PDB-2zbk: Crystal structure of an intact type II DNA topoisomerase: insight...

ID or keywords:

Entry

Database: PDB / ID: 2zbk

Title

Crystal structure of an intact type II DNA topoisomerase: insights into DNA transfer mechanisms

Components

Type 2 DNA topoisomerase 6 subunit B
Type II DNA topoisomerase VI subunit A

Keywords

ISOMERASE / DNA topoisomerase / DNA binding protein / decatenation / ATPase / drug design / DNA-binding / Magnesium / Metal-binding / ATP-binding / Nucleotide-binding / Structural Genomics / Paris-Sud Yeast Structural Genomics / YSG

Function / homology

Function and homology information

DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / chromosome / magnesium ion binding / DNA binding / ATP binding / identical protein binding
Similarity search - Function

Biological species

Sulfolobus shibatae (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3.56 Å

Authors

Graille, M. / Cladiere, L. / Durand, D. / Lecointe, F. / Forterre, P. / van Tilbeurgh, H. / Paris-Sud Yeast Structural Genomics (YSG)

Citation

Journal: Structure / Year: 2008
Title: Crystal Structure of an Intact Type II DNA Topoisomerase: Insights into DNA Transfer Mechanisms
Authors: Graille, M. / Durand, D. / Lecointe, F. / Gadelle, D. / Quevillon-Cheruel, S. / Vachette, P. / Forterre, P. / van Tilbeurgh, H.

History

Deposition	Oct 22, 2007	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Feb 12, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 1, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_site 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2zbk.cif.gz	674.9 KB	Display	PDBx/mmCIF format
PDB format	pdb2zbk.ent.gz	546.4 KB	Display	PDB format
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Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zb/2zbk ftp://data.pdbj.org/pub/pdb/validation_reports/zb/2zbk	HTTPS FTP

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Related structure data

Related structure data	1mu5S 1mx0S S: Starting model for refinement
Similar structure data	2zbk-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	#73 - Jan 2006 Topoisomerase similarity (1) #131 - Nov 2010 Inteins similarity (1)

Deposited unit

A: Type II DNA topoisomerase VI subunit A

B: Type 2 DNA topoisomerase 6 subunit B

C: Type II DNA topoisomerase VI subunit A

D: Type 2 DNA topoisomerase 6 subunit B

E: Type II DNA topoisomerase VI subunit A

F: Type 2 DNA topoisomerase 6 subunit B

G: Type II DNA topoisomerase VI subunit A

H: Type 2 DNA topoisomerase 6 subunit B

hetero molecules

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

1

A: Type II DNA topoisomerase VI subunit A

B: Type 2 DNA topoisomerase 6 subunit B

C: Type II DNA topoisomerase VI subunit A

D: Type 2 DNA topoisomerase 6 subunit B

hetero molecules

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

2

E: Type II DNA topoisomerase VI subunit A

F: Type 2 DNA topoisomerase 6 subunit B

G: Type II DNA topoisomerase VI subunit A

H: Type 2 DNA topoisomerase 6 subunit B

hetero molecules

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

Unit cell

Length a, b, c (Å)	114.960, 200.530, 329.070
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1 / Refine code: 1

