PDB-1z1g: Crystal structure of a lambda integrase tetramer bound to a Holli...

ID or keywords:

Entry

Database: PDB / ID: 1z1g

Title

Crystal structure of a lambda integrase tetramer bound to a Holliday junction

Components

(29-MER) x 4
25-MER
5'-D(*AP*CP*AP*GP*GP*TP*CP*AP*CP*TP*AP*TP*CP*AP*GP*TP*CP*AP*AP*AP*AP*TP*AP*CP*C)-3'
Integrase

Keywords

DNA BINDING PROTEIN/DNA / Protein-DNA complex / DNA BINDING PROTEIN-DNA COMPLEX

Function / homology

Function and homology information

provirus excision / integrase activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / transferase activity / DNA recombination / Hydrolases; Acting on ester bonds / hydrolase activity ...
Similarity search - Function

Biological species

Enterobacteria phage lambda (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MIRAS / Resolution: 4.4 Å

Authors

Biswas, T. / Aihara, H. / Radman-Livaja, M. / Filman, D. / Landy, A. / Ellenberger, T.

Citation

Journal: Nature / Year: 2005
Title: A structural basis for allosteric control of DNA recombination by lambda integrase.
Authors: Biswas, T. / Aihara, H. / Radman-Livaja, M. / Filman, D. / Landy, A. / Ellenberger, T.

History

Deposition	Mar 3, 2005	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 28, 2005	Provider: repository / Type: Initial release
Revision 1.1	Apr 30, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / 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_ref_seq_dif.details
Revision 1.4	Nov 13, 2024	Group: Data collection / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	1z1g.cif.gz	355.9 KB	Display	PDBx/mmCIF format
PDB format	pdb1z1g.ent.gz	264.7 KB	Display	PDB format
PDBx/mmJSON format	1z1g.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	1z1g_validation.pdf.gz	523.9 KB	Display	wwPDB validaton report
Full document	1z1g_full_validation.pdf.gz	787.9 KB	Display
Data in XML	1z1g_validation.xml.gz	80.4 KB	Display
Data in CIF	1z1g_validation.cif.gz	110.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z1/1z1g ftp://data.pdbj.org/pub/pdb/validation_reports/z1/1z1g	HTTPS FTP

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Related structure data

Related structure data	1z19C 1z1bC 1kjk 1p7d C: citing same article (ref.)
Similar structure data	1z1b-1 6olp-d 1suv-d 4zuz-d 6saw-d 8987 9343 5uqg-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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similarity (1)
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Deposited unit

I: 29-MER

J: 29-MER

K: 29-MER

L: 29-MER

E: 5'-D(*AP*CP*AP*GP*GP*TP*CP*AP*CP*TP*AP*TP*CP*AP*GP*TP*CP*AP*AP*AP*AP*TP*AP*CP*C)-3'

F: 25-MER

G: 5'-D(*AP*CP*AP*GP*GP*TP*CP*AP*CP*TP*AP*TP*CP*AP*GP*TP*CP*AP*AP*AP*AP*TP*AP*CP*C)-3'

H: 25-MER

A: Integrase

B: Integrase

C: Integrase

D: Integrase

229 kDa, 12 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)	109.759, 109.759, 265.971
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	144
Space group name H-M	P3₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Refine code: 2

