PDB-4lrv: Crystal structure of DndE from Escherichia coli B7A involved in D...

ID or keywords:

Entry

Database: PDB / ID: 4lrv

Title

Crystal structure of DndE from Escherichia coli B7A involved in DNA phosphorothioation modification

Components

DNA sulfur modification protein DndE

Keywords

DNA BINDING PROTEIN / DNA phosphorothioation

Function / homology

DNA sulphur modification protein DndE / Arc Repressor Mutant / Orthogonal Bundle / Mainly Alpha / :

Function and homology information

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.5 Å

Authors

Hu, W. / Wang, C.K. / Liang, J.D. / Zhang, T.L. / Yang, M. / Hu, Z.P. / Wang, Z.J. / Lan, W.X. / Wu, H.M. / Ding, J.P. ...

Citation

Journal: Cell Res. / Year: 2012
Title: Structural insights into DndE from Escherichia coli B7A involved in DNA phosphorothioation modification
Authors: Hu, W. / Wang, C.K. / Liang, J.D. / Zhang, T.L. / Hu, Z.P. / Wang, Z.J. / Lan, W.X. / Li, F. / Wu, H.M. / Ding, J.P. / Wu, G. / Deng, Z.X. / Cao, C.

History

Deposition	Jul 21, 2013	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Aug 28, 2013	Provider: repository / Type: Initial release
Revision 1.1	Sep 4, 2013	Group: Experimental preparation
Revision 1.2	Oct 30, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4lrv.cif.gz	628.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4lrv.ent.gz	527.4 KB	Display	PDB format
PDBx/mmJSON format	4lrv.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4lrv_validation.pdf.gz	538.5 KB	Display	wwPDB validaton report
Full document	4lrv_full_validation.pdf.gz	574.3 KB	Display
Data in XML	4lrv_validation.xml.gz	71.2 KB	Display
Data in CIF	4lrv_validation.cif.gz	92.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lr/4lrv ftp://data.pdbj.org/pub/pdb/validation_reports/lr/4lrv	HTTPS FTP

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Related structure data

Similar structure data	2vaf-1 2uz3-d 4nge-1 5njc-2 6vrx-5 5vfx-1 5kn2-2 2ra8-1 Search similar-shape structures by Omokage search (details) 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 - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: DNA sulfur modification protein DndE

B: DNA sulfur modification protein DndE

C: DNA sulfur modification protein DndE

D: DNA sulfur modification protein DndE

E: DNA sulfur modification protein DndE

F: DNA sulfur modification protein DndE

G: DNA sulfur modification protein DndE

H: DNA sulfur modification protein DndE

I: DNA sulfur modification protein DndE

J: DNA sulfur modification protein DndE

K: DNA sulfur modification protein DndE

L: DNA sulfur modification protein DndE

M: DNA sulfur modification protein DndE

N: DNA sulfur modification protein DndE

O: DNA sulfur modification protein DndE

P: DNA sulfur modification protein DndE

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

1

A: DNA sulfur modification protein DndE

C: DNA sulfur modification protein DndE

E: DNA sulfur modification protein DndE

M: DNA sulfur modification protein DndE

A: DNA sulfur modification protein DndE

C: DNA sulfur modification protein DndE

E: DNA sulfur modification protein DndE

M: DNA sulfur modification protein DndE

defined by author&software
101 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: DNA sulfur modification protein DndE

D: DNA sulfur modification protein DndE

F: DNA sulfur modification protein DndE

G: DNA sulfur modification protein DndE

I: DNA sulfur modification protein DndE

J: DNA sulfur modification protein DndE

K: DNA sulfur modification protein DndE

P: DNA sulfur modification protein DndE

defined by author&software
101 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

