PDB-5d2q: Crystal structure of STPR from Bombyx Mori in complex with 20-bp ...

ID or keywords:

Entry

Database: PDB / ID: 5d2q

Title

Crystal structure of STPR from Bombyx Mori in complex with 20-bp DNA derived from +290 site of the fibroin gene

Components

DNA (40-MER)
Fibroin-modulator-binding protein-1

Keywords

TRANSCRIPTION/DNA / Protein-DNA complex / All a-helix DNA major groove binding / TRANSCRIPTION-DNA complex

Function / homology

: / STPRs (score and three amino acid peptide repeats) / DNA / DNA (> 10) / Fibroin-modulator-binding protein-1

Function and homology information

Biological species

Bombyx mori (domestic silkworm)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.4 Å

Authors

Cheng, W.

Citation

Journal: Nucleic Acids Res. / Year: 2016
Title: Structures of an all-alpha protein running along the DNA major groove.
Authors: Yu, L.Y. / Cheng, W. / Zhou, K. / Li, W.F. / Yu, H.M. / Gao, X. / Shen, X. / Wu, Q. / Chen, Y. / Zhou, C.Z.

History

Deposition	Aug 6, 2015	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Mar 23, 2016	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5d2q.cif.gz	85.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5d2q.ent.gz	67.4 KB	Display	PDB format
PDBx/mmJSON format	5d2q.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5d2q_validation.pdf.gz	426.9 KB	Display	wwPDB validaton report
Full document	5d2q_full_validation.pdf.gz	431.3 KB	Display
Data in XML	5d2q_validation.xml.gz	7.1 KB	Display
Data in CIF	5d2q_validation.cif.gz	9.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d2/5d2q ftp://data.pdbj.org/pub/pdb/validation_reports/d2/5d2q	HTTPS FTP

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Related structure data

Related structure data	5d23C 5d2sC C: citing same article (ref.)
Similar structure data	6jza-1 1wic-d 4uav-d 4yoe-d 1ox9-2 5yya-d 2fwu-d 1r8h-3 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#67 - Jul 2005 TATA-Binding Protein similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #253 - Jan 2021 Expressome similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #84 - Dec 2006 Transposase similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #227 - Nov 2018 Telomerase similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #135 - Mar 2011 Integrase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #125 - May 2010 Parvoviruses similarity (1) #131 - Nov 2010 Inteins similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #23 - Nov 2001 DNA similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

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Deposited unit

A: Fibroin-modulator-binding protein-1

B: DNA (40-MER)

24.4 kDa, 2 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)	45.890, 45.890, 240.380
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

#1: Protein	Fibroin-modulator-binding protein-1 / Uncharacterized protein Mass: 12047.971 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 99-193 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bombyx mori (domestic silkworm) / Gene: fmbp-1, Fmbp-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5FBS0
#2: DNA chain	DNA (40-MER) Mass: 12307.974 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.62 Å³/Da / Density % sol: 53.11 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 22% PEG 3350, 16% Glycerol,0.2 M ammonium citrate pH7.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 15, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.4→50 Å / Num. obs: 10911 / % possible obs: 99.8 % / Redundancy: 6 % / Net I/σ(I): 12.3

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0049	refinement
HKL-2000		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Resolution: 2.4→45.08 Å / Cor.coef. F_o:F_c: 0.944 / Cor.coef. F_o:F_c free: 0.923 / SU B: 24.299 / SU ML: 0.249 / Cross valid method: THROUGHOUT / ESU R: 0.342 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.29595	523	4.8 %	RANDOM
R_work	0.24671	-	-	-
obs	0.24915	10310	99.42 %	-

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: 61.413 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.64 Å²	0 Å²	-0 Å²
2-	-	2.64 Å²	-0 Å²
3-	-	-	-5.28 Å²

Refinement step

Cycle: 1 / Resolution: 2.4→45.08 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	584	814	0	37	1435

