PDB-3sm4: Crystal Structure of the K131A Mutant of Lambda Exonuclease in Co...

ID or keywords:

Entry

Database: PDB / ID: 3sm4

Title

Crystal Structure of the K131A Mutant of Lambda Exonuclease in Complex with a 5'-Phosphorylated 14-mer/12-mer Duplex and Magnesium

Components

5'-D(*TP*CP*GP*GP*TP*AP*CP*AP*GP*TP*AP*G)-3'
5'-D(P*AP*GP*CP*TP*AP*CP*TP*GP*TP*AP*CP*CP*GP*A)-3'
Exonuclease

Keywords

HYDROLASE/DNA / homologous recombination / DNA repair / recombineering / single-strand annealing / Type II Restriction Endonuclease Fold / 5'-3' dsDNA exonuclease / HYDROLASE-DNA complex

Function / homology

Function and homology information

exodeoxyribonuclease (lambda-induced) / double-stranded DNA 5'-3' DNA exonuclease activity / metal ion binding
Similarity search - Function

Biological species

Enterobacteria phage lambda (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.88 Å

Authors

Bell, C.E. / Zhang, J.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Crystal structures of {lambda} exonuclease in complex with DNA suggest an electrostatic ratchet mechanism for processivity.
Authors: Zhang, J. / McCabe, K.A. / Bell, C.E.

History

Deposition	Jun 27, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 20, 2011	Provider: repository / Type: Initial release
Revision 1.1	Aug 3, 2011	Group: Database references / Experimental preparation / Structure summary
Revision 1.2	Nov 8, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_sheet / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 / _struct_sheet.number_strands / _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	3sm4.cif.gz	323 KB	Display	PDBx/mmCIF format
PDB format	pdb3sm4.ent.gz	258.5 KB	Display	PDB format
PDBx/mmJSON format	3sm4.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3sm4_validation.pdf.gz	443.3 KB	Display	wwPDB validaton report
Full document	3sm4_full_validation.pdf.gz	445.1 KB	Display
Data in XML	3sm4_validation.xml.gz	15.1 KB	Display
Data in CIF	3sm4_validation.cif.gz	25.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sm/3sm4 ftp://data.pdbj.org/pub/pdb/validation_reports/sm/3sm4	HTTPS FTP

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Related structure data

Related structure data	3slpC 1avqS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6dz0-1 1cg6-1 3slp-d 5f7o-d 1dea-2 5f78-1 1dci-d 5f7z-2 5hj5-3 5f78-2 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

A: Exonuclease

B: Exonuclease

C: Exonuclease

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

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

hetero molecules

86.8 kDa, 5 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)	78.391, 78.391, 247.534
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	170
Space group name H-M	P6₅

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Protein , 1 types, 3 molecules ABC

#1: Protein	Exonuclease Mass: 26164.758 Da / Num. of mol.: 3 / Mutation: K131A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage lambda (virus) / Gene: exo, Lambda Exonuclease, red-alpha, redX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI References: UniProt: P03697, exodeoxyribonuclease (lambda-induced)

#1: Protein

Exonuclease

Mass: 26164.758 Da / Num. of mol.: 3 / Mutation: K131A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Enterobacteria phage lambda (virus) / Gene: exo, Lambda Exonuclease, red-alpha, redX / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21-AI
References: UniProt: P03697, exodeoxyribonuclease (lambda-induced)

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DNA chain , 2 types, 2 molecules DE

#2: DNA chain	5'-D(TPCPGPGPTPAPCPAPGPTPAPG)-3' Mass: 3702.428 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain	5'-D(PAPGPCPTPAPCPTPGPTPAPCPCPGPA)-3' Mass: 4264.793 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 5'-phosphorylated

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Non-polymers , 4 types, 590 molecules

#4: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 584 / 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: 2.53 Å³/Da / Density % sol: 51.46 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 19% PEG3350, 0.2 M sodium bromide, 5 mM magnesium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 31-ID / Wavelength: 0.97929 Å

