PDB-4aih: Crystal structure of RovA from Yersinia in its free form

ID or keywords:

Entry

Database: PDB / ID: 4aih

Title

Crystal structure of RovA from Yersinia in its free form

Components

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: 2.4 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 9, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 12, 2012	Provider: repository / Type: Initial release
Revision 1.1	Nov 14, 2012	Group: Database references
Revision 1.2	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/4aih ftp://data.pdbj.org/pub/pdb/validation_reports/ai/4aih	HTTPS FTP

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Related structure data

Related structure data	4aijC 4aikC 3deuS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4qst-2 4qsu-2 2dvp-1 5a83-1 4qsp-2 6cgd-3 6ch4-4 3uzr-d 5a5r-1 6cey-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) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

4aijC

4aikC

3deuS

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: TRANSCRIPTIONAL REGULATOR SLYA

B: TRANSCRIPTIONAL REGULATOR SLYA

C: TRANSCRIPTIONAL REGULATOR SLYA

D: TRANSCRIPTIONAL REGULATOR SLYA

E: TRANSCRIPTIONAL REGULATOR SLYA

F: TRANSCRIPTIONAL REGULATOR SLYA

103 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: TRANSCRIPTIONAL REGULATOR SLYA

B: TRANSCRIPTIONAL REGULATOR SLYA

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

2

C: TRANSCRIPTIONAL REGULATOR SLYA

D: TRANSCRIPTIONAL REGULATOR SLYA

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

3

E: TRANSCRIPTIONAL REGULATOR SLYA

F: TRANSCRIPTIONAL REGULATOR SLYA

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

Unit cell

Length a, b, c (Å)	67.160, 74.780, 181.150
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.54547, 0.14646, 0.82524), (0.18697, -0.98106, 0.05052), (0.81701, 0.12674, -0.56252)	4.61371, 29.22113, -14.48427
2	given	(0.60592, -0.05676, 0.7935), (0.67358, 0.56729, -0.47377), (-0.42325, 0.82156, 0.38197)	9.24712, -29.38224, -10.12216
3	given	(0.10669, 0.66164, 0.74219), (-0.64947, -0.51883, 0.55589), (0.75287, -0.54134, 0.37436)	0.32769, 55.47554, -3.94481
4	given	(0.33108, -0.38757, -0.86033), (-0.33535, -0.90056, 0.27664), (-0.882, 0.19692, -0.42813)	-7.43053, 0.85526, -29.75674
5	given	(-0.55672, -0.09309, -0.82547), (0.32021, 0.89286, -0.31665), (0.7665, -0.44061, -0.46727)	-22.54861, 21.34627, -2.50879

#1: Protein	TRANSCRIPTIONAL REGULATOR SLYA / REGULATOR OF VIRULENCE PROTEIN A / TRANSCRIPTIONAL REGULATOR FOR CRYPTIC HEMOLYSIN / ROVA Mass: 17231.768 Da / Num. of mol.: 6 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) YERSINIA PSEUDOTUBERCULOSIS (bacteria) / Strain: YPIII / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: B1JJ73
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 99 / 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 ENGINEERED RESIDUE IN CHAIN C, CYS 81 TO SER ENGINEERED RESIDUE IN CHAIN C, CYS 108 TO SER ENGINEERED RESIDUE IN CHAIN D, CYS 81 TO SER ENGINEERED RESIDUE IN CHAIN D, CYS 108 TO SER ENGINEERED RESIDUE IN CHAIN E, CYS 81 TO SER ENGINEERED RESIDUE IN CHAIN E, CYS 108 TO SER ENGINEERED RESIDUE IN CHAIN F, CYS 81 TO SER ENGINEERED RESIDUE IN CHAIN F, CYS 108 TO SER

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.2 Å³/Da / Density % sol: 45 % / Description: NONE
Crystal grow	pH: 6.5 / Details: 0.1 M MES PH 6.5, 20% PEG2000MME

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
Detector	Type: ADSC QUANTUM 4 / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.933 Å / Relative weight: 1
Reflection	Resolution: 2.4→90 Å / Num. obs: 36510 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5.9 % / R_merge(I) obs: 0.01 / Net I/σ(I): 16.8
Reflection shell	Resolution: 2.4→2.46 Å / Redundancy: 6.1 % / R_merge(I) obs: 0.07 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.6.0117	refinement
XDS		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DEU

3deu

Resolution: 2.4→90.57 Å / Cor.coef. F_o:F_c: 0.942 / Cor.coef. F_o:F_c free: 0.933 / SU B: 20.138 / SU ML: 0.222 / Cross valid method: THROUGHOUT / ESU R: 0.44 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26612	1824	5 %	RANDOM
R_work	0.22024	-	-	-
obs	0.22262	34623	99.87 %	-

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: 57.224 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.21 Å²	0 Å²	0 Å²
2-	-	1.17 Å²	0 Å²
3-	-	-	-1.38 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→90.57 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6205	0	0	99	6304

