological species

YERSINIA PSEUDOTUBERCULOSIS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Quade, N. / Mendonca, C. / Herbst, K. / Heroven, A.K. / Heinz, D.W. / Dersch, P.

Citation

Journal: J.Biol.Chem. / Year: 2012
Title: Structural Basis for Intrinsic Thermosensing by the Master Virulence Regulator Rova of Yersinia.
Authors: Quade, N. / Mendonca, C. / Herbst, K. / Heroven, A.K. / Ritter, C. / Heinz, D.W. / Dersch, P.

History

Deposition	Feb 10, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 12, 2012	Provider: repository / Type: Initial release
Revision 1.1	Oct 31, 2012	Group: Database references
Revision 1.2	Aug 28, 2019	Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / reflns / reflns_shell Item: _exptl_crystal_grow.method / _reflns.pdbx_Rmerge_I_obs ..._exptl_crystal_grow.method / _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs / _reflns_shell.number_unique_obs
Revision 1.3	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ai/4aik ftp://data.pdbj.org/pub/pdb/validation_reports/ai/4aik	HTTPS FTP

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Related structure data

Related structure data	4aihC 4aijC 3deuS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5oy9-d 4upi-d 4h2t-d 4dq8-d 2bde-d 6uuo-d 1rlz-d 1nt2-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

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Links

PDB pages	PDBj / wwPDB / NCBI
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PDB pages

PDBj /

wwPDB /

NCBI

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Deposited unit

A: TRANSCRIPTIONAL REGULATOR SLYA

B: TRANSCRIPTIONAL REGULATOR SLYA

C: ROVA PROMOTER FRAGMENT, 5'-D(*AP*TP*GP*AP*TP*AP*TP*TP *AP*TP**TP*TP*AP*TP*AP*TP*GP*AP*TP*AP*A)-3'

D: ROVA PROMOTER FRAGMENT, 5'-D(*TP*TP*TP*AP*TP*CP*AP*TP *AP*TP*AP*AP*AP*TP*AP*AP*TP*AP*TP*CP*A)-3'

47.3 kDa, 4 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)	88.678, 88.678, 67.503
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	143
Space group name H-M	P3

Noncrystallographic symmetry (NCS)

NCS oper: (Code: given
Matrix: (-0.49888, -0.86666, -0.00313), (-0.86667, 0.49887, 0.00359), (-0.00155, 0.0045, -0.99999)
Vector: -44.35736, -25.58182, -12.70813)

#1: Protein	TRANSCRIPTIONAL REGULATOR SLYA / REGULATOR OF VIRULENCE PROTEIN A / TRANSCRIPTIONAL REGULATOR FOR CRYPTIC HEMOLYSIN / ROVA Mass: 17231.768 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) YERSINIA PSEUDOTUBERCULOSIS (bacteria) / Strain: YPIII / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: B1JJ73
#2: DNA chain	ROVA PROMOTER FRAGMENT, 5'-D(APTPGPAPTPAPTPTP APTP*TPTPAPTPAPTPGPAPTPAPA)-3' Mass: 6474.244 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) YERSINIA PSEUDOTUBERCULOSIS* (bacteria)
#3: DNA chain	ROVA PROMOTER FRAGMENT, 5'-D(TPTPTPAPTPCPAPTP APTPAPAPAPTPAPAPTPAPTPCPA)-3' Mass: 6403.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) YERSINIA PSEUDOTUBERCULOSIS* (bacteria)
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H₂O
Compound details	ENGINEERED RESIDUE IN CHAIN A, CYS 81 TO SER ENGINEERED RESIDUE IN CHAIN A, CYS 108 TO SER ...ENGINEERED RESIDUE IN CHAIN A, CYS 81 TO SER ENGINEERED RESIDUE IN CHAIN A, CYS 108 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 81 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 108 TO SER
Sequence details	GB AAK01704.1 PROTEIN, GB NC_010465.1 DNA

