PDB-2ihc: Crystal structure of the bric-a-brac (BTB) domain of human BACH1

ID or keywords:

Entry

Database: PDB / ID: 2ihc

Title

Crystal structure of the bric-a-brac (BTB) domain of human BACH1

Components

Transcription regulator protein BACH1

Keywords

TRANSCRIPTION / BACH1 / bric-a-brac domain / transcription factor / protein-protein interaction / cap'n'collar type of basic region leucine zipper factor family / Structural Genomics / Structural Genomics Consortium / SGC

Function / homology

Function and homology information

: / : / : / chromatin => GO:0000785 / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / DNA repair ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.44 Å

Authors

Amos, A.L. / Turnbull, A.P. / Bunkoczi, G. / Papagrigoriou, E. / Gorrec, F. / Umeano, C. / Bullock, A. / von Delft, F. / Weigelt, J. / Edwards, A. ...

Citation

Journal: To be Published
Title: Crystal structure of the bric-a-brac (BTB) domain of human BACH1
Authors: Amos, A.L. / Turnbull, A.P. / Bunkoczi, G. / Papagrigoriou, E. / Gorrec, F. / Umeano, C. / Bullock, A. / von Delft, F. / Weigelt, J. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / Knapp, S.

History

Deposition	Sep 26, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 31, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Aug 30, 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 / struct_ncs_dom_lim / struct_ref_seq_dif 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.end_auth_comp_id / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2ihc.cif.gz	97.8 KB	Display	PDBx/mmCIF format
PDB format	pdb2ihc.ent.gz	74.9 KB	Display	PDB format
PDBx/mmJSON format	2ihc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2ihc_validation.pdf.gz	457 KB	Display	wwPDB validaton report
Full document	2ihc_full_validation.pdf.gz	464.1 KB	Display
Data in XML	2ihc_validation.xml.gz	17.9 KB	Display
Data in CIF	2ihc_validation.cif.gz	24.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ih/2ihc ftp://data.pdbj.org/pub/pdb/validation_reports/ih/2ihc	HTTPS FTP

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Related structure data

Related structure data	1r2bS S: Starting model for refinement
Similar structure data	3e4u-3 4gml-2 3skw-2 2g9c-d 3tmg-3 4gml-3 2ees-d 3skt-2 2eeu-d 4ond-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) 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
Related items in Molecule of the Month	#122 - Feb 2010 Enhanceosome similarity (5) #70 - Oct 2005 Designer Proteins similarity (4) #110 - Feb 2009 Auxin and TIR1 Ubiquitin Ligase similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #218 - Feb 2018 EPSP Synthase and Weedkillers similarity (1)

Deposited unit

A: Transcription regulator protein BACH1

B: Transcription regulator protein BACH1

C: Transcription regulator protein BACH1

D: Transcription regulator protein BACH1

56.2 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Transcription regulator protein BACH1

B: Transcription regulator protein BACH1

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

2

C: Transcription regulator protein BACH1

D: Transcription regulator protein BACH1

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

3

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	83.440, 53.664, 123.891
Angle α, β, γ (deg.)	90.00, 106.15, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-129- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
1	2	A
2	2	D
1	3	B
2	3	C

NCS domain segments:

Component-ID: 1 / Refine code: 2

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	ASN	ASN	LEU	LEU	A	A	19 - 126	15 - 122
2	1	ASN	ASN	GLU	GLU	B	B	19 - 120	15 - 116
3	1	ASN	ASN	LYS	LYS	C	C	19 - 127	15 - 123
4	1	ASN	ASN	LYS	LYS	D	D	19 - 127	15 - 123
1	2	SER	SER	THR	THR	A	A	7 - 18	3 - 14
2	2	SER	SER	THR	THR	D	D	7 - 18	3 - 14
1	3	SER	SER	THR	THR	B	B	-1 - 18	1 - 14
2	3	MET	MET	THR	THR	C	C	0 - 18	2 - 14

NCS ensembles :

ID
1
2
3

#1: Protein	Transcription regulator protein BACH1 / BTB and CNC homolog 1 / HA2303 Mass: 14058.035 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BACH1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: O14867
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Transcription regulator protein BACH1 / BTB and CNC homolog 1 / HA2303

Mass: 14058.035 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: BACH1 / Plasmid: pNIC28-Bsa4 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: O14867