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.019	6268
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.244	1.993	8472
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.906	5	772
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.79	24.672	259
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.113	15	1257
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.673	15	52
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	1050
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	4424
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.211	0.2	2859
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.296	0.2	4344
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.137	0.2	162
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	0.171	0.2	75
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.135	0.2	7
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
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: 2.4→2.462 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.319	109	-
R_work	0.252	2314	-
obs	-	-	99.96 %

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	3.2955	-1.4398	0.4706	10.52	-4.0527	6.3777	-0.1492	-0.4958	0.2799	0.314	0.4092	0.4471	-0.5838	-0.3355	-0.26	0.1365	-0.0015	0.0385	0.2613	-0.0059	0.1853	-32.4732	14.636	-20.9998
2	4.7439	-1.1426	0.5266	3.895	-0.4379	4.0069	-0.0717	-0.1044	-0.1468	0.1341	0.1117	-0.1475	0.2613	0.185	-0.04	0.1494	0.0069	-0.0203	0.1793	-0.0031	0.11	-16.1336	-0.7521	-18.7839
3	16.2955	-0.7462	2.7702	7.2446	8.721	11.3294	-0.0929	0.5884	1.0631	-0.3232	0.0477	-0.1462	-0.3913	0.2294	0.0452	0.3592	0.1085	0.1482	0.2466	-0.053	0.2403	-4.0874	-8.6911	-27.0447
4	12.3094	-5.9448	2.0215	7.3155	-1.7053	3.3424	-0.1272	-0.4306	-1.1235	0.0322	0.4046	0.7371	0.4675	-0.3246	-0.2774	0.252	-0.1027	-0.0258	0.1391	0.0812	0.1722	-25.1623	-8.0474	-16.5253
5	15.4093	6.1493	-3.0495	9.0463	-3.5953	5.6746	-0.0443	0.4137	-0.1624	-0.5174	-0.0341	0.1257	0.1572	-0.0652	0.0784	0.2768	0.1232	-0.0576	0.3269	-0.0672	0.2007	-33.1002	9.8024	-33.983
6	5.2763	3.2622	-0.7602	12.1578	-0.9339	3.1032	0.1295	0.1053	-0.3263	-0.0974	-0.1057	-0.0728	-0.0286	0.2009	-0.0238	0.182	0.0814	0.0218	0.3232	0.0214	0.1843	-24.3329	13.1518	-28.65
7	3.8855	-1.1584	-2.5785	2.208	1.049	9.1103	0.0389	-0.1824	-0.1478	-0.0085	0.0874	-0.1616	0.3712	0.1353	-0.1263	0.1878	-0.0358	0.0115	0.172	0.0509	0.2026	-23.8135	26.4435	-13.5722
8	3.6442	0.6572	1.2269	3.969	0.5714	8.2304	0.0385	-0.3821	0.3245	0.3676	0.2059	-0.4258	-0.4535	0.6718	-0.2444	0.1387	-0.023	0.0239	0.2794	-0.0143	0.1786	-17.3308	31.9881	-11.6326
9	2.6549	0.7306	0.8019	1.9761	-0.2028	0.8412	0.0049	-0.0425	0.0749	-0.046	-0.0714	0.4705	-0.0826	0.0049	0.0665	0.1715	0.0579	0.0343	0.3017	-0.0274	0.2211	-35.3396	19.2584	-28.0743
10	59.7687	-34.0932	58.2221	19.4563	-33.2071	56.7234	-4.8594	-5.9356	2.5392	2.3716	2.9057	-1.4503	-4.2702	-5.7074	1.9537	1.4178	-0.1781	-0.1761	1.3195	-0.1788	0.1232	-38.4784	5.684	-8.9167
11	4.0377	0.3085	-0.6699	3.3715	-4.64	7.6627	0.0507	-0.6398	0.211	0.3835	-0.0598	0.0992	-0.8242	-0.4635	0.0091	0.1963	0.0823	0.0356	0.3834	-0.1256	0.1476	4.0845	16.8541	-46.0189
12	7.6995	-10.3349	-9.2037	16.0753	13.4218	11.5195	-0.5673	-0.3561	-1.584	1.4617	-0.6414	0.8456	0.9804	-0.086	1.2086	0.3924	-0.369	-0.3051	0.5269	0.6783	1.0973	10.0289	-0.3962	-37.8124
13	9.6353	2.2324	2.7522	17.6733	5.5557	13.1347	-0.3658	0.4807	-0.5145	0.2702	0.3116	-0.7137	0.096	-0.1454	0.0542	0.0955	-0.1706	-0.0398	0.3576	0.0611	0.0953	15.3563	9.6814	-36.4575
