PDB-3on0: Crystal structure of the pED208 TraM-sbmA complex

ID or keywords:

Entry

Database: PDB / ID: 3on0

Title

Crystal structure of the pED208 TraM-sbmA complex

Components

Protein traM
sbmA

Keywords

DNA BINDING PROTEIN/DNA / DNA binding protein / DNA Protein-DNA complex / tetramer / cooperative binding / unwinding of DNA / kinking of DNA / plasmid conjugation / bacterial conjugation / ribbon-helix-helix / 4-helix bundle / transcriptional repressor / DNA / DNA BINDING PROTEIN-DNA complex

Function / homology

Function and homology information

DNA binding / cytoplasm
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.874 Å

Authors

Wong, J.J.W. / Lu, J. / Edwards, R.A. / Frost, L.S. / Mark Glover, J.N.

Citation

Journal: Nucleic Acids Res. / Year: 2011
Title: Structural basis of cooperative DNA recognition by the plasmid conjugation factor, TraM.
Authors: Wong, J.J. / Lu, J. / Edwards, R.A. / Frost, L.S. / Glover, J.N.

History

Deposition	Aug 27, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 25, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Sep 7, 2011	Group: Database references
Revision 1.3	Sep 6, 2023	Group: Data collection / Database references / 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 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.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3on0.cif.gz	218.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3on0.ent.gz	176.3 KB	Display	PDB format
PDBx/mmJSON format	3on0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/on/3on0 ftp://data.pdbj.org/pub/pdb/validation_reports/on/3on0	HTTPS FTP

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Related structure data

Related structure data	3omyC 2g7oS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4kro-d 1iyj-d 3iya-d 3m63-d 3ggp-d 1641 6rpj-d 2nqq-d 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
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PDB pages

PDBj /

wwPDB /

NCBI

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Deposited unit

A: Protein traM

B: Protein traM

C: Protein traM

D: Protein traM

P: sbmA

66.1 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Protein traM

B: Protein traM

C: Protein traM

D: Protein traM

P: sbmA

A: Protein traM

B: Protein traM

C: Protein traM

D: Protein traM

P: sbmA

defined by author&software
132 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	93.025, 154.687, 167.565
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
1	2	B
2	2	C
3	2	A
4	2	D
1	3	A
2	3	B
3	3	C
1	4	A
2	4	B
3	4	D

NCS domain segments:

Refine code: 3

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	GLN	GLN	PHE	PHE	A	A	61 - 98	61 - 98
2	1	1	GLN	GLN	PHE	PHE	B	B	61 - 98	61 - 98
3	1	1	GLN	GLN	PHE	PHE	C	C	61 - 98	61 - 98
4	1	1	GLN	GLN	PHE	PHE	D	D	61 - 98	61 - 98
1	2	1	VAL	VAL	PHE	PHE	A	A	102 - 118	102 - 118
2	2	1	VAL	VAL	PHE	PHE	B	B	102 - 118	102 - 118
3	2	1	VAL	VAL	PHE	PHE	C	C	102 - 118	102 - 118
4	2	1	VAL	VAL	PHE	PHE	D	D	102 - 118	102 - 118
1	1	2	PRO	PRO	VAL	VAL	B	B	2 - 47	2 - 47
2	1	2	PRO	PRO	VAL	VAL	C	C	2 - 47	2 - 47
3	1	2	PRO	PRO	VAL	VAL	A	A	2 - 47	2 - 47
4	1	2	PRO	PRO	VAL	VAL	D	D	2 - 47	2 - 47
1	1	3	TYR	TYR	GLN	GLN	A	A	48 - 52	48 - 52
2	1	3	TYR	TYR	GLN	GLN	B	B	48 - 52	48 - 52
3	1	3	TYR	TYR	GLN	GLN	C	C	48 - 52	48 - 52
1	1	4	ASP	ASP	ALA	ALA	A	A	99 - 101	99 - 101
2	1	4	ASP	ASP	ALA	ALA	B	B	99 - 101	99 - 101
3	1	4	ASP	ASP	ALA	ALA	D	D	99 - 101	99 - 101

NCS ensembles :

ID
1
2
3
4

#1: Protein	Protein traM Mass: 14677.630 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: traM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P33788
#2: DNA chain	sbmA Mass: 7367.790 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized oligo

