PDB-2g7o: Protonation-mediated structural flexibility in the F conjugation ...

ID or keywords:

Entry

Database: PDB / ID: 2g7o

Title

Protonation-mediated structural flexibility in the F conjugation regulatory protein, TraM

Components

Protein traM

Keywords

DNA BINDING PROTEIN / four helix bundle / tetramer

Function / homology

Function and homology information

DNA binding / cytoplasm
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.4 Å

Authors

Lu, J. / Edwards, R.A. / Wong, J.J. / Manchak, J. / Scott, P.G. / Frost, L.S. / Glover, J.N.

Citation

Journal: Embo J. / Year: 2006
Title: Protonation-mediated structural flexibility in the F conjugation regulatory protein, TraM.
Authors: Lu, J. / Edwards, R.A. / Wong, J.J. / Manchak, J. / Scott, P.G. / Frost, L.S. / Glover, J.N.

History

Deposition	Feb 28, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 13, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Derived calculations / Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software
Revision 1.4	Feb 14, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

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Related structure data

Related structure data	2g9eC C: citing same article (ref.)
Similar structure data	2g9e-1 2r71-d 4k4b-3 6zdf-1 5zw4-d 3ib0-d 4a51-7 1gp5-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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Deposited unit

A: Protein traM

7.98 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Protein traM

defined by author&software
31.9 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	51.733, 51.733, 49.585
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	79
Space group name H-M	I4

Components on special symmetry positions

ID	Model	Components
1	1	A-37- HOH

Details

The biological assembly is a tetramer generated by the crystallographic four-fold symmetry axis: x+y+z, -x-y+z, -y+x+z, y-x+z

#1: Protein	Protein traM Mass: 7980.898 Da / Num. of mol.: 1 / Fragment: TraM 58-127 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: traM / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P10026
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Protein traM

Mass: 7980.898 Da / Num. of mol.: 1 / Fragment: TraM 58-127
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli (E. coli) / Gene: traM / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P10026

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.08 Å³/Da / Density % sol: 40.81 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30% PEG 400, 0.1M MES pH 6.5, 2mM DTT, 0.5M ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	105	1
2	105	1
1,2		1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	ALS	8.3.1	1	1.11697
SYNCHROTRON	ALS	8.3.1	2	0.979617, 1.019440

Detector

Type	ID	Detector	Date
ADSC QUANTUM 210	1	CCD	Jun 14, 2005
ADSC QUANTUM 210	2	CCD	Jul 20, 2005

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	Double Crystal Si(111)	SINGLE WAVELENGTH	M	x-ray	1
2	Double Crystal Si(111)	MAD	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.11697	1
2	0.979617	1
3	1.01944	1

Reflection

R_merge(I) obs: 0.049 / D res low: 100 Å / Redundancy: 4.1 %

ID	Av σ(I) over netI	Number	Χ²	D res high (Å)	Num. obs	% possible obs
1	20.8	97674	1.06	1.42	23900	98.1
2	19.7	115483	1.03	1.34	28275	97.8

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	Num. obs	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
3.85	100	1168	94.6	1	0.037	0.979	4
3.06	3.85	1196	98.7	1	0.039	0.866	4.1
2.67	3.06	1193	98.7	1	0.042	0.977	4.1
2.43	2.67	1212	98.8	1	0.046	1.094	4.1
2.25	2.43	1205	98.8	1	0.048	1.073	4.1
2.12	2.25	1203	98.9	1	0.052	0.972	4.1
2.01	2.12	1214	98.9	1	0.059	1.056	4.1
1.93	2.01	1209	99.2	1	0.066	1.077	4.1
1.85	1.93	1195	98.7	1	0.08	1.133	4.1
1.79	1.85	1208	98.5	1	0.091	1.064	4.1
1.73	1.79	1200	98	1	0.103	1.29	4.1
1.68	1.73	1218	98.3	1	0.121	1.197	4.1
1.64	1.68	1159	98	1	0.136	1.2	4.1
1.6	1.64	1226	98.5	1	0.147	1.12	4.1
1.56	1.6	1151	98.1	1	0.17	1.084	4.1
1.53	1.56	1181	96.8	1	0.209	1.077	4
1.5	1.53	1219	98.5	1	0.212	1.061	4.2
1.47	1.5	1173	96.9	1	0.28	1.017	3.9
1.44	1.47	1233	97.6	1	0.35	0.924	4.1
1.42	1.44	1137	96.6	1	0.413	0.889	3.9
3.64	100	1398	96.3	2	0.037	0.922	4
2.89	3.64	1460	99.4	2	0.039	0.931	4.2
2.52	2.89	1426	99.4	2	0.042	0.943	4.1
2.29	2.52	1453	99.2	2	0.046	1.051	4.1
2.13	2.29	1393	98.9	2	0.05	1.086	4.1
2	2.13	1431	99.2	2	0.055	1.013	4.1
1.9	2	1441	98.4	2	0.065	1.071	4.2
1.82	1.9	1423	98	2	0.078	1.083	4.1
1.75	1.82	1430	98.2	2	0.086	1.136	4
1.69	1.75	1442	98.2	2	0.099	1.064	4.1
1.64	1.69	1375	97.7	2	0.113	1.25	4.1
1.59	1.64	1427	98	2	0.13	1.198	4.1
1.55	1.59	1443	97.6	2	0.153	1.121	4.1
1.51	1.55	1385	97.4	2	0.177	1.123	4.1
1.47	1.51	1343	96.3	2	0.21	1.093	4
1.44	1.47	1476	97.3	2	0.269	1.027	4.2
1.41	1.44	1373	96.5	2	0.334	0.915	4.1
1.39	1.41	1373	96.5	2	0.433	0.861	4
1.36	1.39	1415	96.3	2	0.46	0.818	4.1
1.34	1.36	1368	96.1	2	0.544	0.799	3.9