14	2.9922	-0.779	-0.1063	1.2772	-0.8292	6.7564	0.1932	-0.6581	-0.3607	-0.0115	0.0519	0.1527	0.3383	-0.9004	-0.2451	0.1636	-0.1512	0.1141	0.3392	0.0581	0.2447	1.3046	7.4112	-44.3571
15	41.1531	5.1587	15.7598	16.2802	-2.204	7.1529	0.9855	1.7527	-2.7108	1.5774	-0.0992	-1.049	0.0018	0.7543	-0.8864	0.4452	0.2782	-0.2243	0.52	-0.3584	0.3878	23.0507	3.8128	-58.4977
16	13.3689	0.2348	1.268	4.3361	-0.0372	3.6499	0.2109	-0.7216	-0.192	0.7072	-0.1487	0.103	0.2933	-0.1223	-0.0621	0.396	0.0512	0.0754	0.1194	0.0128	0.1892	12.2907	9.8945	-53.4301
17	3.8115	0.8304	-0.6011	3.3331	0.9603	4.74	0.0474	0.0192	-0.0722	0.229	-0.0122	-0.2444	-0.1186	0.2207	-0.0352	0.1681	0.0314	-0.0256	0.2238	0.0652	0.1039	24.3966	27.6556	-48.0984
18	2.842	2.656	2.6764	5.8183	3.0712	7.1909	-0.113	0.2372	0.1911	0.3688	-0.1019	-0.0526	-0.3879	0.9155	0.2149	0.1871	-0.0114	0.042	0.3215	0.1294	0.1445	30.1503	29.8024	-54.3855
19	9.2859	-0.4829	-2.5957	2.4751	0.4509	2.7715	-0.0052	0.7968	0.2739	-0.4179	-0.0166	0.0397	0.2359	0.0132	0.0219	0.2063	0.0395	0.0343	0.1529	0.0382	0.1365	8.6274	13.5798	-65.8048
20	26.3736	17.6466	-20.313	33.8532	-30.6129	28.7897	-0.7841	1.7783	-0.6581	0.4444	1.8157	1.6318	-0.1392	-1.8392	-1.0317	0.1381	0.0503	0.1458	0.2576	-0.0622	0.6259	-7.0839	23.3502	-54.6315
21	2.3837	1.4516	-2.3632	3.3734	-2.6405	5.4353	0.061	0.2962	-0.0764	0.2013	0.1358	0.3568	-0.0552	-0.8045	-0.1968	0.1793	0.0512	0.0004	0.3198	0.0298	0.0833	-19.3479	6.7086	10.8161
22	4.8463	-0.1433	2.7186	3.8254	0.5125	4.7703	0.106	0.0039	-0.2392	-0.0549	-0.0709	-0.1424	0.2176	0.0383	-0.0351	0.1787	0.0339	0.0043	0.2284	0.0001	0.0476	-6.8827	4.363	-0.9775
23	19.256	-5.099	2.4963	9.9926	-3.0568	0.99	0.3216	2.0665	-0.09	-0.9764	-0.6222	-1.2608	0.272	0.288	0.3006	0.297	0.0117	0.0943	0.4208	-0.0354	0.2038	-0.9202	8.8741	-6.1133
24	4.4116	0.8661	-8.793	3.2834	-4.895	29.8094	0.6142	-0.1445	0.4147	0.7131	0.2544	0.0646	-1.7853	-0.1695	-0.8686	0.3342	0.0898	0.0189	0.1863	0.0008	0.0881	-14.9061	18.0671	7.7178
25	10.7707	-11.6892	-6.4683	22.3862	10.9003	8.6567	0.5474	0.3317	-0.3811	-0.4269	-0.3038	-0.8745	0.2187	0.6034	-0.2436	0.15	0.0452	-0.0484	0.3835	0.0203	0.1899	-9.2186	3.13	27.0145
26	11.3385	-0.3186	-2.4356	26.9321	0.2045	10.2151	-0.4018	0.3781	-0.7806	-0.761	0.6867	-0.4302	0.4239	1.0248	-0.2849	0.2864	0.1442	0.067	0.4433	0.0305	0.1331	-10.317	-3.1374	17.3144
27	6.8856	2.0798	1.1477	1.0319	0.5104	5.232	0.1651	0.5146	-0.3232	-0.4281	-0.1808	0.0429	0.8944	-0.772	0.0157	0.9863	0.135	-0.0548	0.4729	-0.1913	0.1884	-23.3014	-12.9405	7.8887
28	5.6482	1.0631	3.778	2.6325	3.4813	5.687	0.3615	0.3352	-1.2204	0.7781	-0.5726	0.6615	1.0998	-0.5081	0.2111	0.829	-0.1238	0.1692	0.2275	-0.2681	0.6487	-17.6248	-20.0273	17.7824
29	7.7521	-6.373	2.3312	10.4877	-4.8247	12.7415	0.0758	-0.227	-0.5724	0.5184	0.0684	0.3512	0.3412	0.0874	-0.1442	0.2681	-0.0993	-0.0022	0.2895	0.0318	0.1152	-18.5334	0.9605	30.6469
30	0.947	6.0151	-8.5229	38.2123	-54.1452	76.7218	-0.4331	0.5284	0.304	-1.8297	3.2546	1.8931	2.5813	-4.8295	-2.8215	0.5567	0.4057	-0.1413	1.0645	-0.0087	0.2811	-29.6004	11.7888	19.0678

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 16
2	X-RAY DIFFRACTION	2	A	17 - 77
3	X-RAY DIFFRACTION	3	A	78 - 90
4	X-RAY DIFFRACTION	4	A	91 - 115
5	X-RAY DIFFRACTION	5	A	116 - 143
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