PDB-5itm: The structure of truncated histone-like protein

ID or keywords:

Entry

Database: PDB / ID: 5itm

Title

The structure of truncated histone-like protein

Components

AbrB family transcriptional regulator

Keywords

DNA BINDING PROTEIN / Histone-like protein / Complex / DNA-binding fold

Function / homology

Function and homology information

Biological species

Sulfolobus solfataricus (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.4 Å

Authors

Lin, B.L. / Chen, C.Y. / Huang, C.H. / Ko, T.P. / Chiang, C.H. / Lin, K.F. / Chang, Y.C. / Lin, P.Y. / Tsai, H.H.G. / Wang, A.H.J.

Citation

Journal: PLoS ONE / Year: 2017
Title: The Arginine Pairs and C-Termini of the Sso7c4 from Sulfolobus solfataricus Participate in Binding and Bending DNA.
Authors: Lin, B.L. / Chen, C.Y. / Huang, C.H. / Ko, T.P. / Chiang, C.H. / Lin, K.F. / Chang, Y.C. / Lin, P.Y. / Tsai, H.H.G. / Wang, A.H.J.

History

Deposition	Mar 17, 2016	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Jan 25, 2017	Provider: repository / Type: Initial release
Revision 1.1	Mar 20, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5itm.cif.gz	134.6 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	5itm.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5itm_validation.pdf.gz	453.5 KB	Display	wwPDB validaton report
Full document	5itm_full_validation.pdf.gz	458.6 KB	Display
Data in XML	5itm_validation.xml.gz	16.5 KB	Display
Data in CIF	5itm_validation.cif.gz	24.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/it/5itm ftp://data.pdbj.org/pub/pdb/validation_reports/it/5itm	HTTPS FTP

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Related structure data

Related structure data	5itjC C: citing same article (ref.)
Similar structure data	6mba-d 1y51-d 1j7k-d 3gge-d 3qby-d 3t0f-1 4ety-6 3qf3-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

5itjC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: AbrB family transcriptional regulator

B: AbrB family transcriptional regulator

C: AbrB family transcriptional regulator

D: AbrB family transcriptional regulator

E: AbrB family transcriptional regulator

F: AbrB family transcriptional regulator

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

1

Idetical with deposited unit
defined by author

2

A: AbrB family transcriptional regulator

B: AbrB family transcriptional regulator

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

3

C: AbrB family transcriptional regulator

D: AbrB family transcriptional regulator

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

4

E: AbrB family transcriptional regulator

F: AbrB family transcriptional regulator

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

Unit cell

Length a, b, c (Å)	49.333, 49.333, 82.466
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	144
Space group name H-M	P3₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ALA	ALA	LEU	LEU	A	A	2 - 48	2 - 48
2	1	ALA	ALA	LEU	LEU	B	B	2 - 48	2 - 48
1	2	ALA	ALA	LEU	LEU	A	A	2 - 48	2 - 48
2	2	ALA	ALA	LEU	LEU	C	C	2 - 48	2 - 48
1	3	ALA	ALA	LEU	LEU	A	A	2 - 48	2 - 48
2	3	ALA	ALA	LEU	LEU	D	D	2 - 48	2 - 48
1	4	ALA	ALA	ILE	ILE	A	A	2 - 46	2 - 46
2	4	ALA	ALA	ILE	ILE	E	E	2 - 46	2 - 46
1	5	VAL	VAL	GLN	GLN	A	A	3 - 47	3 - 47
2	5	VAL	VAL	GLN	GLN	F	F	3 - 47	3 - 47
1	6	ALA	ALA	LEU	LEU	B	B	2 - 48	2 - 48
2	6	ALA	ALA	LEU	LEU	C	C	2 - 48	2 - 48
1	7	ALA	ALA	LEU	LEU	B	B	2 - 48	2 - 48
2	7	ALA	ALA	LEU	LEU	D	D	2 - 48	2 - 48
1	8	ALA	ALA	ILE	ILE	B	B	2 - 46	2 - 46
2	8	ALA	ALA	ILE	ILE	E	E	2 - 46	2 - 46
1	9	VAL	VAL	GLN	GLN	B	B	3 - 47	3 - 47
2	9	VAL	VAL	GLN	GLN	F	F	3 - 47	3 - 47
1	10	ALA	ALA	LEU	LEU	C	C	2 - 48	2 - 48
2	10	ALA	ALA	LEU	LEU	D	D	2 - 48	2 - 48
1	11	ALA	ALA	ILE	ILE	C	C	2 - 46	2 - 46
2	11	ALA	ALA	ILE	ILE	E	E	2 - 46	2 - 46
1	12	VAL	VAL	GLN	GLN	C	C	3 - 47	3 - 47
2	12	VAL	VAL	GLN	GLN	F	F	3 - 47	3 - 47
1	13	ALA	ALA	ILE	ILE	D	D	2 - 46	2 - 46
2	13	ALA	ALA	ILE	ILE	E	E	2 - 46	2 - 46
1	14	VAL	VAL	GLN	GLN	D	D	3 - 47	3 - 47
2	14	VAL	VAL	GLN	GLN	F	F	3 - 47	3 - 47
1	15	VAL	VAL	ILE	ILE	E	E	3 - 46	3 - 46
2	15	VAL	VAL	ILE	ILE	F	F	3 - 46	3 - 46