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	ASP	ASP	MET	MET	A	A	10 - 44	10 - 44
2	1	GLU	GLU	VAL	VAL	B	B	14 - 229	14 - 229
3	1	ASP	ASP	MET	MET	C	C	10 - 44	10 - 44
4	1	GLU	GLU	VAL	VAL	D	D	14 - 229	14 - 229
5	1	ASP	ASP	MET	MET	E	E	10 - 44	10 - 44
6	1	GLU	GLU	VAL	VAL	F	F	14 - 229	14 - 229
7	1	ASP	ASP	MET	MET	G	G	10 - 44	10 - 44
8	1	GLU	GLU	VAL	VAL	H	H	14 - 229	14 - 229
1	2	LEU	LEU	LYS	LYS	A	A	66 - 158	66 - 158
2	2	LYS	LYS	ASP	ASP	B	B	230 - 312	230 - 312
3	2	LEU	LEU	LYS	LYS	C	C	66 - 158	66 - 158
4	2	LYS	LYS	ASP	ASP	D	D	230 - 312	230 - 312
5	2	LEU	LEU	LYS	LYS	E	E	66 - 158	66 - 158
6	2	LYS	LYS	ASP	ASP	F	F	230 - 312	230 - 312
7	2	LEU	LEU	LYS	LYS	G	G	66 - 158	66 - 158
8	2	LYS	LYS	ASP	ASP	H	H	230 - 312	230 - 312
1	3	GLU	GLU	ALA	ALA	A	A	159 - 389	159 - 389
2	3	SER	SER	LYS	LYS	B	B	313 - 450	313 - 450
3	3	GLU	GLU	ALA	ALA	C	C	159 - 389	159 - 389
4	3	SER	SER	LYS	LYS	D	D	313 - 450	313 - 450
5	3	GLU	GLU	ALA	ALA	E	E	159 - 389	159 - 389
6	3	SER	SER	LYS	LYS	F	F	313 - 450	313 - 450
7	3	GLU	GLU	ALA	ALA	G	G	159 - 389	159 - 389
8	3	SER	SER	LYS	LYS	H	H	313 - 450	313 - 450
2	4	LEU	LEU	GLU	GLU	B	B	451 - 519	451 - 519
4	4	LEU	LEU	GLU	GLU	D	D	451 - 519	451 - 519
6	4	LEU	LEU	GLU	GLU	F	F	451 - 519	451 - 519
8	4	LEU	LEU	GLU	GLU	H	H	451 - 519	451 - 519

NCS ensembles :

ID	Details
1	A B C D E F G H
2	A B C D E F G H
3	A B C D E F G H
4	B D F H
5	A B C D
6	A B C D
7	A B C D
8	A B C D

#1: Protein	Type II DNA topoisomerase VI subunit A Mass: 45121.980 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus shibatae (archaea) / Gene: top6A / Plasmid: pET3b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O05208, EC: 5.99.1.3
#2: Protein	Type 2 DNA topoisomerase 6 subunit B / Type II DNA topoisomerase VI subunit B / TopoVI-B Mass: 60614.555 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus shibatae (archaea) / Gene: top6B / Plasmid: pET3b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O05207, EC: 5.99.1.3
#3: Chemical	ChemComp-RDC / RADICICOL / MONORDEN Mass: 364.777 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₈H₁₇ClO₆

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 4.48 Å³/Da / Density % sol: 72.57 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 25mM sodium acetate pH4.6, 50mM ammonium sulphate, 6.6% PEG-MME-2000, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9798 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 20, 2006
Radiation	Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9798 Å / Relative weight: 1
Reflection	Av σ(I) over netI: 8.1 / Number: 460374 / R_merge(I) obs: 0.108 / D res high: 3.5 Å / Num. obs: 167444 / % possible obs: 90.4
Diffraction reflection shell	Highest resolution: 3.5 Å / Lowest resolution: 3.6 Å / Num. obs: 46207 / % possible obs: 75.6 % / R_merge(I) obs: 0.524
Reflection	Resolution: 3.5→40 Å / Num. obs: 88994 / % possible obs: 90.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.7 % / B_iso Wilson estimate: 79.165 Å² / R_merge(I) obs: 0.108 / Net I/σ(I): 8.1
Reflection shell	Resolution: 3.55→3.6 Å / Redundancy: 2.4 % / R_merge(I) obs: 0.524 / Mean I/σ(I) obs: 1.9 / Num. measured obs: 110502 / Num. unique obs: 46207 / R_sym value: 0.524 / % possible all: 75.6

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Phasing

Phasing

Method:

SAD

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	32.048	151.003	71.965	S	20	1
2	37.578	147.868	65.663	S	20	0.937
3	25.087	202.6	72.223	S	20	0.932
4	-11.672	205.159	98.552	S	20	0.921
5	57.036	132.946	97.073	S	20	0.903
6	-16.723	202.144	91.086	S	20	0.877
7	0.322	220.823	96.702	S	20	0.853
8	19.735	205.857	65.55	S	20	0.83
9	68.946	148.644	98.886	S	20	0.824
10	23.105	193.759	62.741	S	20	0.822
11	-14.001	192.978	99.027	S	20	0.819
12	49.637	132.482	67.825	S	20	0.812
13	63.46	154.761	106.084	S	20	0.792
14	41.743	168.959	17.771	S	20	0.786
15	-6.371	198.824	105.574	S	20	0.772
16	56.508	125.952	106.907	S	20	0.759
17	74.307	151.412	91.399	S	20	0.744
18	43.358	153.981	58.704	S	20	0.739
19	7.135	228.717	58.044	S	20	0.732
20	1.336	227.845	106.631	S	20	0.727
21	8.101	173.691	9.735	S	20	0.703
22	7.77	221.179	66.429	S	20	0.701
23	47.041	177.648	10.781	S	20	0.68
24	23.455	174.047	16.428	S	20	0.679
25	-6.251	172.24	151.046	S	20	0.633
26	-45.049	170.748	144.079	S	20	0.631
27	34.877	160.802	64.471	S	20	0.628
28	-19.77	170.106	140.61	S	20	0.604
29	9.176	227.853	137.627	S	20	0.603
30	14.815	184.32	16.385	S	20	0.597
31	50.753	125.027	57.531	S	20	0.586
32	-11.563	181.368	142.465	S	20	0.566
33	-48.588	178.551	154.421	S	20	0.557
34	14.608	199.693	58.232	S	20	0.553
35	73.063	160.347	100.435	S	20	0.546
36	31.704	180.39	18.376	S	20	0.546
37	61.49	124.029	25.95	S	20	0.496

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
SHELX		phasing
REFMAC	5.2.0019	refinement
PDB_EXTRACT	3	data extraction
ADSC	Quantum	data collection
SHELXD		phasing

Refinement

Method to determine structure:

SAD
Starting model: PDB ENTRY 1MU5, 1MX0

1mu5

1mx0

Resolution: 3.56→19.99 Å / Cor.coef. F_o:F_c: 0.867 / Cor.coef. F_o:F_c free: 0.851 / SU B: 110.496 / SU ML: 0.759 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.693 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.333	4471	5 %	RANDOM
R_work	0.312	-	-	-
all	0.313	98444	-	-
obs	0.313	84522	100 %	-

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: 66.325 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-5.07 Å²	0 Å²	0 Å²
2-	-	6.77 Å²	0 Å²
3-	-	-	-1.71 Å²

Refinement step

Cycle: LAST / Resolution: 3.56→19.99 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	27676	0	100	0	27776

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	28324
X-RAY DIFFRACTION	r_angle_refined_deg	1.308	1.984	38208
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.523	5	3392
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.74	24.369	1300
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	22.2	15	5388
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.538	15	184
X-RAY DIFFRACTION	r_chiral_restr	0.086	0.2	4232
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	21024
X-RAY DIFFRACTION	r_nbd_refined	0.324	0.3	13286
X-RAY DIFFRACTION	r_nbtor_refined	0.351	0.5	19104
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.298	0.5	1341
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.369	0.3	85
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.412	0.5	2
X-RAY DIFFRACTION	r_mcbond_it	0.95	2	17389
X-RAY DIFFRACTION	r_mcangle_it	1.705	3	27684
X-RAY DIFFRACTION	r_scbond_it	0.365	2	12252
X-RAY DIFFRACTION	r_scangle_it	0.591	3	10512

