PDB-1p51: Anabaena HU-DNA cocrystal structure (AHU6)

ID or keywords:

Entry

Database: PDB / ID: 1p51

Title

Anabaena HU-DNA cocrystal structure (AHU6)

Components

5'-D(*GP*CP*AP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP*AP*T)-3'
DNA-binding protein HU

Keywords

DNA Binding Protein/DNA / protein-DNA complex / DNA bending / HU / DNA Binding Protein-DNA COMPLEX

Function / homology

Function and homology information

heterocyst development / chromosome condensation / structural constituent of chromatin / DNA binding / cytosol
Similarity search - Function

Biological species

Anabaena sp. (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Swinger, K.K. / Lemberg, K.M. / Zhang, Y. / Rice, P.A.

Citation

Journal: Embo J. / Year: 2003
Title: Flexible DNA bending in HU-DNA cocrystal structures
Authors: Swinger, K.K. / Lemberg, K.M. / Zhang, Y. / Rice, P.A.

History

Deposition	Apr 24, 2003	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 13, 2003	Provider: repository / Type: Initial release
Revision 1.1	Apr 29, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Aug 16, 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	1p51.cif.gz	122.4 KB	Display	PDBx/mmCIF format
PDB format	pdb1p51.ent.gz	93.5 KB	Display	PDB format
PDBx/mmJSON format	1p51.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/p5/1p51 ftp://data.pdbj.org/pub/pdb/validation_reports/p5/1p51	HTTPS FTP

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Related structure data

Related structure data	1p71SC 1p78C 1b8z 1ihf S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1p78-d 1p71-d 6d21-d 5wwz-d 2qko-2 3ech-d 3wrk-1 6fp6-3 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	#67 - Jul 2005 TATA-Binding Protein similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #253 - Jan 2021 Expressome similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #135 - Mar 2011 Integrase similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #227 - Nov 2018 Telomerase similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #84 - Dec 2006 Transposase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #125 - May 2010 Parvoviruses similarity (1) #131 - Nov 2010 Inteins similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #23 - Nov 2001 DNA similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

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Deposited unit

E: 5'-D(*GP*CP*AP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP*AP*T)-3'

F: 5'-D(*GP*CP*AP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP*AP*T)-3'

I: 5'-D(*GP*CP*AP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP*AP*T)-3'

H: 5'-D(*GP*CP*AP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP*AP*T)-3'

A: DNA-binding protein HU

B: DNA-binding protein HU

C: DNA-binding protein HU

D: DNA-binding protein HU

63.6 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

E: 5'-D(*GP*CP*AP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP*AP*T)-3'

F: 5'-D(*GP*CP*AP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP*AP*T)-3'

A: DNA-binding protein HU

B: DNA-binding protein HU

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

2

I: 5'-D(*GP*CP*AP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP*AP*T)-3'

H: 5'-D(*GP*CP*AP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP*AP*T)-3'

C: DNA-binding protein HU

D: DNA-binding protein HU

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

Unit cell

Length a, b, c (Å)	37.646, 107.836, 83.464
Angle α, β, γ (deg.)	90.00, 92.25, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Details

The functional complex is a protein homodimer bound to a DNA duplex. The assymetric unit contains two copies of the functional complex.

#1: DNA chain	5'-D(GPCPAPTPAPTPCPAPAPTPTPTPGPTPTPGPCPAPT)-3' Mass: 5809.782 Da / Num. of mol.: 4 / Source method: obtained synthetically Details*: chemically synthesized DNA with a 5' phosphate modification
#2: Protein	DNA-binding protein HU Mass: 10089.584 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anabaena sp. (bacteria) / Gene: HUP OR HANA OR ASR3935 / Plasmid: pET21a (pETAHU) / Production host: Escherichia coli (E. coli) / Strain (production host): RJ1878 lacks functional HU genes / References: UniProt: P05514
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.75 Å³/Da / Density % sol: 54.94 %

Crystal grow

Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Peg 5000 monomethyl ether, glycerol, tris, jeffamine, potassium chloride, calcium chloride, sodium azide, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Components of the solutions

ID	Name	Crystal-ID	Sol-ID
1	Peg 5000	1	1
2	monomethyl ether	1	1
3	glycerol	1	1
4	tris	1	1
5	jeffamine	1	1
6	potassium chloride	1	1
7	calcium chloride	1	1
8	sodium azide	1	1
9	H2O	1	1
10	Peg 5000	1	2
11	glycerol	1	2
12	potassium chloride	1	2
13	calcium chloride	1	2
14	sodium azide	1	2
15	H2O	1	2