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 4.56 Å³/Da / Density % sol: 73.03 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 36% MPD, 5% PEG 2000, 100mM cacodylic acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.1158 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 16, 2009
Radiation	Monochromator: Si(111) Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.1158 Å / Relative weight: 1
Reflection	Resolution: 2.87→83.789 Å / Num. all: 27939 / Num. obs: 27538 / % possible obs: 81 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / R_sym value: 0.07 / Net I/σ(I): 23
Reflection shell	Resolution: 2.87→3 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 3 / Num. unique all: 2568 / R_sym value: 0.433 / % possible all: 94.2

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Processing

Software

Name	Version	Classification
Blu-Ice		data collection
MOLREP		phasing
REFMAC	5.5.0066	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2G7O, C-terminal domain with residues mutated to pED208

2g7o

Resolution: 2.874→83.78 Å / Cor.coef. F_o:F_c: 0.928 / Cor.coef. F_o:F_c free: 0.909 / SU B: 29.321 / SU ML: 0.293 / Cross valid method: THROUGHOUT / ESU R: 0.497 / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27811	1383	5 %	RANDOM
R_work	0.25016	-	-	-
obs	0.25156	26155	98.57 %	-

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: 78.074 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.32 Å²	0 Å²	0 Å²
2-	-	-0.02 Å²	0 Å²
3-	-	-	-0.29 Å²

Refinement step

Cycle: LAST / Resolution: 2.874→83.78 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3737	489	0	0	4226

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	4326
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.348	2.111	5916
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.485	5	457
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.358	25.632	190
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	21.349	15	742
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.352	15	22
X-RAY DIFFRACTION	r_chiral_restr	0.064	0.2	678
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	3014
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	0.697	1.5	2306
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.286	2	3736
X-RAY DIFFRACTION	r_scbond_it	1.305	3	2020
X-RAY DIFFRACTION	r_scangle_it	2.197	4.5	2180
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	220	TIGHT POSITIONAL	0.04	0.05
1	2	B	220	TIGHT POSITIONAL	0.04	0.05
1	3	C	220	TIGHT POSITIONAL	0.05	0.05
1	4	D	220	TIGHT POSITIONAL	0.03	0.05
1	1	A	219	LOOSE POSITIONAL	0.06	5
1	2	B	219	LOOSE POSITIONAL	0.06	5
1	3	C	219	LOOSE POSITIONAL	0.07	5
1	4	D	219	LOOSE POSITIONAL	0.05	5
1	1	A	220	TIGHT THERMAL	0.08	0.5
1	2	B	220	TIGHT THERMAL	0.07	0.5
1	3	C	220	TIGHT THERMAL	0.09	0.5
1	4	D	220	TIGHT THERMAL	0.06	0.5
1	1	A	219	LOOSE THERMAL	0.1	10
1	2	B	219	LOOSE THERMAL	0.09	10
1	3	C	219	LOOSE THERMAL	0.09	10
1	4	D	219	LOOSE THERMAL	0.08	10
2	1	B	184	TIGHT POSITIONAL	0.03	0.05
2	2	C	184	TIGHT POSITIONAL	0.03	0.05
2	3	A	184	TIGHT POSITIONAL	0.03	0.05
2	4	D	184	TIGHT POSITIONAL	0.04	0.05
2	1	B	180	LOOSE POSITIONAL	0.09	5
2	2	C	180	LOOSE POSITIONAL	0.05	5
2	3	A	180	LOOSE POSITIONAL	0.04	5
2	4	D	180	LOOSE POSITIONAL	0.05	5
2	1	B	184	TIGHT THERMAL	0.04	0.5
2	2	C	184	TIGHT THERMAL	0.05	0.5
2	3	A	184	TIGHT THERMAL	0.06	0.5
2	4	D	184	TIGHT THERMAL	0.09	0.5
2	1	B	180	LOOSE THERMAL	0.05	10
2	2	C	180	LOOSE THERMAL	0.06	10
2	3	A	180	LOOSE THERMAL	0.05	10
2	4	D	180	LOOSE THERMAL	0.08	10
3	1	A	20	TIGHT POSITIONAL	0.03	0.05
3	2	B	20	TIGHT POSITIONAL	0.03	0.05
3	3	C	20	TIGHT POSITIONAL	0.04	0.05
3	1	A	26	LOOSE POSITIONAL	0.05	5
3	2	B	26	LOOSE POSITIONAL	0.05	5
3	3	C	26	LOOSE POSITIONAL	0.04	5
3	1	A	20	TIGHT THERMAL	0.2	0.5
3	2	B	20	TIGHT THERMAL	0.21	0.5
3	3	C	20	TIGHT THERMAL	0.07	0.5
3	1	A	26	LOOSE THERMAL	0.09	10
3	2	B	26	LOOSE THERMAL	0.12	10
3	3	C	26	LOOSE THERMAL	0.07	10
4	1	A	12	TIGHT POSITIONAL	0.04	0.05
4	2	B	12	TIGHT POSITIONAL	0.04	0.05
4	3	D	12	TIGHT POSITIONAL	0.02	0.05
4	1	A	13	LOOSE POSITIONAL	0.11	5
4	2	B	13	LOOSE POSITIONAL	0.12	5
4	3	D	13	LOOSE POSITIONAL	0.03	5
4	1	A	12	TIGHT THERMAL	0.04	0.5
4	2	B	12	TIGHT THERMAL	0.04	0.5
4	3	D	12	TIGHT THERMAL	0.04	0.5
4	1	A	13	LOOSE THERMAL	0.05	10
4	2	B	13	LOOSE THERMAL	0.07	10
4	3	D	13	LOOSE THERMAL	0.05	10

LS refinement shell

Resolution: 2.874→2.949 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.502	73	-
R_work	0.409	1655	-
obs	-	-	84.29 %

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	2.6449	0.8542	-0.4735	2.0772	-0.0922	2.1212	-0.0229	0.0089	0.2212	-0.1509	-0.0588	0.4751	-0.027	-0.1991	0.0817	0.7139	0.0418	-0.104	0.1167	0.0719	0.2248	7.784	12.876	-1.884
2	2.6862	1.7495	1.0673	2.7371	2.158	5.4403	0.0031	0.4052	0.3121	-0.8604	0.1561	-0.4873	-0.1439	0.4651	-0.1591	1.0465	0.0961	0.2479	0.127	0.1406	0.4437	19.051	18.679	-10.355
3	0.9089	0.0008	0.2377	4.4153	1.692	2.3097	0.047	0.1294	-0.0343	-0.393	0.1523	-0.4272	0.0712	0.1979	-0.1994	0.7347	-0.0292	0.0292	0.1027	0.0111	0.2188	17.302	9.333	-5.742
4	2.7833	-0.276	2.1156	4.5896	1.2767	5.2033	0.0883	0.2906	0.3293	-0.353	-0.0471	0.2393	-0.3244	-0.182	-0.0413	0.7455	0.0257	-0.0013	0.1168	0.1505	0.2342	9.529	22.191	-6.658
5	5.6147	-0.188	-3.7455	2.156	-0.0427	5.4844	0.0841	0.0772	0.1209	-0.028	-0.4	0.0213	-0.1336	-0.3287	0.3159	0.9874	0.0609	-0.0937	0.1111	-0.0296	0.2114	46.01	30.315	42.087
6	4.2069	-5.5068	3.2199	10.9812	-1.0684	8.4635	0.5683	0.6631	-0.6791	-1.2429	0.2161	-0.1141	1.4143	1.1153	-0.7844	1.1534	-0.184	0.2458	0.6016	-0.2975	0.6108	58.404	25.394	9.084
7	2.7125	-0.0681	2.9368	10.7212	2.3109	4.4898	-0.4764	-0.2265	0.6743	-0.604	-0.1982	1.4255	-0.8864	-0.672	0.6746	0.8827	0.0948	-0.0976	0.4443	-0.0114	0.599	23.636	29.846	38.547
8	9.927	-2.0735	5.52	5.7081	-0.135	3.3968	0.4553	0.3393	-0.56	-0.4203	-0.1578	0.0842	0.5718	0.1407	-0.2975	1.2176	0.0274	-0.0604	0.1676	-0.1665	0.1741	31.456	17.75	37.196
9	4.9351	0.9513	-0.6684	13.1175	-0.5219	9.9923	-0.2668	-0.0865	0.2799	-0.1452	0.2025	1.0098	-0.0296	-0.8172	0.0643	0.5592	-0.014	-0.0203	0.1755	0.1294	0.2536	52.028	36.927	14.881

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	61 - 118
2	X-RAY DIFFRACTION	2	B	61 - 118
3	X-RAY DIFFRACTION	3	C	61 - 118
4	X-RAY DIFFRACTION	4	D	61 - 118
5	X-RAY DIFFRACTION	5	P	1 - 24
6	X-RAY DIFFRACTION	6	A	2 - 47
7	X-RAY DIFFRACTION	7	B	2 - 47
8	X-RAY DIFFRACTION	8	C	2 - 47
9	X-RAY DIFFRACTION	9	D	2 - 47

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News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
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