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

#1: Protein/peptide	AbrB family transcriptional regulator / Histone-like protein Mass: 5499.421 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 1-48 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: SULA_1064, SULB_1065, SULC_1064 / Plasmid: pET-29a / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E3K9N8
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein/peptide

AbrB family transcriptional regulator / Histone-like protein

Mass: 5499.421 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 1-48
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Sulfolobus solfataricus (archaea) / Gene: SULA_1064, SULB_1065, SULC_1064 / Plasmid: pET-29a / Production host:

Escherichia coli (E. coli) / References: UniProt: A0A0E3K9N8

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.8 Å³/Da / Density % sol: 31.62 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M Tris-Cl, pH 7.5, 40% PEG 400

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Data collection

Diffraction

Mean temperature: 123 K

Diffraction source

Source:

SYNCHROTRON / Site:

NSRRC

/ Beamline: BL13C1 / Wavelength: 0.976 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 25, 2015

Radiation

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

Radiation wavelength

Wavelength: 0.976 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.33
1	1	K, H, -L	2	0.67

Reflection

Resolution: 1.4→30 Å / Num. obs: 43748 / % possible obs: 99.2 % / Redundancy: 4.5 % / Net I/σ(I): 30.6

Reflection shell

Resolution: 1.4→1.45 Å

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
REFMAC	5.8.0135	refinement
PDB_EXTRACT	3.2	data extraction
HKL-2000		data reduction
PHASER		phasing

Refinement

Resolution: 1.4→27.49 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.955 / SU B: 2.166 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.015 / ESU R Free: 0.015 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1974	2228	5.1 %	RANDOM
R_work	0.168	-	-	-
obs	0.1696	41484	99.15 %	-

Solvent computation

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

Displacement parameters

B_iso max: 54.74 Å² / B_iso mean: 22.409 Å² / B_iso min: 10.35 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.61 Å²	0 Å²	0 Å²
2-	-	2.61 Å²	0 Å²
3-	-	-	-5.23 Å²

Refinement step

Cycle: final / Resolution: 1.4→27.49 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2255	0	0	311	2566
B_iso mean	-	-	-	30.24	-
Num. residues	-	-	-	-	280

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.023	0.019	2273
X-RAY DIFFRACTION	r_bond_other_d	0.022	0.02	2372
X-RAY DIFFRACTION	r_angle_refined_deg	2.301	1.978	3054
X-RAY DIFFRACTION	r_angle_other_deg	3.092	3	5460
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.668	5	274
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	42.772	25.882	102
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.736	15	472
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.47	15	12
X-RAY DIFFRACTION	r_chiral_restr	0.133	0.2	369
X-RAY DIFFRACTION	r_gen_planes_refined	0.017	0.02	2488
X-RAY DIFFRACTION	r_gen_planes_other	0.015	0.02	460
X-RAY DIFFRACTION	r_mcbond_it	1.405	1.479	1114
X-RAY DIFFRACTION	r_mcbond_other	1.405	1.478	1113
X-RAY DIFFRACTION	r_mcangle_it	2.088	2.219	1382

