PDB-1zr4: Structure of a Synaptic gamma-delta Resolvase Tetramer Covalently...

ID or keywords:

Entry

Database: PDB / ID: 1zr4

Title

Structure of a Synaptic gamma-delta Resolvase Tetramer Covalently linked to two Cleaved DNAs

Components

AAA
TCAGTGTCCGATAATTTAT
TTATCGGACACTG
Transposon gamma-delta resolvase

Keywords

RECOMBINATION/DNA / resolvase / site-specific / recombination / flat interface / cross-crystal averaging / multi-crystal averaging / RECOMBINATION-DNA COMPLEX

Function / homology

Function and homology information

DNA strand exchange activity / DNA integration / DNA binding
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.4 Å

Authors

Li, W. / Kamtekar, S. / Xiong, Y. / Sarkis, G.J. / Grindley, N.D. / Steitz, T.A.

Citation

Journal: Science / Year: 2005
Title: Structure of a synaptic gamma delta resolvase tetramer covalently linked to two cleaved DNAs.
Authors: Li, W. / Kamtekar, S. / Xiong, Y. / Sarkis, G.J. / Grindley, N.D. / Steitz, T.A.

History

Deposition	May 19, 2005	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 30, 2005	Provider: repository / Type: Initial release
Revision 1.1	Apr 30, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.3	Oct 20, 2021	Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	1zr4.cif.gz	218.1 KB	Display	PDBx/mmCIF format
PDB format	pdb1zr4.ent.gz	179 KB	Display	PDB format
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Validation report

Summary document	1zr4_validation.pdf.gz	502.8 KB	Display	wwPDB validaton report
Full document	1zr4_full_validation.pdf.gz	538 KB	Display
Data in XML	1zr4_validation.xml.gz	32.7 KB	Display
Data in CIF	1zr4_validation.cif.gz	45.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zr/1zr4 ftp://data.pdbj.org/pub/pdb/validation_reports/zr/1zr4	HTTPS FTP

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Related structure data

Related structure data	1zr2C 1gdr 1gdt 2rsl C: citing same article (ref.)
Similar structure data	1zr2-1 2gm4-1 4cnj-d 5tch-d 6ub9-d 6u6c-d 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
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PDB pages