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.014	1510
X-RAY DIFFRACTION	r_bond_other_d	0.005	0.02	1042
X-RAY DIFFRACTION	r_angle_refined_deg	1.792	1.465	2205
X-RAY DIFFRACTION	r_angle_other_deg	2.27	3	2407
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.569	5	77
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	26.418	20	29
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.412	15	107
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.569	15	13
X-RAY DIFFRACTION	r_chiral_restr	0.095	0.2	208
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	1164
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	331
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	5.115	4.473	311
X-RAY DIFFRACTION	r_mcbond_other	5.072	4.472	310
X-RAY DIFFRACTION	r_mcangle_it	7.589	6.672	387
X-RAY DIFFRACTION	r_mcangle_other	7.597	6.678	388
X-RAY DIFFRACTION	r_scbond_it	4.701	3.885	1199
X-RAY DIFFRACTION	r_scbond_other	4.698	3.884	1198
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	6.912	5.791	1818
X-RAY DIFFRACTION	r_long_range_B_refined	9.695	34.257	2006
X-RAY DIFFRACTION	r_long_range_B_other	9.693	34.217	1996
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	0.417	37	-
R_work	0.429	724	-
obs	-	-	100 %

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	13.8281	34.5053	-4.2056	86.2	-10.4983	1.28	0.772	-0.3172	1.3437	1.1025	-0.5895	3.5384	-0.1552	0.0855	-0.1825	0.7406	0.089	-0.445	0.3039	-0.2337	0.5923	0.5227	7.369	-58.5095
2	3.6088	-4.0961	-8.5784	4.656	9.7398	20.3959	-0.1943	0.2681	-0.1914	0.2041	-0.2509	0.2245	0.4827	-0.6364	0.4451	0.2962	-0.1321	-0.0175	0.3195	0.1586	0.3368	4.9485	-2.4915	-55.1175
3	10.2971	-21.4837	-12.2615	46.3406	20.9039	29.1815	0.8692	0.2408	-0.1515	-1.8855	-0.1345	0.5716	-0.4083	-1.3427	-0.7347	0.4517	-0.0212	-0.1524	0.1032	-0.0222	0.4421	10.4318	-8.7994	-45.8296
4	0.1397	-0.2682	-0.0689	13.1279	5.5929	5.193	-0.0683	0.0414	0.1516	-0.5964	0.236	-0.4678	-0.1109	0.2822	-0.1677	0.2092	-0.0014	0.0308	0.121	0.0113	0.266	13.5528	5.0276	-39.1613
5	8.6954	4.8866	0.952	2.7618	0.5138	1.2482	0.0211	0.2072	0.2318	-0.0123	0.0736	0.1372	-0.075	0.0151	-0.0947	0.1362	0.0763	-0.0146	0.1069	-0.0002	0.2266	-1.45	15.0754	-32.0824
6	6.1283	0.9971	5.2139	1.7439	-1.2788	7.3328	0.3557	-0.3536	0.0371	0.1988	-0.4599	-0.0049	0.1603	0.1778	0.1042	0.1844	-0.0456	0.0274	0.2067	-0.0432	0.3393	-11.2146	-1.174	-22.4203
7	2.8394	0.2758	-2.2273	1.1535	1.2621	4.7416	0.0307	0.1625	0.3514	-0.0306	0.0679	-0.0202	0.2494	-0.2229	-0.0986	0.2436	0.0357	-0.0026	0.1366	0.0092	0.2338	-2.2816	6.6372	-29.4965
8	0.4906	0.1426	-0.6751	3.8164	0.6582	8.121	0.0414	0.1139	0.3118	0.0629	0.4479	-0.1969	0.4797	0.1593	-0.4892	0.274	0.012	0.0601	0.2386	0.0254	0.2265	12.6772	8.5664	-53.3718
9	1.7034	0.1492	-1.2165	1.7076	0.9694	6.7118	0.0428	-0.019	0.1684	0.1084	0.0386	-0.0748	0.3055	-0.3201	-0.0814	0.0887	0.0006	0.0063	0.0899	0.0101	0.2287	-5.8491	7.4338	-23.5729

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	113 - 116
2	X-RAY DIFFRACTION	2	A	117 - 123
3	X-RAY DIFFRACTION	3	A	124 - 128
4	X-RAY DIFFRACTION	4	A	129 - 144
5	X-RAY DIFFRACTION	5	A	145 - 168
6	X-RAY DIFFRACTION	6	A	169 - 189
7	X-RAY DIFFRACTION	7	B	-20 - -3
8	X-RAY DIFFRACTION	8	B	-2 - 7
9	X-RAY DIFFRACTION	9	B	8 - 20

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