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	285	TIGHT POSITIONAL	0.03	0.05
1	2	B	285	TIGHT POSITIONAL	0.03	0.05
1	3	C	285	TIGHT POSITIONAL	0.03	0.05
1	4	D	285	TIGHT POSITIONAL	0.03	0.05
1	1	A	285	TIGHT THERMAL	0.06	0.5
1	2	B	285	TIGHT THERMAL	0.04	0.5
1	3	C	285	TIGHT THERMAL	0.03	0.5
1	4	D	285	TIGHT THERMAL	0.03	0.5
2	1	A	716	TIGHT POSITIONAL	0.03	0.05
2	2	B	716	TIGHT POSITIONAL	0.03	0.05
2	3	C	716	TIGHT POSITIONAL	0.03	0.05
2	4	D	716	TIGHT POSITIONAL	0.02	0.05
2	1	A	716	TIGHT THERMAL	0.06	0.5
2	2	B	716	TIGHT THERMAL	0.04	0.5
2	3	C	716	TIGHT THERMAL	0.04	0.5
2	4	D	716	TIGHT THERMAL	0.04	0.5
3	1	A	1841	TIGHT POSITIONAL	0.04	0.05
3	2	B	1841	TIGHT POSITIONAL	0.03	0.05
3	3	C	1841	TIGHT POSITIONAL	0.04	0.05
3	4	D	1841	TIGHT POSITIONAL	0.03	0.05
3	1	A	1841	TIGHT THERMAL	0.08	0.5
3	2	B	1841	TIGHT THERMAL	0.05	0.5
3	3	C	1841	TIGHT THERMAL	0.06	0.5
3	4	D	1841	TIGHT THERMAL	0.05	0.5
4	1	B	1741	TIGHT POSITIONAL	0.03	0.05
4	2	D	1741	TIGHT POSITIONAL	0.02	0.05
4	3	F	1741	TIGHT POSITIONAL	0.02	0.05
4	4	H	1741	TIGHT POSITIONAL	0.02	0.05
4	1	B	1741	TIGHT THERMAL	0.05	0.5
4	2	D	1741	TIGHT THERMAL	0.04	0.5
4	3	F	1741	TIGHT THERMAL	0.03	0.5
4	4	H	1741	TIGHT THERMAL	0.03	0.5
5	1	A	679	TIGHT POSITIONAL	0.03	0.05
5	2	B	679	TIGHT POSITIONAL	0.02	0.05
5	3	C	679	TIGHT POSITIONAL	0.02	0.05
5	4	D	679	TIGHT POSITIONAL	0.02	0.05
5	1	A	679	TIGHT THERMAL	0.03	0.5
5	2	B	679	TIGHT THERMAL	0.03	0.5
5	3	C	679	TIGHT THERMAL	0.02	0.5
5	4	D	679	TIGHT THERMAL	0.02	0.5
6	1	A	1092	TIGHT POSITIONAL	0.04	0.05
6	2	B	1092	TIGHT POSITIONAL	0.03	0.05
6	3	C	1092	TIGHT POSITIONAL	0.03	0.05
6	4	D	1092	TIGHT POSITIONAL	0.03	0.05
6	1	A	1092	TIGHT THERMAL	0.05	0.5
6	2	B	1092	TIGHT THERMAL	0.04	0.5
6	3	C	1092	TIGHT THERMAL	0.03	0.5
6	4	D	1092	TIGHT THERMAL	0.03	0.5
7	1	A	556	TIGHT POSITIONAL	0.02	0.05
7	2	B	556	TIGHT POSITIONAL	0.03	0.05
7	3	C	556	TIGHT POSITIONAL	0.02	0.05
7	4	D	556	TIGHT POSITIONAL	0.03	0.05
7	1	A	556	TIGHT THERMAL	0.03	0.5
7	2	B	556	TIGHT THERMAL	0.04	0.5
7	3	C	556	TIGHT THERMAL	0.03	0.5
7	4	D	556	TIGHT THERMAL	0.02	0.5
8	1	A	25	TIGHT POSITIONAL	0.01	0.05
8	2	B	25	TIGHT POSITIONAL	0.02	0.05
8	3	C	25	TIGHT POSITIONAL	0.02	0.05
8	4	D	25	TIGHT POSITIONAL	0.02	0.05
8	1	A	25	TIGHT THERMAL	0.04	0.5
8	2	B	25	TIGHT THERMAL	0.03	0.5
8	3	C	25	TIGHT THERMAL	0.04	0.5
8	4	D	25	TIGHT THERMAL	0.04	0.5

LS refinement shell

Resolution: 3.563→3.653 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.439	286	-
R_work	0.414	5314	-
all	-	5600	-
obs	-	-	100 %

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