PDBj /

wwPDB /

NCBI

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Deposited unit

X: TCAGTGTCCGATAATTTAT

Z: AAA

Y: TTATCGGACACTG

J: TCAGTGTCCGATAATTTAT

I: AAA

K: TTATCGGACACTG

U: TCAGTGTCCGATAATTTAT

W: AAA

V: TTATCGGACACTG

M: TCAGTGTCCGATAATTTAT

O: AAA

N: TTATCGGACACTG

A: Transposon gamma-delta resolvase

B: Transposon gamma-delta resolvase

E: Transposon gamma-delta resolvase

D: Transposon gamma-delta resolvase

124 kDa, 16 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	119.158, 127.290, 140.419
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg label comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	LEU	SER	1	A	M	3 - 15	3 - 15
2	1	1	LEU	SER	1	B	N	3 - 15	3 - 15
3	1	1	LEU	SER	1	E	O	3 - 15	3 - 15
4	1	1	LEU	SER	1	D	P	3 - 15	3 - 15
1	2	1	LEU	THR	6	A	M	16 - 99	16 - 99
2	2	1	LEU	THR	6	B	N	16 - 99	16 - 99
3	2	1	LEU	THR	6	E	O	16 - 99	16 - 99
4	2	1	LEU	THR	6	D	P	16 - 99	16 - 99
1	3	1	ASP	THR	6	A	M	100 - 126	100 - 126
2	3	1	ASP	THR	6	B	N	100 - 126	100 - 126
3	3	1	ASP	THR	6	E	O	100 - 126	100 - 126
4	3	1	ASP	THR	6	D	P	100 - 126	100 - 126
1	4	1	ARG	ASN	6	A	M	144 - 183	144 - 183
2	4	1	ARG	ASN	6	B	N	144 - 183	144 - 183
3	4	1	ARG	ASN	6	E	O	144 - 183	144 - 183
4	4	1	ARG	ASN	6	D	P	144 - 183	144 - 183
1	1	2	DA	DT	6	X	A	3 - 17	3 - 17
2	1	2	DA	DT	6	J	D	3 - 17	3 - 17
3	1	2	DA	DT	6	U	G	3 - 17	3 - 17
4	1	2	DA	DT	6	M	J	3 - 17	3 - 17
1	1	3	DA	DA	2	Z	B	20 - 22	1 - 3
2	1	3	DA	DA	2	I	E	20 - 22	1 - 3
3	1	3	DA	DA	2	W	H	20 - 22	1 - 3
4	1	3	DA	DA	2	O	K	20 - 22	1 - 3
1	1	4	DT	DC	6	Y	C	23 - 33	1 - 11
2	1	4	DT	DC	6	K	F	23 - 33	1 - 11
3	1	4	DT	DC	6	V	I	23 - 33	1 - 11
4	1	4	DT	DC	6	N	L	23 - 33	1 - 11

NCS ensembles :

ID
1
2
3
4

Details

Biological Tetramer in Assymetric Unit

#1: DNA chain	TCAGTGTCCGATAATTTAT Mass: 5809.782 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: symmetrized RESOLVASE sites
#2: DNA chain	AAA Mass: 894.663 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: symmetrized RESOLVASE sites
#3: DNA chain	TTATCGGACACTG Mass: 3966.597 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: symmetrized RESOLVASE sites
#4: Protein	Transposon gamma-delta resolvase / Transposon Tn1000 resolvase Mass: 20353.477 Da / Num. of mol.: 4 / Mutation: G101S, E102Y, M103I, E124Q, R2A, E56K Source method: isolated from a genetically manipulated source Details: Activated gamma-delta resolvase mutant / Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pSW26131 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03012

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal

Density Matthews: 3.93 Å³/Da / Density % sol: 68 %

Crystal grow

Temperature: 303 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.2M NaCl, 0.1M Magnesium Formate, 0.1M Sodium Acetate, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 303K

Components of the solutions

ID	Name	Crystal-ID	Sol-ID
1	Sodium Chloride	1	1
2	Magnesium Formate	1	1
3	Sodium Acetate	1	1
4	H2O	1	1
5	Sodium Chloride	1	2
6	Magnesium Formate	1	2
7	Sodium Acetate	1	2
8	H2O	1	2

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.99 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 15, 2005
Radiation	Monochromator: double flat Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99 Å / Relative weight: 1
Reflection	Resolution: 3.4→50 Å / Num. all: 33298 / Num. obs: 33091 / % possible obs: 99.8 % / Observed criterion σ(F): 1.45 / Observed criterion σ(I): 2 / Redundancy: 8 % / R_merge(I) obs: 0.047 / R_sym value: 0.047 / Net I/σ(I): 25.7
Reflection shell	Resolution: 3.4→3.55 Å / Redundancy: 8 % / R_merge(I) obs: 0.01 / Mean I/σ(I) obs: 2 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.4→50 Å / Cor.coef. F_o:F_c: 0.904 / Cor.coef. F_o:F_c free: 0.877 / SU B: 67.9 / SU ML: 0.497 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.558 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.29469	1510	5 %	RANDOM
R_work	0.26399	-	-	-
obs	0.26554	28441	99.74 %	-
all	-	28497	-	-

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: 111.263 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.1 Å²	0 Å²	0 Å²
2-	-	-1.99 Å²	0 Å²
3-	-	-	-0.11 Å²

Refinement step

Cycle: LAST / Resolution: 3.4→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5672	2844	0	0	8516

