PDB-4aij: Crystal structure of RovA from Yersinia in complex with a rovA pr...

ID or keywords:

Entry

Database: PDB / ID: 4aij

Title

Crystal structure of RovA from Yersinia in complex with a rovA promoter fragment

Components

ROVA PROMOTER FRAGMENT, 5'-D(*AP*AP*TP*TP*AP*TP*AP*TP *TP*AP*TP*TP*TP*GP*AP*AP*TP*TP*AP*AP*T)-3'
ROVA PROMOTER FRAGMENT, 5'-D(*TP*AP*TP*TP*AP*AP*TP*TP *CP*AP*AP*AP*TP*AP*AP*TP*AP*TP*AP*AP*T)-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 / response to stress / 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: 2.05 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	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

Summary document	4aij_validation.pdf.gz	425.1 KB	Display	wwPDB validaton report
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Data in XML	4aij_validation.xml.gz	9.1 KB	Display
Data in CIF	4aij_validation.cif.gz	13.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ai/4aij ftp://data.pdbj.org/pub/pdb/validation_reports/ai/4aij	HTTPS FTP

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Related structure data

Related structure data	4aihC 4aikC 3deuS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3zpl-1 1fn7-d 6m2t-1 1hzu-d 3zpl-2 4rlf-2 6bi8-1 6mon-2 5xwk-d 5ex3-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*AP*TP*TP*AP*TP*AP*TP *TP*AP*TP*TP*TP*GP*AP*AP*TP*TP*AP*AP*T)-3'

D: ROVA PROMOTER FRAGMENT, 5'-D(*TP*AP*TP*TP*AP*AP*TP*TP *CP*AP*AP*AP*TP*AP*AP*TP*AP*TP*AP*AP*T)-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)	88.779, 88.779, 67.729
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: (0.99997, -0.00456, -0.00695), (-0.00462, -0.99995, -0.00866), (-0.00691, 0.00869, -0.99994)
Vector: -0.07246, -51.19507, -2.99423)

#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 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: B1JJ73
#2: DNA chain	ROVA PROMOTER FRAGMENT, 5'-D(APAPTPTPAPTPAPTP TPAPTPTPTPGPAPAPTPTPAPAPT)-3' Mass: 6449.231 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) YERSINIA PSEUDOTUBERCULOSIS* (bacteria)
#3: DNA chain	ROVA PROMOTER FRAGMENT, 5'-D(TPAPTPTPAPAPTPTP CPAPAPAPTPAPAPTPAPTPAPAPT)-3' Mass: 6427.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) YERSINIA PSEUDOTUBERCULOSIS* (bacteria)
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 76 / 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	CROSS-REFERENCE FOR DNA SEQUENCE IS NC_010465.1

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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	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	K,H,-L	2	0.498

Reflection

Resolution: 2.1→37 Å / Num. obs: 39678 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 5.3 % / R_merge(I) obs: 0.01 / Net I/σ(I): 15.3

Reflection shell

Resolution: 2.1→2.2 Å / Redundancy: 2.5 % / R_merge(I) obs: 0.05 / Mean I/σ(I) obs: 2 / % possible all: 89

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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: 2.05→76.9 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.933 / SU B: 13.561 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25132	1905	5.1 %	RANDOM
R_work	0.20303	-	-	-
obs	0.20562	35093	98.56 %	-

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: 65.609 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	5.54 Å²	0 Å²	0 Å²
2-	-	5.54 Å²	0 Å²
3-	-	-	-11.09 Å²

Refinement step

Cycle: LAST / Resolution: 2.05→76.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2227	855	0	76	3158

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	3209
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.664	2.317	4518
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.649	5	279
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	42.665	24.227	97
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.948	15	451
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.509	15	22
X-RAY DIFFRACTION	r_chiral_restr	0.097	0.2	538
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	2051
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.242	0.2	1442
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.301	0.2	2050
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.21	0.2	132
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	0.229	0.2	68
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.177	0.2	5
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	0.717	1.5	1399
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.181	2	2281
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.272	3	1810
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.662	4.5	2237
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: 2.049→2.102 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.264	117	-
R_work	0.231	2490	-
obs	-	-	93.51 %

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	2.8729	-2.3751	0.9066	18.7085	0.2988	1.6447	-0.1377	-0.0804	0.1209	0.3735	0.2078	-0.0983	0.0158	0.016	-0.0701	0.2493	0.032	0.0542	0.266	0.031	0.6632	4.67	-23.9812	3.5245
2	3.7772	-0.6332	-0.5962	3.8106	-1.1203	6.422	-0.036	0.1483	0.0371	-0.3365	0.1849	0.1035	0.038	0.0977	-0.1489	0.3151	-0.0313	-0.0335	0.2218	0.0068	0.719	13.9422	-39.2403	-5.0666
3	10.6348	-0.8074	1.6292	10.7212	0.6801	2.4045	0.1135	0.4313	0.3007	-0.3949	-0.1901	0.1188	-0.4018	0.9495	0.0766	0.2752	-0.0716	0.1068	0.3277	0.0503	0.5035	21.1721	-33.9816	-12.9043
4	0.2805	-1.4634	-3.1694	7.0788	-13.1462	35.5081	0.5658	1.4566	-0.5686	-1.6731	-0.0988	0.343	0.3248	1.6573	-0.467	0.6413	0.1746	0.17	0.9988	-0.0586	0.6946	22.1888	-43.5277	-20.7795
5	6.3955	-0.8301	1.8	1.4749	-6.1271	18.5724	0.2327	1.1967	-0.3438	-0.6043	-0.6132	-0.1132	-0.1798	0.7352	0.3805	0.7469	0.1205	0.0868	0.1732	-0.0204	0.7398	19.0807	-45.466	-17.6291
6	3.9991	-2.1022	-1.888	1.6672	1.7331	4.5079	-0.0169	-0.2039	-0.1994	-0.0317	-0.0216	0.2914	0.1093	0.1152	0.0385	0.2971	-0.0309	0.0169	0.2279	0.0216	0.7574	4.3065	-42.8913	-0.5139
7	7.7295	2.9117	-1.5961	5.2149	-1.9484	3.4982	-0.0693	0.5225	0.3777	0.1005	0.3112	0.1199	-0.3156	0.0294	-0.2419	0.3474	-0.0132	-0.0265	0.1825	-0.0477	0.657	-4.0504	-24.7017	-7.846
8	0.3998	1.7035	-0.8761	16.7948	-3.4154	0.7563	-0.2787	0.2917	-0.1167	-0.5325	0.4308	0.1669	0.1503	0.0592	-0.1521	0.2385	-0.0055	-0.0418	0.2709	0.015	0.6897	5.4748	-25.8245	-6.874
9	1.8109	1.0341	2.5271	3.7641	0.4589	7.9024	0.04	0.2205	0.0396	0.0624	0.0582	-0.0511	-0.1301	0.1456	-0.0982	0.2654	-0.0177	0.0162	0.1944	0.0168	0.7206	15.3826	-10.9007	-1.6089
10	9.4041	-3.7712	-4.0033	5.6712	-0.0597	2.7263	-0.2732	-1.4807	-0.6919	0.892	0.2018	0.4666	0.3528	-0.4612	0.0714	0.4126	-0.1054	0.0079	0.3697	0.0701	0.5861	13.491	-17.0857	13.5998
11	9.3307	1.9833	-3.1381	9.4348	-1.3667	5.8188	-0.1284	-0.0028	-0.1824	-0.2616	-0.0608	-0.7005	0.4017	0.2411	0.1892	0.2573	0.044	-0.0951	0.2629	0.0403	0.5555	24.7294	-15.8302	8.6254
12	1.9087	-2.5757	5.6766	2.0707	-8.5624	10.2327	-0.5653	-0.4577	0.5457	0.9566	0.2166	-0.3037	-0.3066	0.0265	0.3487	0.8596	-0.0679	0.0301	0.6334	0.035	0.5913	22.1279	-9.7717	19.6917
13	3.1533	2.0567	-0.6906	5.621	1.3743	1.9745	0.0168	-0.4495	0.1548	0.2341	-0.0317	0.0691	-0.2539	0.1088	0.0149	0.2655	0.0063	0.0396	0.2799	0.0184	0.8012	10.9582	-5.0975	3.4255
14	4.1824	-1.2149	1.0924	4.8449	-1.5711	2.7487	-0.0817	-0.3997	0.0685	0.215	0.0544	-0.0145	0.1065	0.3185	0.0273	0.3033	0.056	0.0224	0.2607	-0.0386	0.6575	-3.2845	-26.1995	4.5241
15	12.2142	-0.915	-1.6711	20.1951	-3.8009	0.3863	0.4366	-0.4552	-0.1799	-0.6426	0.0277	0.0078	0.1262	-0.1382	-0.4644	0.6837	-0.0386	0.0074	0.769	0.1671	0.3666	26.0125	-28.4474	-22.7697
16	-0.113	-3.7454	3.4452	16.8944	10.1172	8.3064	-0.0608	0.1326	0.8933	-0.6771	0.4916	-1.3148	-0.5518	0.4515	-0.4308	0.4416	-0.0683	-0.1027	0.6884	0.2703	0.6203	30.9675	-21.6616	-4.4999
17	4.6278	3.7006	3.4147	12.5687	3.1216	11.6724	0.4454	0.3548	-1.0098	0.4491	0.4245	-0.1514	0.6708	1.2443	-0.8699	0.5461	0.0676	-0.0109	0.6723	0.0209	0.3558	29.1846	-29.5956	12.6804
18	22.183	3.6549	-9.1079	7.1763	2.6356	14.1754	-0.33	-0.2634	2.2201	0.8057	1.1493	-1.2376	0.7248	1.21	-0.8193	0.895	0.036	-0.0829	0.9025	-0.0192	0.6323	28.2488	-21.1091	27.5876
19	21.9387	-3.2956	1.9494	41.2594	-13.1843	4.5977	0.5023	0.6175	-1.3924	0.7483	-0.1324	2.5564	-0.0313	0.0607	-0.3699	0.9772	0.0625	0.0265	0.8638	0.0263	0.4329	22.3362	-27.9682	28.4957
20	16.4413	-5.3809	-5.4073	10.2435	0.601	0.82	-0.201	-0.4095	0.4526	0.8342	0.5494	-1.5958	-0.056	0.1561	-0.3484	0.5156	0.0011	-0.2304	0.7579	-0.0602	0.4921	31.0565	-22.4875	13.3222
21	0.4442	-0.01	-1.6817	12.5905	1.1327	-0.6452	0.0987	0.7005	-1.4062	-0.4676	-0.5108	0.1724	0.3544	-0.403	0.4121	0.4812	0.048	-0.1826	0.9618	-0.2152	0.7354	29.7816	-29.9639	-1.1669
22	8.2397	-0.7272	0.331	15.5578	1.6461	4.6958	0.5809	0.6776	1.1054	-1.0961	0.3649	-0.3907	-1.0587	0.3644	-0.9458	0.7858	-0.1305	0.0557	0.711	0.1501	0.513	29.1829	-23.5761	-19.4271

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 16
2	X-RAY DIFFRACTION	2	A	17 - 49
3	X-RAY DIFFRACTION	3	A	50 - 72
4	X-RAY DIFFRACTION	4	A	73 - 84
5	X-RAY DIFFRACTION	5	A	85 - 99
6	X-RAY DIFFRACTION	6	A	100 - 116
7	X-RAY DIFFRACTION	7	A	117 - 141
8	X-RAY DIFFRACTION	8	B	2 - 20
9	X-RAY DIFFRACTION	9	B	21 - 41
10	X-RAY DIFFRACTION	10	B	42 - 58
11	X-RAY DIFFRACTION	11	B	59 - 72
12	X-RAY DIFFRACTION	12	B	73 - 88
13	X-RAY DIFFRACTION	13	B	89 - 113
14	X-RAY DIFFRACTION	14	B	114 - 143
15	X-RAY DIFFRACTION	15	C	1 - 7
16	X-RAY DIFFRACTION	16	C	8 - 12
17	X-RAY DIFFRACTION	17	C	13 - 17
18	X-RAY DIFFRACTION	18	C	18 - 21
19	X-RAY DIFFRACTION	19	D	1 - 5
20	X-RAY DIFFRACTION	20	D	6 - 10
21	X-RAY DIFFRACTION	21	D	11 - 14
22	X-RAY DIFFRACTION	22	D	15 - 21

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