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	4766	0.15
1	2	B	4766	0.15
2	1	A	4934	0.13
2	2	C	4934	0.13
3	1	A	4808	0.14
3	2	D	4808	0.14
4	1	A	4612	0.14
4	2	E	4612	0.14
5	1	A	4490	0.16
5	2	F	4490	0.16
6	1	B	4754	0.16
6	2	C	4754	0.16
7	1	B	5112	0.12
7	2	D	5112	0.12
8	1	B	4496	0.15
8	2	E	4496	0.15
9	1	B	4568	0.13
9	2	F	4568	0.13
10	1	C	4828	0.15
10	2	D	4828	0.15
11	1	C	4606	0.15
11	2	E	4606	0.15
12	1	C	4474	0.17
12	2	F	4474	0.17
13	1	D	4646	0.12
13	2	E	4646	0.12
14	1	D	4670	0.12
14	2	F	4670	0.12
15	1	E	4484	0.15
15	2	F	4484	0.15

LS refinement shell

Resolution: 1.401→1.438 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.246	158	-
R_work	0.18	3065	-
all	-	3223	-
obs	-	-	99.2 %

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	0.2954	-0.345	-0.3202	0.8553	-0.1842	1.4531	-0.0177	0.0318	-0.0368	0.0338	0.0016	0.0502	0.0196	-0.1281	0.0161	0.0077	-0.0071	0.0077	0.0161	-0.0069	0.0118	-24.5004	15.6412	3.7328
2	0.3771	-0.0212	-0.0695	0.1926	-0.0204	1.3234	-0.0059	0.0421	-0.0134	0.0607	0.0153	-0.0032	0.0692	-0.0257	-0.0093	0.03	0.0037	0.0058	0.0068	-0.0025	0.0101	-19.395	14.0489	4.3641
3	0.4599	-0.5497	-0.0527	1.3973	-0.2992	0.9377	0.0643	0.0129	0.0269	0.0029	-0.0745	-0.0055	-0.0288	0.0677	0.0103	0.0207	-0.005	-0.0002	0.0192	0.0048	0.0229	-1.0436	0.9023	-3.6731
4	0.255	-0.4386	0.0714	1.3681	-0.1737	0.9591	0.0591	0.0246	-0.0018	-0.0358	-0.0852	0.0652	0.0144	0.0539	0.0261	0.0207	0.0021	0.0065	0.0157	-0.0009	0.0079	-2.0989	-4.4147	-4.3932
5	0.8068	0.1498	-0.8672	1.6941	-0.0155	1.2505	0.0313	-0.0263	-0.0559	0.0437	-0.1896	0.0035	0.0917	0.1208	0.1584	0.0769	0.0236	0.0216	0.0703	0.0361	0.0404	1.0962	27.9532	13.7193
6	0.6805	-0.0227	-0.0679	1.9457	-0.0405	1.6497	0.1184	0.0562	0.0815	0.0509	-0.1469	0.0473	0.0503	-0.0062	0.0285	0.0255	0.0046	0.0168	0.0344	-0.0026	0.0137	-1.0606	32.6386	12.9938
7	0.2003	-0.0352	-0.0582	0.0677	-0.0606	0.1638	0.0312	0.0086	-0.0171	-0.0027	-0.0315	0.0103	-0.0086	0.007	0.0003	0.044	0.0042	0.0126	0.0264	-0.0024	0.0094	-9.4569	13.3593	4.382

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 48
2	X-RAY DIFFRACTION	2	B	2 - 48
3	X-RAY DIFFRACTION	3	C	2 - 48
4	X-RAY DIFFRACTION	4	D	2 - 48
5	X-RAY DIFFRACTION	5	E	2 - 47
6	X-RAY DIFFRACTION	6	F	3 - 48
7	X-RAY DIFFRACTION	7	A	101 - 155
8	X-RAY DIFFRACTION	7	B	101 - 167
9	X-RAY DIFFRACTION	7	C	101 - 152
10	X-RAY DIFFRACTION	7	D	101 - 152
11	X-RAY DIFFRACTION	7	E	101 - 140
12	X-RAY DIFFRACTION	7	F	101 - 145

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