Crystal grow

*PLUS

pH: 7.5

Components of the solutions

*PLUS

ID	Conc.	Common name	Crystal-ID	Sol-ID	Chemical formula	Details
1	50 mM		1	reservoir	KCl
2	10 %	glycerol	1	reservoir
3	50 mM	Tris	1	reservoir		pH7.5 or pH8.0
4	0.02 %		1	reservoir	NaN3
5	1 %	Jaffamine	1	reservoir		pH7.0
6	12-22.5 %	PEG5000 MME	1	reservoir
7	10 mM		1	reservoir	CaCl2
8			1
9			1
10			1
11			1
12			1
13			1
14			1
15			1

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 29, 2002
Radiation	Monochromator: Ge 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9 Å / Relative weight: 1
Reflection	Resolution: 2.48→99 Å / Num. all: 23324 / Num. obs: 23324 / % possible obs: 93.3 % / Observed criterion σ(I): -3 / Redundancy: 3 % / R_merge(I) obs: 0.107
Reflection shell	Resolution: 2.48→2.57 Å / Redundancy: 2.2 % / R_merge(I) obs: 0.359 / % possible all: 46.5
Reflection	PLUS Lowest resolution: 99 Å / R_merge(I) obs*: 0.11

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Processing

Software

Name	Version	Classification
REFMAC	5.1.24	refinement
DENZO		data reduction
SCALEPACK		data scaling
EPMR		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P71 with nonidentical sidechains pruned back to a common atom

1p71

Resolution: 2.5→25 Å / Cor.coef. F_o:F_c: 0.821 / Cor.coef. F_o:F_c free: 0.751 / SU B: 18.487 / SU ML: 0.417 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: restrained individual isotropic (after TLS refinement)
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.477
Details: Data is anisotropic with limits 2.5 x 2.5 x 2.8. Data were truncated to an ellipsoid and reflections with an average (I/sigI) ratio less than 2 were removed. The completeness above is ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.338	1828	9.8 %	RANDOM
R_work	0.286	-	-	-
obs	0.291	16900	81.39 %	-
all	-	23042	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 28.115 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.44 Å²	0 Å²	0.09 Å²
2-	-	-0.62 Å²	0 Å²
3-	-	-	2.07 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2767	1556	0	72	4395

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.022	4535
X-RAY DIFFRACTION	r_angle_refined_deg	0.927	2.404	6435
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.511	5	364
X-RAY DIFFRACTION	r_chiral_restr	0.046	0.2	664
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	2832
X-RAY DIFFRACTION	r_nbd_refined	0.175	0.2	1770
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.124	0.2	186
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.157	0.2	48
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.136	0.2	8
X-RAY DIFFRACTION	r_mcbond_it	0.431	1.5	1831
X-RAY DIFFRACTION	r_mcangle_it	0.81	2	2939
X-RAY DIFFRACTION	r_scbond_it	0.894	3	2704
X-RAY DIFFRACTION	r_scangle_it	1.668	4.5	3496

LS refinement shell

Resolution: 2.5→2.635 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.39	72
R_work	0.31	140