Detector

Type: RAYONIX MX225HE / Detector: CCD / Date: Aug 3, 2010

Radiation

Monochromator: Diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97929 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.563
1	1	-H-K, K, -L	2	0.437

Reflection

Resolution: 1.88→67.9 Å / Num. all: 65978 / Num. obs: 65978 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.9 % / R_merge(I) obs: 0.084 / Net I/σ(I): 20.3

Reflection shell

Resolution: 1.88→1.98 Å / Redundancy: 9.1 % / R_merge(I) obs: 0.48 / Mean I/σ(I) obs: 4.2 / % possible all: 100

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Processing

Software

Name	Version	Classification
MAR345		data collection
PHASER		phasing
REFMAC	5.5.0109	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AVQ

1avq

Resolution: 1.88→67.89 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.946 / SU B: 5.388 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.026 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18578	3584	5.2 %	RANDOM
R_work	0.15976	-	-	-
all	0.16113	65978	-	-
obs	0.16113	65978	99.83 %	-

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: 24.638 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-7.59 Å²	0 Å²	0 Å²
2-	-	-7.59 Å²	0 Å²
3-	-	-	15.19 Å²

Refine analyze

	Free	Obs
Luzzati coordinate error	0.024 Å	0.026 Å
Luzzati sigma a	-	0.072 Å

Refinement step

Cycle: LAST / Resolution: 1.88→67.89 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5476	533	14	584	6607

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.022	6218
X-RAY DIFFRACTION	r_angle_refined_deg	0.919	2.054	8517
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.536	5	679
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.863	23.491	275
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.929	15	958
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.465	15	42
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.021	4593

LS refinement shell

Resolution: 1.879→1.928 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.353	243	-
R_work	0.249	4805	-
obs	-	-	98.65 %

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	2.3713	1.3179	1.3319	4.4758	0.7379	10.5555	0.2306	0.1331	0.0393	-0.6716	0.0404	-0.1121	0.3846	0.5155	-0.271	0.2737	0.0658	-0.0196	0.1326	-0.0109	0.3895	-23.829	-36.264	-10.673
2	2.074	-0.0098	0.8875	2.0152	0.0372	1.6153	0.0073	0.0301	-0.0614	0.0062	0.0362	-0.0609	-0.0658	0.1801	-0.0435	0.0637	0.0262	0.0194	0.041	0.0143	0.1406	-19.563	-20.726	4.285
3	2.6025	-1.713	0.9085	8.1018	-3.4366	2.6211	0.0339	0.1165	-0.0931	-0.0519	0.0727	0.555	-0.0551	-0.2318	-0.1066	0.0464	0.0146	-0.0167	0.0734	-0.0105	0.126	-0.5	-31.522	-10.767
4	3.9904	-1.383	-0.906	1.1659	0.1916	0.4987	0.0722	0.1137	-0.4503	-0.1025	-0.139	0.1835	0.1547	-0.048	0.0669	0.102	0.0164	-0.0309	0.0528	0.0054	0.2019	-14.934	-37.785	-1.191
5	2.09	1.5804	-0.0167	4.3935	-0.2272	-0.0793	0.0505	-0.1305	-0.0124	0.0871	-0.0453	0.1248	0.0747	-0.0005	-0.0053	0.1138	0.0317	0.0114	0.0543	0.0135	0.1214	2.048	-30.094	0.919
6	5.1444	-0.6185	-0.8503	2.5559	0.1459	3.6068	-0.0346	-0.1122	0.0079	-0.0054	0.0047	0.0763	-0.0366	-0.0121	0.0299	0.053	0.0152	0.0016	0.0264	0.048	0.1083	-9.183	-34.753	7.164
7	2.5104	-0.4923	-0.4717	0.7099	-0.1904	0.4222	-0.0593	-0.1716	-0.1863	0.0715	0.0704	0.1275	0.0022	-0.0271	-0.0111	0.0805	0.0077	-0.0179	0.0242	0.003	0.1055	-13.991	-29.339	4.649
8	4.1418	3.0876	1.0501	3.3146	1.4879	0.8794	0.0612	0.0377	-0.2041	0.1451	0.0269	-0.4244	0.247	0.1927	-0.0881	0.1187	0.0528	-0.005	0.1151	0.0078	0.2094	32.691	-12.692	-9.713
9	3.0976	1.2989	-0.145	4.0057	-1.6286	8.53	-0.0454	0.4799	0.2562	-0.5901	0.0436	0.0234	-0.331	0.1041	0.0018	0.148	0.0384	-0.0127	0.1098	0.0218	0.1642	20.908	-9.279	-11.912
10	2.3888	1.1482	-2.9402	2.1999	-4.3687	12.8536	0.0943	-0.0697	0.1992	0.3782	0.1387	0.2069	-0.004	-0.5431	-0.233	0.2177	-0.0044	0.0149	0.1122	-0.0289	0.1521	11.254	-8.842	9.927
11	2.8303	-0.6499	-1.073	3.2361	3.4761	4.9283	0.0256	-0.0879	-0.0405	0.1076	-0.0062	-0.0329	0.1066	-0.0658	-0.0194	0.016	0.0068	-0.0128	0.0114	0.0226	0.0816	11.723	-17.242	1.374
12	2.4337	3.9057	-0.297	6.5378	-0.5339	1.1885	-0.1407	0.2574	-0.0133	-0.5253	0.1609	-0.0961	0.177	-0.0441	-0.0202	0.1418	0.0721	-0.0094	0.1021	0.0313	0.1397	6.835	1.597	-13.605
13	1.4473	-0.9257	0.3255	1.5582	-0.1028	0.3531	-0.0633	-0.0506	0.2104	-0.0253	0.053	-0.1796	-0.0473	0.0655	0.0103	0.0446	-0.0082	-0.0133	0.031	0.0024	0.1421	16.101	5.512	-4.255
14	0.8704	-0.4345	0.1918	1.6523	-0.186	0.3689	-0.0576	-0.0957	0.0788	0.1598	0.0701	-0.1081	0.008	0.0222	-0.0124	0.0432	0.0184	-0.0206	0.0456	-0.005	0.0967	17.849	-2.594	2.018
15	4.8991	-3.386	-4.2081	3.4779	3.883	4.6794	0.1443	-0.0869	0.2918	-0.1326	-0.0194	-0.0302	-0.0809	0.3106	-0.125	0.1381	0.0484	-0.0262	0.1156	-0.0025	0.1875	-22.973	26.468	-10.21
16	0.8145	-0.7307	1.1979	1.9251	-1.9147	5.4842	0.0866	0.0216	-0.0729	-0.0745	-0.0585	0.0537	0.1804	0.0151	-0.0281	0.0242	0.0352	0.012	0.0597	0.0031	0.1756	-15.499	11.235	0.373
17	2.488	-0.0572	-1.2446	3.309	-1.2413	8.7807	0.039	-0.0564	-0.181	-0.033	-0.0502	0.0967	0.2615	-0.1248	0.0112	0.0136	0.0134	0.0012	0.013	0.0156	0.1693	-7.595	12.116	-2.208
18	0.4401	0.9217	0.1392	2.0409	0.2063	0.502	-0.0425	0.0694	0.0605	-0.1052	0.0465	0.0572	0.0088	-0.0213	-0.004	0.0536	0.0131	0.0054	0.073	0.0227	0.1678	-29.591	7.036	-7.104
19	3.6803	-1.6362	-0.0813	3.2896	-1.099	2.2012	-0.0489	-0.0457	0.0108	0.2728	-0.075	-0.2167	-0.1275	0.0098	0.124	0.0406	-0.0251	-0.0108	0.0184	-0.0114	0.1293	-27.343	-6.777	1.197
20	0.9983	0.653	0.3561	3.406	1.5737	1.2735	0.0428	-0.0471	0.0354	0.2467	-0.0021	0.1189	0.1246	-0.031	-0.0406	0.0521	0.0248	0.0192	0.0259	0.0226	0.1187	-30.066	4.097	4.135
21	5.8572	1.4782	-2.465	1.9876	-0.635	1.6084	0.0701	-0.2976	0.1589	0.0827	-0.0648	-0.0846	-0.1872	0.2319	-0.0053	0.0959	-0.0076	-0.0296	0.0449	-0.0053	0.1781	-10.102	22.159	2.239
22	7.1011	1.6004	-2.0307	2.6277	-0.9968	3.9151	-0.0216	0.082	0.2835	-0.1753	0.141	0.4277	0.1002	-0.4537	-0.1194	0.137	-0.0273	0.012	0.1179	0.0414	0.1163	-17.094	-3.991	19.697
23	3.0457	-0.5916	-3.7658	3.6922	1.1907	2.8954	0.0016	0.2209	0.0507	0.1041	0.0217	-0.365	0.0281	-0.1766	-0.0232	0.18	0.0061	0.0181	0.164	-0.027	0.1612	-4.318	-2.441	11.464
24	0.2683	-0.3335	0.0609	2.0547	-0.5989	-0.9073	-0.0359	-0.0691	-0.0313	-0.0676	0.0929	0.1837	0.0313	-0.0851	-0.057	0.0626	-0.0061	0.0041	0.1257	0.0077	0.1678	0.045	-10.792	-0.849
25	9.1926	1.1738	-1.7761	0.135	0.553	1.4718	-0.1604	0.2491	-0.4208	0.0388	-0.0014	0.0055	0.1563	-0.064	0.1617	0.0546	0.01	-0.0017	0.0582	0.0248	0.1491	6.947	-2.685	-5.994
26	3.4392	0.1197	-1.85	1.5756	-6.5137	9.4698	0.4896	0.0312	0.716	-0.2919	0.0687	0.5523	0.5172	-0.2819	-0.5582	0.3551	0.0053	0.0724	0.261	-0.0231	0.3843	-7.476	-7.117	2.346
27	5.404	1.5093	0.6675	5.8755	1.5341	7.9891	-0.0699	0.0162	-0.0914	0.2813	0.0688	-0.3402	0.1869	0.2504	0.0011	0.1026	-0.0269	0.0006	0.1396	0.0516	0.1411	-8.808	-3.993	20.565

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 22
2	X-RAY DIFFRACTION	2	A	23 - 73
3	X-RAY DIFFRACTION	3	A	74 - 94
4	X-RAY DIFFRACTION	4	A	95 - 119
5	X-RAY DIFFRACTION	5	A	120 - 149
6	X-RAY DIFFRACTION	6	A	150 - 171
7	X-RAY DIFFRACTION	7	A	172 - 226
8	X-RAY DIFFRACTION	8	B	-1 - 13
9	X-RAY DIFFRACTION	9	B	14 - 32
10	X-RAY DIFFRACTION	10	B	33 - 49
11	X-RAY DIFFRACTION	11	B	50 - 71
12	X-RAY DIFFRACTION	12	B	72 - 90
13	X-RAY DIFFRACTION	13	B	91 - 148
14	X-RAY DIFFRACTION	14	B	149 - 226
15	X-RAY DIFFRACTION	15	C	-2 - 14
16	X-RAY DIFFRACTION	16	C	15 - 52
17	X-RAY DIFFRACTION	17	C	53 - 72
18	X-RAY DIFFRACTION	18	C	73 - 128
19	X-RAY DIFFRACTION	19	C	129 - 147
20	X-RAY DIFFRACTION	20	C	148 - 197
21	X-RAY DIFFRACTION	21	C	198 - 226
22	X-RAY DIFFRACTION	22	D	1 - 4
23	X-RAY DIFFRACTION	23	D	5 - 8
24	X-RAY DIFFRACTION	24	D	9 - 12
25	X-RAY DIFFRACTION	25	E	1 - 4
26	X-RAY DIFFRACTION	26	E	5 - 8
27	X-RAY DIFFRACTION	27	E	9 - 14

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