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.33 Å³/Da / Density % sol: 62 % / Description: NONE
Crystal grow	Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 10 MM MGCL2, 50 MM MES PH 5.6, 2.3 M LISO4

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID14-4 / Wavelength: 0.95

Detector

Type: ADSC CCD / Detector: CCD / Date: Jun 28, 2010

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.95 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.502
1	1	h,-h-k,-l	2	0.498

Reflection

Resolution: 1.85→76 Å / Num. obs: 49796 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / R_merge(I) obs: 0.034 / Net I/σ(I): 13.9

Reflection shell

Resolution: 1.85→2.1 Å / Redundancy: 2.5 % / R_merge(I) obs: 0.487 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 7414 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0109	refinement
XDS		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DEU

3deu

Resolution: 1.85→76.81 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.938 / SU B: 7.557 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23025	2504	5 %	RANDOM
R_work	0.19833	-	-	-
obs	0.19988	47218	97.97 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 50.527 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	6.61 Å²	0 Å²	0 Å²
2-	-	6.61 Å²	0 Å²
3-	-	-	-13.21 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→76.81 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2227	855	0	184	3266

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	3227
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.281	2.316	4548
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.399	5	284
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.632	24.286	98
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.523	15	456
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.733	15	22
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	543
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	2067
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.203	0.2	1498
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.293	0.2	2107
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.168	0.2	164
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	0.232	0.2	92
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.114	0.2	9
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	0.477	1.5	1408
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.808	2	2301
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.902	3	1819
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.277	4.5	2244
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.849→1.897 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.296	192	-
R_work	0.232	3439	-
obs	-	-	97.5 %