Dom-ID	Component-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	1	THR	THR	VAL	VAL	A	I	75 - 175	75 - 175
2	1	1	THR	THR	VAL	VAL	B	J	75 - 175	75 - 175
3	1	1	THR	THR	VAL	VAL	C	K	75 - 175	75 - 175
4	1	1	THR	THR	VAL	VAL	D	L	75 - 175	75 - 175
5	2	1	ARG	ARG	LEU	LEU	A	I	176 - 330	176 - 330
6	2	1	ARG	ARG	LEU	LEU	B	J	176 - 330	176 - 330
7	2	1	ARG	ARG	LEU	LEU	C	K	176 - 330	176 - 330
8	2	1	ARG	ARG	LEU	LEU	D	L	176 - 330	176 - 330
1	1	2	ASP	ASP	ASP	ASP	A	I	11 - 40	11 - 40
2	1	2	ASP	ASP	ASP	ASP	B	J	11 - 40	11 - 40
3	1	2	ASP	ASP	ASP	ASP	C	K	11 - 40	11 - 40
4	1	2	ASP	ASP	ASP	ASP	D	L	11 - 40	11 - 40
1	1	3	ARG	ARG	LEU	LEU	A	I	41 - 55	41 - 55
2	1	3	ARG	ARG	LEU	LEU	B	J	41 - 55	41 - 55
3	1	3	ARG	ARG	LEU	LEU	C	K	41 - 55	41 - 55
4	1	3	ARG	ARG	LEU	LEU	D	L	41 - 55	41 - 55
1	1	4	DC	DC	DC	DC	E	E	2 - 24	2 - 24
2	1	4	DC	DC	DC	DC	G	G	2 - 24	2 - 24
1	1	5	DG	DG	DG	DG	F	F	2 - 24	2 - 24
2	1	5	DG	DG	DG	DG	H	H	2 - 24	2 - 24
1	1	6	DA	DA	DT	DT	I	A	2 - 13	2 - 13
2	1	6	DT	DT	DT	DT	K	C	2 - 13	2 - 13
1	1	7	DA	DA	DT	DT	J	B	17 - 28	17 - 28
2	1	7	DA	DA	DA	DA	L	D	17 - 28	17 - 28
1	1	8	DA	DA	DC	DC	I	A	16 - 29	16 - 29
2	1	8	DT	DT	DG	DG	K	C	16 - 29	16 - 29
1	1	9	DA	DA	DT	DT	L	D	2 - 14	2 - 14
2	1	9	DG	DG	DA	DA	J	B	2 - 14	2 - 14

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9

Details

The biological assembly is a tetramer contained in an asymetric unit

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DNA chain , 6 types, 8 molecules IJKLEGFH

#1: DNA chain	29-MER Mass: 8867.746 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain	29-MER Mass: 8940.810 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain	29-MER Mass: 8898.756 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: DNA chain	29-MER Mass: 8941.797 Da / Num. of mol.: 1 / Source method: obtained synthetically
#5: DNA chain	5'-D(APCPAPGPGPTPCPAPCPTPAPTPCPAPGPTPCPAPAPAPAPTPAPCPC)-3' Mass: 7619.965 Da / Num. of mol.: 2 / Source method*: obtained synthetically
#6: DNA chain	25-MER Mass: 7734.991 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Protein , 1 types, 4 molecules ABCD

#7: Protein	Integrase Mass: 40732.324 Da / Num. of mol.: 4 / Mutation: Y342F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage lambda (virus) / Genus: Lambda-like viruses / Gene: INT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: P03700

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Details

Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal

Density Matthews: 3.96 Å³/Da / Density % sol: 71 %

Crystal grow

Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, bis-tris-propane, di-ammonium hydrogen phosphate, glycerol, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Components of the solutions

ID	Name	Crystal-ID	Sol-ID
1	PEG 8000	1	1
2	bis-tris-propane	1	1
3	di-ammonium hydrogen phosphate	1	1
4	glycerol	1	1
5	DTT	1	1
6	H2O	1	1
7	PEG 8000	1	2
8	bis-tris-propane	1	2
9	di-ammonium hydrogen phosphate	1	2

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X25 / Wavelength: 0.9793,0.9795,0.9709

Detector

Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 15, 2003

Radiation

Monochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9793	1
2	0.9795	1
3	0.9709	1

Reflection

Resolution: 4.4→45 Å / Num. all: 22852 / Num. obs: 22783 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3

Reflection shell

Resolution: 4.4→4.56 Å / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.1.24	refinement
HKL-2000		data reduction
CCP4	(TRUNCATE)	data scaling
SHARP		phasing

Refinement

Method to determine structure:

MIRAS / Resolution: 4.4→20 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.93 / SU B: 115.312 / SU ML: 1.31 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 1.102
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.29207	1146	5.1 %	RANDOM
R_work	0.24444	-	-	-
obs	0.24683	21338	99.96 %	-
all	-	22525	-	-

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: 108.297 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.63 Å²	-0.81 Å²	0 Å²
2-	-	-1.63 Å²	0 Å²
3-	-	-	2.44 Å²

Refinement step

Cycle: LAST / Resolution: 4.4→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10790	4366	0	0	15156