Reflection

Resolution: 1.4→36.58 Å / Num. all: 12828 / Num. obs: 12828 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / R_merge(I) obs: 0.039 / Χ²: 1.032 / Net I/σ(I): 27.6

Reflection shell

Resolution: 1.4→1.42 Å / % possible obs: 86.6 % / Redundancy: 2.8 % / R_merge(I) obs: 0.371 / Mean I/σ(I) obs: 3.12 / Num. unique all: 548 / Num. unique obs: 548 / Χ²: 0.973 / % possible all: 86.6

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Phasing

Phasing

Method:

MAD

Phasing set

ID
1
2

Phasing MAD set

Clust-ID	Expt-ID	Set-ID	Wavelength (Å)	F double prime refined	F prime refined
1	2 wavelength	1	0.9796	2.8	-10.2
1	2 wavelength	2	1.0194	0.54	-2.8

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy
1	Se	17.784	0.105	0.186	0	1.083
2	Se	20.165	0.444	0.272	0.096	0.785
3	Se	30.723	0.046	0.262	0.427	0.295

Phasing dm

FOM : 0.76 / FOM acentric: 0.76 / FOM centric: 0.77 / Reflection: 10410 / Reflection acentric: 9964 / Reflection centric: 446

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
4.3-35.85	0.95	0.96	0.92	454	404	50
2.7-4.3	0.96	0.96	0.95	1410	1320	90
2.1-2.7	0.91	0.91	0.89	1770	1690	80
1.9-2.1	0.84	0.84	0.72	1778	1709	69
1.6-1.9	0.69	0.69	0.65	3090	2993	97
1.5-1.6	0.5	0.5	0.47	1908	1848	60

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SOLVE	2.08	phasing
RESOLVE	2.08	phasing
REFMAC		refinement
PDB_EXTRACT	1.701	data extraction

Refinement

Method to determine structure:

MAD / Resolution: 1.4→36.58 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.938 / SU B: 2.067 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.224	626	4.9 %	RANDOM
R_work	0.193	-	-	-
all	0.195	12827	-	-
obs	0.195	12827	99.43 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 17.335 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.03 Å²	0 Å²	0 Å²
2-	-	-0.03 Å²	0 Å²
3-	-	-	0.06 Å²

Refinement step

Cycle: LAST / Resolution: 1.4→36.58 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	544	0	0	55	599

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	559
X-RAY DIFFRACTION	r_angle_refined_deg	1.233	1.971	748
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.684	5	67
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.961	26.071	28
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.366	15	113
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	28.655	15	2
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	82
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	415
X-RAY DIFFRACTION	r_nbd_refined	0.218	0.2	228
X-RAY DIFFRACTION	r_nbtor_refined	0.307	0.2	400
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.14	0.2	31
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.172	0.2	48
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.123	0.2	8
X-RAY DIFFRACTION	r_mcbond_it	0.744	1.5	350
X-RAY DIFFRACTION	r_mcangle_it	1.243	2	554
X-RAY DIFFRACTION	r_scbond_it	2.233	3	227
X-RAY DIFFRACTION	r_scangle_it	3.528	4.5	194

LS refinement shell

Resolution: 1.4→1.437 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.272	39	-
R_work	0.246	854	-
obs	-	893	95.82 %

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