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	11.8068	1.8192	-0.8293	1.8301	-0.476	0.6963	0.0145	0.5349	-0.1524	-0.044	0.0629	0.1386	0.1066	-0.1117	-0.0774	0.0927	0.0087	0.0157	0.124	0.0096	0.3863	-16.8856	-17.2235	-11.7937
2	3.8339	-0.1974	0.3794	3.1464	-1.2436	4.5566	0.1271	-0.3769	0.0173	0.2809	-0.0625	0.1316	0.1045	-0.1672	-0.0646	0.1131	-0.0624	0.0231	0.165	-0.0178	0.4358	-2.7938	-18.3012	-0.5567
3	8.5224	-0.1675	0.0247	5.314	0.3797	4.1612	0.1222	-0.488	-0.1997	-0.0128	-0.0456	0.1776	0.5889	-0.1611	-0.0766	0.1451	-0.0465	0.0332	0.186	0.0755	0.3464	-4.2121	-26.8822	4.4978
4	-1.4199	0.6693	-2.0949	0.7687	-5.9634	18.4092	0.0493	-0.6026	0.3409	0.6505	0.1163	-0.4516	0.0781	1.1426	-0.1656	0.5896	0.0424	-0.0611	0.6192	-0.0967	0.4409	3.9934	-23.5398	14.3128
5	4.2004	6.761	-9.5248	8.6739	-13.7459	28.0726	-0.4485	-0.5087	0.2707	0.6573	0.3107	-0.4704	0.1457	-0.1737	0.1378	0.3457	0.0637	-0.1037	0.3756	-0.1036	0.3888	4.1208	-20.4875	11.4154
6	12.9398	-4.0428	5.5028	2.7043	-2.1441	4.8207	0.0915	0.0903	0.305	-0.0888	-0.0499	0.0205	-0.0143	-0.065	-0.0416	0.0858	-0.0172	0.0391	0.0532	-0.0244	0.4361	-3.532	-8.6328	-6.6362
7	3.3716	1.2538	-0.3723	7.8946	-4.1527	11.0536	-0.0848	0.2346	0.1253	-0.2184	0.1438	0.0339	0.2475	-0.2094	-0.059	0.1061	-0.0473	-0.0092	0.1343	-0.0265	0.4255	-22.1014	-2.2299	-6.3503
8	7.2536	1.3786	-0.0073	10.5138	1.3632	5.5988	0.2059	-0.5655	-0.2106	1.6642	-0.2773	-0.0069	-0.0001	-0.1015	0.0714	0.2622	-0.0535	0.0101	0.0821	-0.0125	0.3895	-26.9844	-16.0325	4.894
9	7.5625	7.8527	-0.2874	11.9018	-1.0691	0.0203	0.4777	-0.3426	-0.0525	0.6483	-0.4174	-0.3271	-0.0891	0.1489	-0.0603	0.1194	-0.047	0.0477	0.1168	-0.032	0.3972	-20.6356	-19.4272	-0.819
10	1.7521	0.5714	-0.711	3.9214	-0.7611	5.4987	0.0494	-0.0425	-0.2253	0.2756	0.0938	-0.0399	0.3	0.2948	-0.1432	0.0681	-0.0171	-0.021	0.1333	0.0177	0.3817	-26.6645	-34.557	-5.2089
11	8.9156	0.1002	6.4559	1.753	-1.629	4.9434	0.1013	1.0947	0.0922	-0.6359	-0.2545	0.346	-0.1097	0.0857	0.1532	0.6109	0.0043	-0.0538	0.1894	0.0681	0.3854	-27.4253	-29.8724	-21.313
12	6.7224	1.4416	-0.3275	5.8919	-0.1627	3.9843	-0.2396	0.1227	0.0423	-0.1811	0.3584	-0.2015	-0.0519	0.6226	-0.1188	0.0872	-0.0329	0.0762	0.1218	-0.0346	0.2623	-19.0431	-35.5298	-17.0902
13	2.9781	-1.4688	-0.0063	3.031	0.2171	2.7403	-0.1619	0.86	-0.088	-0.8542	0.0423	0.1929	0.1401	-0.1331	0.1196	0.3701	-0.2579	0.0045	0.2899	0.004	0.4248	-29.781	-37.4472	-20.4625
14	-1.1207	-0.2467	-2.6878	4.9208	4.8714	9.5959	0.0222	-0.2893	-0.0151	0.4805	-0.2994	0.5022	-0.1266	-0.1011	0.2772	0.0997	-0.0234	0.0225	0.1573	0.0197	0.5265	-34.91	-19.1794	-3.0272
15	5.3116	-0.7922	-1.1727	2.321	0.278	1.2517	0.1406	0.3074	-0.0287	-0.1644	-0.1526	-0.0401	0.0474	0.0737	0.0121	0.0772	-0.0072	-0.0351	0.1311	0.0087	0.3776	-25.4851	-8.4294	-11.4495
16	9.104	5.4297	5.1457	0.314	1.2808	19.4452	-0.1606	0.7349	-0.161	-0.9661	-0.0146	-0.2211	-0.4075	1.0511	0.1752	0.463	0.2999	0.2174	0.542	0.1063	0.5335	-9.63	-10.2715	-21.5592
17	7.6218	2.2824	1.6833	15.9208	4.3477	3.498	0.1059	0.1503	1.2426	1.0806	0.485	-0.7292	0.2972	0.2656	-0.5909	0.2727	-0.0131	-0.01	0.4249	-0.0273	0.2646	-4.7351	-34.7553	49.8968
18	1.8067	-3.4569	1.2768	11.0001	4.1552	7.207	-0.3846	-0.4092	-2.2562	-0.2041	0.5652	-0.1613	0.6923	-0.1778	-0.1806	0.4687	-0.0348	0.2187	0.4299	-0.0868	0.8691	-9.2593	-40.9087	35.0218
19	15.9556	7.7349	-2.3397	5.434	-2.2788	0.1507	0.3812	0.0059	1.3011	0.202	0.0983	0.8552	0.2367	-0.2991	-0.4794	0.493	-0.058	0.1613	0.6228	0.0683	0.1944	-12.0989	-31.9181	22.5154
20	11.5395	-6.1677	-5.1412	10.9411	-0.3917	3.4836	0.4157	0.5743	-1.0948	0.1036	-0.5114	-0.4064	1.02	-0.1074	0.0957	0.555	-0.0213	-0.1946	0.4713	0.0444	0.2723	-3.5613	-36.4671	9.9441
21	-0.8401	3.4858	-5.3686	-0.1732	6.3317	-1.3146	-0.2432	0.4599	-1.1697	-0.6446	0.6872	0.0658	-0.7971	-0.3582	-0.444	0.5664	-0.0792	-0.0502	0.6459	-0.0753	0.5212	-9.6085	-43.0432	-2.7938
22	12.426	-5.1179	-14.995	10.9551	13.7955	21.084	-0.2441	0.9154	0.3574	-0.9265	0.9734	-0.601	-0.3826	0.3677	-0.7293	0.5278	0.0521	0.0994	0.4916	0.1175	0.2469	-3.3982	-36.36	-6.6292
23	11.984	-0.6237	0.6199	-0.5901	2.6569	3.6134	0.3733	-0.6351	0.0017	0.1099	-0.3712	0.4999	0.3976	-1.403	-0.002	0.3661	-0.0922	0.0794	0.3265	0.1809	0.5964	-12.4596	-38.9692	6.3689
24	-1.0252	-0.982	-0.3011	16.2525	-3.3695	5.95	0.4216	-1.4618	-0.7116	0.9901	-0.0638	-1.4784	0.667	0.0273	-0.3578	0.4008	-0.2192	-0.0877	0.7596	0.3608	0.4013	-4.4299	-37.7275	19.8355
25	9.2627	2.7751	-4.6156	7.5581	-3.7332	8.5932	0.0551	0.6017	1.0122	-0.2651	0.1691	0.2463	-0.3605	0.293	-0.2242	0.4624	-0.0855	0.1097	0.498	0.0908	0.1319	-11.5005	-32.1299	33.5891
26	10.2431	2.6681	-4.1265	8.0349	-2.1716	-0.2241	-0.4589	-0.257	-1.3392	0.7535	0.3317	-0.5677	0.3473	0.2769	0.1272	0.3895	0.0281	-0.0495	0.4213	-0.0625	0.3709	-7.7514	-42.3311	47.5588