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.37 Å³/Da / Density % sol: 48.07 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 20 % PEG3350, 200 mM MgCl2, 0.1M Tris buffer, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.978 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 16, 2006
Radiation	Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.978 Å / Relative weight: 1
Reflection	Resolution: 2.45→50 Å / Num. obs: 19702 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 %
Reflection shell	Resolution: 2.45→2.54 Å / % possible all: 99.4

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: Molecular replacement search model = pdb entry 1R2B

1r2b

Resolution: 2.44→33.3 Å / Cor.coef. F_o:F_c: 0.935 / Cor.coef. F_o:F_c free: 0.914 / SU B: 23.58 / SU ML: 0.261 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.506 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2777	1010	5.1 %	RANDOM
R_work	0.2467	-	-	-
all	0.24841	18692	-	-
obs	0.24841	18692	98.81 %	-

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: 54.379 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.55 Å²	0 Å²	-3.41 Å²
2-	-	-0.86 Å²	0 Å²
3-	-	-	-3.59 Å²

Refinement step

Cycle: LAST / Resolution: 2.44→33.3 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3382	0	0	33	3415

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.021	3440
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	2092
X-RAY DIFFRACTION	r_angle_refined_deg	1.453	1.933	4690
X-RAY DIFFRACTION	r_angle_other_deg	1.098	3	5124
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.944	5	454
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.393	23.835	133
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.665	15	485
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.506	15	12
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	585
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	3900
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	724
X-RAY DIFFRACTION	r_nbd_refined	0.213	0.2	733
X-RAY DIFFRACTION	r_nbd_other	0.188	0.2	2078
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	1738
X-RAY DIFFRACTION	r_nbtor_other	0.087	0.2	1752
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.175	0.2	65
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	0.216	0.2	7
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.193	0.2	34
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.169	0.2	3
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	0.57	1.5	2348
X-RAY DIFFRACTION	r_mcbond_other	0.137	1.5	922
X-RAY DIFFRACTION	r_mcangle_it	0.932	2	3665
X-RAY DIFFRACTION	r_scbond_it	1.471	3	1209
X-RAY DIFFRACTION	r_scangle_it	2.133	4.5	1025
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	572	tight positional	0.06	0.05
1	2	B	572	tight positional	0.05	0.05
1	3	C	572	tight positional	0.06	0.05
1	4	D	572	tight positional	0.04	0.05
2	1	A	71	tight positional	0.05	0.05
3	1	B	77	tight positional	0.04	0.05
1	1	A	429	medium positional	0.41	0.5
1	2	B	429	medium positional	0.38	0.5
1	3	C	429	medium positional	0.36	0.5
1	4	D	429	medium positional	0.38	0.5
2	1	A	63	medium positional	0.19	0.5
3	1	B	84	medium positional	0.45	0.5
1	1	A	572	tight thermal	1.49	10
1	2	B	572	tight thermal	1.24	10
1	3	C	572	tight thermal	2.5	10
1	4	D	572	tight thermal	1.04	10
2	1	A	71	tight thermal	1.03	10
3	1	B	77	tight thermal	0.49	10
1	1	A	429	medium thermal	1.08	2
1	2	B	429	medium thermal	0.89	2
1	3	C	429	medium thermal	1.42	2
1	4	D	429	medium thermal	0.73	2
2	1	A	63	medium thermal	0.95	2
3	1	B	84	medium thermal	0.62	2

LS refinement shell

Resolution: 2.437→2.5 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.331	61	-
R_work	0.305	1310	-
obs	-	-	92.89 %