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	1.3324	-0.1824	-0.6087	1.9985	-0.7982	1.1348	-0.0561	-0.1089	-0.136	-0.1734	-0.0574	0.0377	0.1103	0.0258	0.1135	0.2892	0.001	0.0253	0.2728	-0.0004	0.3185	7.8298	5.382	17.2572
2	4.824	-0.703	0.5186	1.733	0.059	0.7836	0.0714	-0.107	0.7545	-0.0201	-0.0559	-0.2528	-0.0024	-0.052	-0.0155	0.2417	-0.0113	-0.0045	0.2628	-0.0355	0.4342	7.7777	27.0397	59.9312
3	0.8123	-3.1444	-3.1692	2.0218	0.6734	-3.7609	0.0759	-0.0218	0.2115	0.4048	0.19	-0.3798	0.5375	0.2416	-0.2659	0.4645	-0.0386	-0.0658	0.2807	0.0183	0.3498	21.2179	30.5111	28.5245
4	4.3538	1.3031	-2.052	-0.0045	0.962	3.8106	0.003	0.181	-0.06	-0.3051	0.0258	0.0592	-0.1621	-0.289	-0.0288	0.3408	-0.0075	-0.0218	0.3342	-0.0361	0.2477	-5.4766	32.1591	11.227
5	5.7687	-0.1685	2.9875	-3.5416	-2.0305	0.4349	0.0157	0.2033	0.3075	-0.1793	-0.0125	0.408	0.1706	0.7276	-0.0032	0.4473	0.0507	-0.0007	0.2415	0.0519	0.2749	20.7561	0.7458	52.0494
6	2.4041	1.8847	4.1565	4.7171	-0.8202	4.984	0.2123	-0.0649	0.2357	-0.0776	0.055	0.1214	0.4746	0.1753	-0.2673	0.3211	0.0399	0.0323	0.2886	-0.0036	0.3101	-5.761	2.0301	69.3889
7	1.382	0.4081	-3.539	-0.7263	0.8352	8.7836	0.6462	-0.7433	0.3504	-0.0064	-0.5371	0.1724	-0.1249	0.408	-0.1091	0.4957	-0.0195	-0.0379	0.1403	0.2246	0.4133	12.4969	24.8779	38.4396
8	0.3373	1.3161	1.6508	-2.1982	-0.54	2.4037	0.1449	0.0625	-0.1077	0.0923	-0.0614	-0.1468	-0.0744	-0.0801	-0.0835	0.4024	0.0566	-0.0494	0.3776	-0.012	0.2937	7.7542	33.0003	20.1204
9	-4.1065	-10.9281	-4.1435	10.7907	3.6279	4.8841	0.5468	0.7105	-0.3362	-0.1443	-0.2493	-0.6014	-0.1406	-0.2549	-0.2975	0.4112	0.039	-0.0349	0.5318	-0.0199	0.2695	2.5288	29.0493	-0.6332
10	11.3236	-10.8578	6.254	8.938	-6.016	-0.7317	0.1819	0.7231	-0.1545	-0.1361	-0.1297	0.6	0.282	0.4575	-0.0521	0.3858	-0.0073	0.054	0.4154	-0.057	0.1937	12.0689	4.657	40.6155
11	-0.2713	-0.1199	-1.0482	-2.1532	-0.2888	3.0841	0.2961	-0.045	0.0785	0.1146	0.0203	0.0326	-0.1105	-0.0222	-0.3164	0.3993	0.013	0.0543	0.3448	0.0009	0.3118	7.8106	-0.3182	61.0571
12	4.9999	5.6818	3.4039	9.7298	11.5854	-4.823	-0.4904	0.5455	-0.0204	-0.1451	0.3518	-0.0662	0.326	-0.2265	0.1385	0.3759	-0.0501	0.0693	0.4754	0.1557	0.3449	1.1297	8.7167	79.4664

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	E	1 - 53	1 - 53
2	X-RAY DIFFRACTION	1	B	F	1 - 53	1 - 53
3	X-RAY DIFFRACTION	1	A	E	76 - 92	76 - 92
4	X-RAY DIFFRACTION	1	B	F	76 - 92	76 - 92
5	X-RAY DIFFRACTION	2	C	G	1 - 53	1 - 53
6	X-RAY DIFFRACTION	2	D	H	1 - 53	1 - 53
7	X-RAY DIFFRACTION	2	C	G	76 - 92	76 - 92
8	X-RAY DIFFRACTION	2	D	H	76 - 92	76 - 92
9	X-RAY DIFFRACTION	3	A	E	54 - 75	54 - 75
10	X-RAY DIFFRACTION	4	B	F	54 - 75	54 - 75
11	X-RAY DIFFRACTION	5	C	G	54 - 75	54 - 75
12	X-RAY DIFFRACTION	6	D	H	54 - 75	54 - 75
13	X-RAY DIFFRACTION	7	E	A	2 - 5	1 - 4
14	X-RAY DIFFRACTION	7	F	B	16 - 18	15 - 17
15	X-RAY DIFFRACTION	8	E	A	6 - 15	5 - 14
16	X-RAY DIFFRACTION	8	F	B	6 - 15	5 - 14
17	X-RAY DIFFRACTION	9	E	A	16 - 18	15 - 17
18	X-RAY DIFFRACTION	9	F	B	2 - 5	1 - 4
19	X-RAY DIFFRACTION	10	I	C	2 - 5	1 - 4
20	X-RAY DIFFRACTION	10	H	D	16 - 18	15 - 17
21	X-RAY DIFFRACTION	11	I	C	6 - 15	5 - 14
22	X-RAY DIFFRACTION	11	H	D	6 - 15	5 - 14
23	X-RAY DIFFRACTION	12	I	C	16 - 18	15 - 17
24	X-RAY DIFFRACTION	12	H	D	2 - 5	1 - 4

Refinement

*PLUS

Highest resolution: 2.5 Å / Lowest resolution: 25 Å / % reflection R_free: 10 %

Solvent computation

*PLUS

Displacement parameters

*PLUS

Refine LS restraints

*PLUS

Refine-ID	Type	Dev ideal
X-RAY DIFFRACTION	r_bond_d	0.005
X-RAY DIFFRACTION	r_angle_d	0.927

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