H: DNA sulfur modification protein DndE

L: DNA sulfur modification protein DndE

N: DNA sulfur modification protein DndE

O: DNA sulfur modification protein DndE

H: DNA sulfur modification protein DndE

L: DNA sulfur modification protein DndE

N: DNA sulfur modification protein DndE

O: DNA sulfur modification protein DndE

defined by author&software
101 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	97.845, 97.306, 218.532
Angle α, β, γ (deg.)	90.00, 95.81, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	DNA sulfur modification protein DndE Mass: 12574.100 Da / Num. of mol.: 16 / Fragment: UNP RESIDUES 1-108 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: B7A / Gene: dndE, EcB7A_5348 / Production host: Escherichia coli (E. coli) / References: UniProt: B3HI59
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 384 / Source method: isolated from a natural source / Formula: H₂O
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: 2.4 Å³/Da / Density % sol: 48.66 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion / pH: 6.6 Details: 1.5M sodium citrate (pH 6.6), 1M cesium chloride, VAPOR DIFFUSION, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 24, 2011
Radiation	Monochromator: Si 111 CHANNEL / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97 Å / Relative weight: 1
Reflection	Resolution: 2.5→50 Å / Num. obs: 62884 / % possible obs: 96.8 % / Observed criterion σ(F): 23.2 / Observed criterion σ(I): 2

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHENIX		model building
REFMAC	5.5.0109	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.5→50 Å / Cor.coef. F_o:F_c: 0.927 / Cor.coef. F_o:F_c free: 0.902 / SU B: 17.3 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R Free: 0.308 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24166	3139	5 %	RANDOM
R_work	0.20106	-	-	-
obs	0.20306	59323	88.33 %	-

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: 24.325 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.23 Å²	0 Å²	0.17 Å²
2-	-	-1.96 Å²	0 Å²
3-	-	-	1.76 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13375	0	0	384	13759

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	13594
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.105	1.987	18319
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.615	5	1652
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.377	23.765	571
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.428	15	2629
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.526	15	105
X-RAY DIFFRACTION	r_chiral_restr	0.079	0.2	2107
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	9817
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
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
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	0.793	1.5	8336
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.583	2	13363
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.409	3	5258
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.823	4.5	4956
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr	1.182	3	13594
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.5→2.565 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.257	231	-
R_work	0.192	4137	-
obs	-	-	83.06 %

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	0.5247	0.2197	0.0381	0.4934	0.116	0.2178	0.0013	-0.0056	-0.0004	0.0143	-0.0077	0.0051	0.0166	0.0003	0.0064	0.0272	-0.0005	0.0012	0.0302	0.0046	0.0068	32.383	20.7293	12.0563
2	0.6521	0.2633	-0.2128	0.4956	-0.1477	0.2271	-0.0019	0.0086	-0.0072	-0.0093	-0.0064	0.0015	-0.0032	-0.0088	0.0083	0.0208	-0.0006	-0.0018	0.0329	-0.0056	0.0039	32.0761	21.0312	42.4744
3	0.4093	0.263	-0.0557	0.6462	-0.1335	0.2348	-0.0061	0.0117	-0.0207	0.0057	0.0123	-0.0305	-0.0131	-0.0028	-0.0061	0.0268	0.0019	-0.0013	0.0321	0.0005	0.0077	68.2619	43.1456	11.3239
4	1.22	-0.1962	-0.2336	0.6891	0.0768	0.4447	-0.0009	0.039	-0.0128	-0.0249	-0.0171	0.0659	0.0048	-0.0228	0.018	0.0236	0.0062	-0.0057	0.0185	-0.006	0.0079	26.0612	50.863	40.8575
5	0.6158	-0.1943	-0.0635	1.0309	0.3364	0.5979	-0.0083	-0.0215	-0.045	0.0244	-0.0157	0.0057	0.0251	-0.0114	0.0241	0.0193	-0.0003	0.0035	0.0207	0.0076	0.0066	62.1247	14.7771	13.3518
6	0.4978	-0.2426	0.2173	0.5835	-0.109	0.2988	-0.005	-0.0017	0.0094	0.001	-0.0157	-0.002	0.0042	-0.0031	0.0207	0.0157	-0.0019	0.0009	0.0398	0.0036	0.005	32.2379	54.3352	66.1439
7	0.6377	0.3912	0.0576	0.6026	0.0187	0.3112	-0.0118	0.0187	0.0479	-0.0015	0.0046	0.0105	0.0169	0.0147	0.0072	0.0235	0.004	-0.0027	0.0313	-0.0024	0.0052	54.7022	56.7568	43.1961
8	0.6216	-0.4207	-0.0585	0.4869	0.158	0.2363	0.0005	0.0082	-0.0206	-0.0204	0.0011	0.037	-0.0159	-0.0184	-0.0016	0.0284	-0.0047	0.0029	0.0342	0.0015	0.006	18.5045	37.7399	97.1826
9	1.2225	0.0122	0.3027	0.3643	0.0848	0.3183	-0.0159	-0.0304	-0.0041	0.0163	0.0058	0.0318	-0.0294	-0.0284	0.0101	0.0277	-0.002	0.0064	0.0248	-0.0018	0.0052	26.4305	24.6026	67.6301
10	0.6624	-0.3133	-0.2198	0.5211	0.048	0.1681	0.0027	0.0039	-0.0291	-0.001	-0.006	0.0132	0.0073	0.0066	0.0034	0.0278	-0.0015	-0.0062	0.0313	0.0005	0.0029	54.6878	18.4615	65.9395
11	0.6749	-0.2022	0.0266	0.7268	-0.156	0.3146	-0.0093	-0.0191	0.0035	0	0.0002	-0.0558	0.0293	0.0052	0.0091	0.0271	0.001	0.0019	0.024	-0.0014	0.0049	59.2249	26.9493	41.4275
12	0.9012	0.2112	-0.0448	1.2309	-0.4745	0.5157	-0.0357	0.0103	-0.0633	-0.0169	0.0097	-0.0079	0.0319	-0.0035	0.026	0.0096	-0.0037	0.0085	0.0217	-0.0129	0.0142	24.933	9.4458	95.8157
13	0.6657	-0.1078	0.0495	0.4923	-0.1006	0.4068	0.0025	-0.0097	0.0495	-0.0103	-0.0064	0.0053	-0.0031	-0.0033	0.0039	0.0256	0.0029	-0.003	0.0281	-0.0074	0.0058	38.3288	47.6304	13.1001
14	0.2752	0.1413	0.0948	0.4543	0.1787	0.4049	-0.0045	-0.0044	0.0253	-0.0069	-0.0068	-0.0221	-0.0139	-0.0041	0.0112	0.0301	0	0.0009	0.037	0.0038	0.0067	48.0158	42.808	96.2542
15	0.5205	-0.3805	0.0696	0.6648	-0.2077	0.2279	-0.0064	0.0015	-0.0045	-0.0032	0.0022	0.0106	0.0165	0.011	0.0041	0.027	-0.002	0.0006	0.0347	-0.0017	0.0036	54.3712	15.5613	96.751
16	0.6798	0.1403	-0.1919	0.98	-0.0812	0.3512	-0.0009	-0.0052	0.0155	0.005	-0.0302	-0.1002	-0.007	0.0181	0.0311	0.0189	-0.0032	-0.0056	0.0255	0.0071	0.0159	59.5265	48.1058	67.5735

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 108
2	X-RAY DIFFRACTION	2	B	3 - 108
3	X-RAY DIFFRACTION	3	C	3 - 107
4	X-RAY DIFFRACTION	4	D	2 - 108
5	X-RAY DIFFRACTION	5	E	3 - 107
6	X-RAY DIFFRACTION	6	F	3 - 106
7	X-RAY DIFFRACTION	7	G	2 - 107
8	X-RAY DIFFRACTION	8	H	2 - 107
9	X-RAY DIFFRACTION	9	I	2 - 107
10	X-RAY DIFFRACTION	10	J	3 - 108
11	X-RAY DIFFRACTION	11	K	3 - 109
12	X-RAY DIFFRACTION	12	L	3 - 107
13	X-RAY DIFFRACTION	13	M	3 - 110
14	X-RAY DIFFRACTION	14	N	3 - 108
15	X-RAY DIFFRACTION	15	O	2 - 107
16	X-RAY DIFFRACTION	16	P	2 - 108

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