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	5.4152	-0.9747	1.5602	6.4741	-1.0054	3.8442	-0.5057	-0.3373	0.7208	0.2663	0.1549	0.3306	-0.5711	-0.2462	0.3508	-0.3817	-0.0466	0.034	-0.2953	0.0171	-0.0699	12.9817	10.7482	49.1885
2	3.557	-0.9564	-1.5693	3.7539	-0.1515	7.8671	0.0866	-0.1423	-0.2205	0.141	-0.0824	-0.3903	0.6222	0.2931	-0.0042	-0.3269	0.0294	-0.0068	-0.2895	-0.0132	-0.0589	24.8445	1.9035	47.9482
3	5.2387	-1.8871	-0.5431	2.5908	0.6006	5.1453	0.1388	-0.169	0.1051	0.3059	-0.0042	-0.6119	0.3145	0.5259	-0.1347	-0.2696	0.045	-0.0467	-0.2605	-0.0161	-0.0076	27.7578	3.8037	44.584
4	4.2339	0.8335	-0.1675	8.4236	-1.9613	4.4137	0.2298	0.5347	0.1835	-0.6711	-0.2938	-0.7899	-0.1121	0.3564	0.064	-0.1458	0.0575	0.092	-0.2138	-0.0083	-0.0632	26.5163	14.0793	33.3565
5	3.6689	3.2782	-2.3581	7.0698	-0.5987	5.2518	-0.0019	0.1263	-0.5305	-0.8008	0.1251	0.1292	0.6382	-0.1008	-0.1232	-0.2446	-0.0833	-0.0807	-0.2835	0.0006	0.0738	9.9083	-0.8702	40.4122
6	10.0047	-0.3991	2.6981	4.9603	1.0701	7.0064	0.2875	-1.5276	-0.7359	0.665	0.0884	0.1611	0.6874	-1.1221	-0.3759	-0.1194	-0.2199	0.028	0.0512	0.1953	0.0041	1.8381	-2.2358	55.1852
7	10.2499	-0.7791	3.1415	0.0707	-0.0265	4.8994	-0.3989	-0.8512	0.3929	0.0129	0.132	0.2199	-0.355	-1.0508	0.2669	-0.2028	-0.097	0.0035	-0.0051	0.0312	0.1554	-6.3327	5.4368	44.8292
8	15.3038	9.8066	-10.5274	7.0775	-6.6089	11.3463	-1.1499	1.8289	-1.2297	-1.4755	0.56	-1.2391	0.9865	-0.4492	0.5899	0.0554	0.0097	0.1198	0.1912	-0.2416	-0.2392	23.2604	24.7988	15.7684
9	13.9273	4.2686	3.7965	8.5153	4.4716	14.2159	-1.039	2.1091	0.8541	-2.0582	0.5523	0.6487	-2.1231	-0.0818	0.4866	0.5432	-0.2298	-0.0312	0.3327	0.4893	-0.4	22.2791	42.2438	11.6416
10	6.6915	3.7168	3.5956	12.2839	2.2631	7.2657	-0.338	0.2909	0.7548	-0.1853	0.0864	-0.2816	-0.8048	-0.0749	0.2516	-0.1224	0.0757	0.0067	-0.1593	0.0842	-0.0939	27.4496	41.0491	26.5311
11	28.5667	-3.1273	14.6042	6.511	-0.2712	10.9758	-0.0577	0.5599	0.9592	-0.6281	-0.042	0.5646	-0.2493	-1.3445	0.0997	-0.1486	0.0946	-0.064	0.1049	0.0313	-0.301	10.6215	30.3841	18.8275
12	7.827	3.3829	-2.5449	5.9589	-2.0972	6.1052	-0.6868	2.1024	-1.2829	-1.1447	0.5548	-0.0241	0.9231	-1.2678	0.132	0.1123	-0.1348	-0.0415	0.4986	-0.4269	-0.0432	8.8724	15.0196	14.5947

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	15 - 33	11 - 29
2	X-RAY DIFFRACTION	2	A	A	34 - 61	30 - 57
3	X-RAY DIFFRACTION	3	A	A	62 - 66	58 - 62
4	X-RAY DIFFRACTION	3	A	A	70 - 92	66 - 88
5	X-RAY DIFFRACTION	4	A	A	93 - 126	89 - 122
6	X-RAY DIFFRACTION	4	B	B	-1 - 14	1 - 10
7	X-RAY DIFFRACTION	5	B	B	15 - 33	11 - 29
8	X-RAY DIFFRACTION	6	B	B	34 - 66	30 - 62
9	X-RAY DIFFRACTION	6	B	B	70 - 85	66 - 81
10	X-RAY DIFFRACTION	7	B	B	86 - 120	82 - 116
11	X-RAY DIFFRACTION	7	A	A	7 - 14	3 - 10
12	X-RAY DIFFRACTION	8	C	C	15 - 33	11 - 29
13	X-RAY DIFFRACTION	9	C	C	34 - 64	30 - 60
14	X-RAY DIFFRACTION	9	C	C	70 - 83	66 - 79
15	X-RAY DIFFRACTION	10	C	C	84 - 127	80 - 123
16	X-RAY DIFFRACTION	10	D	D	7 - 14	3 - 10
17	X-RAY DIFFRACTION	11	D	D	15 - 33	11 - 29
18	X-RAY DIFFRACTION	12	D	D	34 - 64	30 - 60
19	X-RAY DIFFRACTION	12	D	D	71 - 127	67 - 123
20	X-RAY DIFFRACTION	12	C	C	0 - 14	2 - 10

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