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.025	0.021	15870
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.831	2.311	22327
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.46	5	1364
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.165	0.2	2286
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	10426
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.331	0.2	8695
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	0.278	0.3	697
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	0.368	0.2	79
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.498	0.3	4
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scangle_it
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	1016	tight positional	0.08	0.05
1	2	B	1016	tight positional	0.09	0.05
1	3	C	1016	tight positional	0.08	0.05
1	4	D	1016	tight positional	0.07	0.05
2	1	A	120	tight positional	0.11	0.05
2	2	B	120	tight positional	0.1	0.05
2	3	C	120	tight positional	0.11	0.05
2	4	D	120	tight positional	0.14	0.05
3	1	A	60	tight positional	0.09	0.05
3	2	B	60	tight positional	0.1	0.05
3	3	C	60	tight positional	0.1	0.05
3	4	D	60	tight positional	0.12	0.05
1	1	A	960	medium positional	0.79	0.5
1	2	B	960	medium positional	0.82	0.5
1	3	C	960	medium positional	0.89	0.5
1	4	D	960	medium positional	0.85	0.5
2	1	A	131	medium positional	1.2	0.5
2	2	B	131	medium positional	1.45	0.5
2	3	C	131	medium positional	1.19	0.5
2	4	D	131	medium positional	1.13	0.5
3	1	A	59	medium positional	1.25	0.5
3	2	B	59	medium positional	1.17	0.5
3	3	C	59	medium positional	1.19	0.5
3	4	D	59	medium positional	1.46	0.5
4	1	E	469	medium positional	0.32	0.5
5	1	F	474	medium positional	0.35	0.5
6	1	I	140	medium positional	0.36	0.5
7	1	J	147	medium positional	0.28	0.5
8	1	I	146	medium positional	0.35	0.5
9	1	L	141	medium positional	0.32	0.5

LS refinement shell

Resolution: 4.4→4.626 Å / Total num. of bins used: 10 /

	R_factor	Num. reflection
R_free	0.39	150
R_work	0.378	3021

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	0.9452	-2.0521	-0.8699	3.2428	-1.0963	3.7001	0.3401	-0.5312	-1.0097	1.0517	-0.1489	-0.0011	0.7567	-0.2419	-0.1912	0.1447	0.4982	0.1455	2.2111	-0.5262	2.2717	36.7222	-19.1301	43.3496
2	3.5963	-0.0667	0.1207	3.4823	0.8801	3.9059	-0.4424	1.3172	1.1585	-1.6333	0.4992	-0.6426	-2.0655	0.7003	-0.0568	2.1913	-0.5277	0.1008	2.0766	0.089	1.351	37.2115	14.1505	-0.504

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	I	11 - 74	11 - 74
2	X-RAY DIFFRACTION	1	B	J	10 - 74	10 - 74
3	X-RAY DIFFRACTION	1	C	K	11 - 74	11 - 74
4	X-RAY DIFFRACTION	1	D	L	10 - 74	10 - 74
5	X-RAY DIFFRACTION	1	E	E	1 - 24	1 - 24
6	X-RAY DIFFRACTION	1	F	F	1 - 25	1 - 25
7	X-RAY DIFFRACTION	1	G	G	1 - 24	1 - 24
8	X-RAY DIFFRACTION	1	H	H	1 - 25	1 - 25
9	X-RAY DIFFRACTION	2	A	I	75 - 356	75 - 356
10	X-RAY DIFFRACTION	2	B	J	75 - 356	75 - 356
11	X-RAY DIFFRACTION	2	C	K	75 - 356	75 - 356
12	X-RAY DIFFRACTION	2	D	L	75 - 356	75 - 356
13	X-RAY DIFFRACTION	2	I	A	1 - 29	1 - 29
14	X-RAY DIFFRACTION	2	J	B	1 - 29	1 - 29
15	X-RAY DIFFRACTION	2	K	C	1 - 29	1 - 29
16	X-RAY DIFFRACTION	2	L	D	1 - 29	1 - 29

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DNA chain , 6 types, 8 molecules IJKLEGFH

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Protein , 1 types, 4 molecules ABCD

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-DNA chain , 6 types, 8 molecules IJKLEGFH

-Protein , 1 types, 4 molecules ABCD

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Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
DNA chain , 6 types, 8 molecules IJKLEGFH

-
Protein , 1 types, 4 molecules ABCD

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi