PDB-2jj7: Crystal structure of the HlyIIR mutant protein with residues 170-...

ID or keywords:

Entry

Database: PDB / ID: 2jj7

Title

Crystal structure of the HlyIIR mutant protein with residues 170-185 substituted by alanine

Components

HEMOLYSIN II REGULATORY PROTEIN

Keywords

TRANSCRIPTION / DNA-BINDING PROTEIN / TRANSCRIPTION REGULATION / DNA-BINDING / TETR FAMILY / TRANSCRIPTIONAL REGULATOR

Function / homology

Function and homology information

DNA binding / identical protein binding
Similarity search - Function

Biological species

BACILLUS CEREUS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Kovalevskiy, O.V. / Antson, A.A. / Solonin, A.S.

Citation

Journal: Mol.Biol.(Moscow) / Year: 2009
Title: [Contraction of the disordered loop located within C-terminal domain of the transcriptional regulator HlyIIR causes its structural rearrangement].
Authors: Kovalevskii, O.V. / Antson, A.A. / Solonin, A.S.

History

Deposition	Mar 18, 2008	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 8, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Dec 28, 2011	Group: Other
Revision 1.3	Oct 9, 2019	Group: Data collection / Database references / Other / Category: citation / pdbx_database_status Item: _citation.page_last / _citation.title / _pdbx_database_status.status_code_sf
Revision 1.4	Dec 13, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2jj7.cif.gz	90 KB	Display	PDBx/mmCIF format
PDB format	pdb2jj7.ent.gz	70.1 KB	Display	PDB format
PDBx/mmJSON format	2jj7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2jj7_validation.pdf.gz	437.4 KB	Display	wwPDB validaton report
Full document	2jj7_full_validation.pdf.gz	440 KB	Display
Data in XML	2jj7_validation.xml.gz	16.3 KB	Display
Data in CIF	2jj7_validation.cif.gz	23.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jj/2jj7 ftp://data.pdbj.org/pub/pdb/validation_reports/jj/2jj7	HTTPS FTP

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Related structure data

Related structure data	2fx0S S: Starting model for refinement
Similar structure data	6e0k-d 3qdq-d 1w1w-1 1x3z-d 1w1w-4 5lgb-d 6ncr-2 4rs1-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

Deposited unit

A: HEMOLYSIN II REGULATORY PROTEIN

B: HEMOLYSIN II REGULATORY PROTEIN

43.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	66.831, 120.414, 55.178
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	HEMOLYSIN II REGULATORY PROTEIN / HLYIIRDA / HEMOLYSIN II REGULATORY PROTEIN MUTANT Mass: 21610.795 Da / Num. of mol.: 2 / Fragment: RESIDUES 4-169,186-201 Source method: isolated from a genetically manipulated source Details: RESIDUES 170-185 SUBSTITUTED BY ALANINE / Source: (gene. exp.) BACILLUS CEREUS (bacteria) / Strain: B771 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: Q7X506
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	SEGMENT OF 15 AMINO ACIDS 170-185 IS DELETED AND SUBSTITUTED WITH SINGLE ALANINE RESIDUE.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.3 Å³/Da / Density % sol: 47 % / Description: NONE
Crystal grow	pH: 7.5 / Details: TRIS, AMMONIUM SULFATE, PEG3350, pH 7.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
Detector	Type: ADSC CCD / Detector: CCD / Date: Jan 30, 2008
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.934 Å / Relative weight: 1
Reflection	Resolution: 2.1→25 Å / Num. obs: 26373 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / B_iso Wilson estimate: 34 Å² / R_merge(I) obs: 0.07 / Net I/σ(I): 15
Reflection shell	Resolution: 2.1→2.18 Å / Redundancy: 3.2 % / R_merge(I) obs: 0.5 / Mean I/σ(I) obs: 1.8 / % possible all: 86.1

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Processing

Software

Name	Version	Classification
REFMAC	5.4.0065	refinement
DENZO		data reduction
SCALEPACK		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FX0

2fx0

Resolution: 2.1→25 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.932 / SU B: 10.017 / SU ML: 0.132 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.237	1062	4.1 %	RANDOM
R_work	0.179	-	-	-
obs	0.181	25102	98 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 39.83 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.51 Å²	0 Å²	0 Å²
2-	-	-1.14 Å²	0 Å²
3-	-	-	-0.37 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2953	0	0	195	3148

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	3051
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.101	1.953	4108
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.858	5	365
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.355	24.768	151
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.425	15	573
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.615	15	11
X-RAY DIFFRACTION	r_chiral_restr	0.086	0.2	441
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	2290
X-RAY DIFFRACTION	r_gen_planes_other
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	1.109	3	1804
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.892	4	2917
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	4.387	8	1247
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	6.68	12	1188
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: 2.1→2.15 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.321	69
R_work	0.238	1622

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	4.7388	5.0404	0.7957	12.2883	-0.2722	3.4221	-0.0224	-0.0804	0.3089	-0.1372	0.1405	0.4393	-0.1635	-0.195	-0.1182	-0.0646	-0.0117	0.0048	-0.0055	0.048	-0.0919	-2.437	37.063	-18.183
2	2.8965	-6.171	-1.8482	19.8394	-1.795	6.0897	0.3783	0.7105	-0.9682	-0.9608	-0.1994	-0.8585	0.5359	0.3301	-0.1789	0.067	0.0453	0.0203	0.0152	-0.0232	0.0664	3.189	26.461	-22.457
3	8.6074	3.0879	1.1455	8.3964	-5.5334	5.0005	0.0581	0.3976	0.3329	-0.3227	-0.0124	-0.0103	0.2648	-0.0845	-0.0457	-0.0488	0.001	0.0376	-0.0426	0.012	-0.0849	4.108	38.428	-22.123
4	3.2095	1.0408	-2.1082	3.3974	-0.0073	7.3446	-0.0098	-0.0131	0.1675	0.2433	0.0089	-0.1931	-0.0984	0.414	0.0009	-0.0801	-0.0366	-0.0228	-0.1206	0.0143	-0.0532	-0.156	30.173	-7.905
5	2.0557	1.3778	-0.12	3.4873	-2.7322	2.7497	0.177	-0.0072	0.2068	0.6454	0.0395	0.1848	-0.6556	-0.1129	-0.2166	0.0182	0.0239	0.0505	-0.1705	-0.0072	-0.0904	-12.947	22.266	-1.402
6	7.4452	-3.5002	-6.0381	5.6468	-0.274	7.7826	0.0129	-0.1147	-0.1723	0.4769	-0.0658	-0.9509	0.1445	0.5066	0.0529	-0.0896	-0.0187	-0.0621	-0.1333	0.0074	0.0665	1.457	22.76	-5.865
7	6.4174	3.7637	-4.1479	4.9375	-2.994	4.2844	-0.02	-0.2348	-0.2405	0.3075	-0.0486	-0.111	-0.0819	0.1055	0.0686	-0.0719	0.033	-0.0026	-0.1723	0.0179	-0.1425	-14.419	12.381	4.806
8	3.0409	1.4088	-0.2478	10.582	-3.9753	7.2009	-0.1206	0.1674	0.0248	-0.0548	0.2346	0.1655	-0.0126	-0.0312	-0.114	-0.132	-0.0161	0.0202	-0.0782	-0.0232	-0.1108	-15.463	12.829	-7.684
9	52.4656	0.1327	-2.6228	0.0003	-0.0066	0.1311	0.9334	-0.4556	1.974	-0.9129	-1.2294	0.9363	-1.1766	-1.3989	0.296	0.2825	0.0816	0.1758	0.2294	0.1692	0.3979	-25.625	23.201	-9.118
10	9.8834	1.4976	-1.441	15.2255	-6.9742	15.9404	0.0713	0.3916	-0.09	-0.475	0.7039	1.0947	0.4056	-1.2286	-0.7752	-0.0665	0.0634	0.0337	0.1435	0.0924	0.0112	-26.143	13.534	-0.574
11	15.1618	2.0674	-5.6465	18.8263	-5.0609	14.6192	-0.1553	0.2766	0.3749	-0.6698	0.3111	1.2636	0.3083	-0.8235	-0.1558	0.0427	0.0147	-0.1065	-0.0357	-0.028	0.0409	-32.487	-25.951	-6.09
12	3.3835	3.8103	0.0803	11.5016	0.1098	3.4079	0.1473	-0.1591	0.0803	0.4773	-0.1002	0.2463	-0.372	-0.0161	-0.0471	0.0584	0.006	-0.0074	-0.1057	0.07	-0.0729	-20.794	-11.146	-2.8
13	28.0342	1.8719	-0.4564	14.6759	-4.6427	5.374	0.4631	-0.4899	0.4243	1.1278	-0.3019	0.0476	-0.2773	0.274	-0.1612	0.1421	-0.076	-0.0091	-0.1348	0.0175	-0.0892	-22.011	-15.384	3.468
14	2.4064	4.2095	-2.132	9.9109	-4.8283	2.3629	-0.0328	-0.2556	-0.2986	-0.0342	-0.26	-0.9794	0.1603	0.1642	0.2928	0.0991	-0.009	-0.0698	-0.1093	0.0384	0.1273	-17.855	-19.029	-5.733
15	0.0101	0.2739	-0.0665	7.4372	-1.2666	15.2683	-0.1228	0.144	-0.1757	-0.5843	0.0706	-0.0536	0.6689	-0.2027	0.0522	0.0521	-0.0577	-0.0106	-0.0717	0.0078	-0.0135	-21.568	-4.904	-24.986
16	1.6907	0.0974	0.8625	4.2695	-3.0253	4.8677	-0.1222	0.0867	0.0199	-0.1537	0.2074	0.2918	0.0996	-0.3102	-0.0851	-0.1586	-0.0218	-0.042	-0.1962	0.0139	-0.0856	-23.284	3.67	-21.604
17	9.9036	1.4346	1.4834	10.8304	-0.536	1.4873	0.0731	0.0351	-0.188	0.267	0.1445	-0.9853	0.2134	0.5811	-0.2176	-0.111	0.0639	-0.0081	-0.0989	0.0421	-0.0172	-9.244	-4.913	-13.525
18	2.7822	1.5962	-0.3182	4.561	-0.6601	3.9316	-0.2012	0.1633	0.1014	-0.2107	0.1539	-0.1441	-0.2174	0.4327	0.0473	-0.128	-0.0309	-0.0292	-0.0825	0.0233	-0.1435	-12.786	9.082	-24.985
19	3.8956	-1.015	2.9407	2.7778	1.1622	3.6995	0.0906	-0.3199	-0.0042	0.208	-0.0746	0.6484	-0.1412	-0.6688	-0.0161	-0.0675	0.0211	0.0352	-0.0583	0.0243	-0.0083	-23.624	9.66	-12.156
20	9.089	9.1744	-5.3465	13.7803	-7.0246	14.6064	-0.0148	-0.099	0.8337	0.3444	0.114	0.5179	-1.1626	0.1779	-0.0993	0.0124	0.0289	-0.1063	-0.1117	0.0113	0.0017	-21.618	18.537	-22.993

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 24
2	X-RAY DIFFRACTION	2	A	25 - 31
3	X-RAY DIFFRACTION	3	A	32 - 48
4	X-RAY DIFFRACTION	4	A	49 - 69
5	X-RAY DIFFRACTION	5	A	70 - 111
6	X-RAY DIFFRACTION	6	A	112 - 122
7	X-RAY DIFFRACTION	7	A	123 - 144
8	X-RAY DIFFRACTION	8	A	145 - 162
9	X-RAY DIFFRACTION	9	A	163 - 171
10	X-RAY DIFFRACTION	10	A	172 - 183
11	X-RAY DIFFRACTION	11	B	1 - 7
12	X-RAY DIFFRACTION	12	B	8 - 29
13	X-RAY DIFFRACTION	13	B	30 - 38
14	X-RAY DIFFRACTION	14	B	39 - 59
15	X-RAY DIFFRACTION	15	B	60 - 74
16	X-RAY DIFFRACTION	16	B	75 - 104
17	X-RAY DIFFRACTION	17	B	105 - 120
18	X-RAY DIFFRACTION	18	B	121 - 152
19	X-RAY DIFFRACTION	19	B	153 - 172
20	X-RAY DIFFRACTION	20	B	173 - 183

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