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 22
2	X-RAY DIFFRACTION	2	A	23 - 49
3	X-RAY DIFFRACTION	3	A	50 - 73
4	X-RAY DIFFRACTION	4	A	74 - 84
5	X-RAY DIFFRACTION	5	A	85 - 97
6	X-RAY DIFFRACTION	6	A	98 - 115
7	X-RAY DIFFRACTION	7	A	116 - 129
8	X-RAY DIFFRACTION	8	A	130 - 141
9	X-RAY DIFFRACTION	9	B	2 - 22
10	X-RAY DIFFRACTION	10	B	23 - 37
11	X-RAY DIFFRACTION	11	B	38 - 49
12	X-RAY DIFFRACTION	12	B	50 - 74
13	X-RAY DIFFRACTION	13	B	75 - 108
14	X-RAY DIFFRACTION	14	B	109 - 116
15	X-RAY DIFFRACTION	15	B	117 - 138
16	X-RAY DIFFRACTION	16	B	139 - 143
17	X-RAY DIFFRACTION	17	C	1 - 5
18	X-RAY DIFFRACTION	18	C	6 - 9
19	X-RAY DIFFRACTION	19	C	10 - 13
20	X-RAY DIFFRACTION	20	C	14 - 17
21	X-RAY DIFFRACTION	21	C	18 - 21
22	X-RAY DIFFRACTION	22	D	1 - 4
23	X-RAY DIFFRACTION	23	D	5 - 8
24	X-RAY DIFFRACTION	24	D	9 - 12
25	X-RAY DIFFRACTION	25	D	13 - 17
26	X-RAY DIFFRACTION	26	D	18 - 21

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