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	8896
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.453	2.367	12532
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.15	5	726
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.679	23.438	256
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.111	15	1154
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.786	15	64
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	1434
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	5552
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.241	0.2	3129
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.305	0.2	5657
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.145	0.2	172
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	0.308	0.2	34
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.13	0.2	1
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	2.006	1.5	3710
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	3.414	2	5748
X-RAY DIFFRACTION	r_scbond_it	1.85	3	6655
X-RAY DIFFRACTION	r_scangle_it	2.144	4.5	6784
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	101	tight positional	0.03	0.05
1	2	B	101	tight positional	0.02	0.05
1	3	E	101	tight positional	0.03	0.05
1	4	D	101	tight positional	0.03	0.05
3	3	Z	63	medium positional	0.18	0.5
3	2	I	63	medium positional	0.15	0.5
3	3	W	63	medium positional	0.24	0.5
3	4	O	63	medium positional	0.2	0.5
1	1	A	1177	loose positional	2.06	5
1	2	B	1177	loose positional	1.04	5
1	3	E	1177	loose positional	3.06	5
1	4	D	1177	loose positional	0.87	5
2	1	X	308	loose positional	0.49	5
2	2	J	308	loose positional	0.36	5
2	3	U	308	loose positional	0.26	5
2	4	M	308	loose positional	0.52	5
4	1	Y	221	loose positional	0.33	5
4	2	K	221	loose positional	0.34	5
4	4	V	221	loose positional	0.27	5
4	3	N	221	loose positional	0.42	5
1	1	A	101	tight thermal	0.05	0.5
1	2	B	101	tight thermal	0.05	0.5
1	3	E	101	tight thermal	0.05	0.5
1	4	D	101	tight thermal	0.03	0.5
3	1	Z	63	medium thermal	0.28	2
3	2	I	63	medium thermal	0.26	2
3	3	W	63	medium thermal	0.22	2
3	4	O	63	medium thermal	0.27	2
1	1	A	1177	loose thermal	2.65	10
1	2	B	1177	loose thermal	2.75	10
1	3	E	1177	loose thermal	2.08	10
1	4	D	1177	loose thermal	2.52	10
2	1	X	308	loose thermal	6.87	10
2	2	J	308	loose thermal	2.49	10
2	3	U	308	loose thermal	2.89	10
2	4	M	308	loose thermal	4.21	10
4	1	Y	221	loose thermal	5.25	10
4	2	K	221	loose thermal	1.93	10
4	2	V	221	loose thermal	3.62	10
4	4	N	221	loose thermal	2.84	10

LS refinement shell

Resolution: 3.4→3.583 Å / Total num. of bins used: 10

	R_factor	Num. reflection	% reflection
R_free	0.379	202	-
R_work	0.364	4089	-
obs	-	-	99.91 %

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	1.5593	-0.4214	2.6179	4.8684	2.7585	8.7844	-0.4153	-0.1203	0.6473	-0.1585	0.0829	0.0785	-1.0293	-0.3145	0.3325	-0.3512	-0.0457	-0.0207	-0.3822	0.036	-0.3577	20.5619	4.1004	15.5522
2	2.2579	-3.0221	2.4773	7.8754	-7.329	15.1058	-0.1075	0.3705	0.3944	0.4794	-0.8689	-0.5441	-1.7126	1.2484	0.9765	-0.2653	-0.0437	-0.2636	-0.2676	0.0043	-0.3433	32.345	21.6172	17.4676
3	7.6141	-1.1431	5.2767	4.6953	-3.2355	15.077	0.5795	1.6107	0.7525	-0.1927	-1.1748	-0.0853	0.5368	1.4683	0.5953	-0.6219	0.3114	0.2407	-0.2039	0.2249	-0.4666	23.9855	31.2223	-14.8901
4	10.3865	-0.9743	-3.7958	6.1539	3.6554	7.7323	0.1367	0.3627	-0.2466	0.5197	-0.1478	0.711	-0.1209	-0.7049	0.0111	-0.3772	0.1322	0.066	-0.4646	-0.0165	-0.1393	12.5994	28.4161	39.2018
5	12.0221	2.5903	-0.8335	6.733	-0.2808	6.4245	-0.0401	-1.5881	-1.4274	1.0419	-0.3411	1.104	0.5088	-0.5933	0.3812	-0.1945	0.1431	0.2544	-0.2959	-0.0859	0.0177	15.3565	7.9938	44.3795
6	17.7615	2.3647	-7.4321	2.6422	0.2099	4.161	-1.2756	-0.7557	0.2787	-0.6851	0.3635	2.4314	0.0783	-2.518	0.9122	0.6207	-0.151	0.6149	1.9344	-0.0368	2.3089	-17.7358	5.0153	52.7936
7	15.5337	-0.4968	-4.672	3.9384	-0.638	5.734	-0.1877	-0.4914	-0.2671	-0.1582	0.0903	0.0796	0.0081	0.6486	0.0974	-0.3484	-0.1105	-0.0799	-0.2604	0.1668	-0.3634	52.8863	22.7752	31.9996
8	9.1794	-6.2884	-1.5941	4.8967	-0.4327	4.2262	0.7532	1.2513	-0.8933	-1.1428	-1.3023	-0.1905	0.4278	-0.2167	0.5491	-0.3846	0.0466	0.1312	-0.2411	0.1523	-0.1481	44.1611	4.326	25.1124
9	17.2041	-10.34	0.149	9.9514	1.0178	2.0204	-0.0196	1.4607	0.8272	0.1551	-0.3365	-1.1618	0.1337	0.1973	0.3561	-0.1251	0.376	0.2425	-0.0845	-0.0286	-0.0974	73.9836	-11.3309	19.7378
10	2.3598	2.2048	-0.1547	11.0711	-2.879	12.0247	-0.1046	-0.3031	0.2047	1.1086	-0.0446	-0.5444	-0.2745	0.5402	0.1492	-0.076	0.2015	-0.061	-0.32	-0.0084	-0.3812	36.9818	-1.3693	52.4899
11	2.3326	1.6622	2.1858	1.5158	3.436	12.698	-0.4834	-0.4406	0.2197	0.025	0.2181	-0.1759	-0.9367	0.4836	0.2653	-0.2229	0.0812	-0.1059	-0.4207	0.1273	-0.3707	31.2871	19.3491	52.9812
12	8.8533	-1.7388	-0.1728	7.0303	-0.9252	9.8154	0.2196	-1.4946	1.1742	0.2273	-0.1673	-0.7283	-1.8244	0.2744	-0.0524	-0.6361	-0.2919	0.1285	-0.5725	-0.1873	-0.4942	41.3419	23.0314	85.2616

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 99
2	X-RAY DIFFRACTION	2	A	100 - 143
3	X-RAY DIFFRACTION	3	A	144 - 183
4	X-RAY DIFFRACTION	3	Z	20 - 22
5	X-RAY DIFFRACTION	3	X	2 - 19
6	X-RAY DIFFRACTION	3	Y	23 - 35
7	X-RAY DIFFRACTION	4	B	3 - 99
8	X-RAY DIFFRACTION	5	B	100 - 143
9	X-RAY DIFFRACTION	6	I	20 - 22
10	X-RAY DIFFRACTION	6	J	2 - 19
11	X-RAY DIFFRACTION	6	K	23 - 35
12	X-RAY DIFFRACTION	7	E	3 - 99
13	X-RAY DIFFRACTION	8	E	100 - 143
14	X-RAY DIFFRACTION	9	W	20 - 22
15	X-RAY DIFFRACTION	9	U	2 - 19
16	X-RAY DIFFRACTION	9	V	23 - 35
17	X-RAY DIFFRACTION	10	D	3 - 99
18	X-RAY DIFFRACTION	11	D	100 - 143
19	X-RAY DIFFRACTION	12	O	20 - 22
20	X-RAY DIFFRACTION	12	M	2 - 19
21	X-RAY DIFFRACTION	12	N	23 - 35

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