PDB-3ub1: Ntf2 like protein involved in plasmid conjugation

ID or keywords:

Entry

Database: PDB / ID: 3ub1

Title

Ntf2 like protein involved in plasmid conjugation

Components

ORF13-like protein

Keywords

TRANSPORT PROTEIN / NTF2-LIKE

Function / homology

Function and homology information

identical protein binding / membrane
Similarity search - Function

Biological species

Clostridium perfringens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.8 Å

Authors

Porter, C.J. / Rosado, C.J. / Bantwal, R. / Bannam, T.L. / Rood, J.I. / Whisstock, J.C.

Citation

Journal: Mol.Microbiol. / Year: 2012
Title: The conjugation protein TcpC from Clostridium perfringens is structurally related to the type IV secretion system protein VirB8 from Gram-negative bacteria.
Authors: Porter, C.J. / Bantwal, R. / Bannam, T.L. / Rosado, C.J. / Pearce, M.C. / Adams, V. / Lyras, D. / Whisstock, J.C. / Rood, J.I.

History

Deposition	Oct 22, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 8, 2012	Provider: repository / Type: Initial release
Revision 1.1	Feb 15, 2012	Group: Structure summary
Revision 1.2	Nov 20, 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_site 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_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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PDBx/mmCIF format	3ub1.cif.gz	679.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3ub1.ent.gz	565.5 KB	Display	PDB format
PDBx/mmJSON format	3ub1.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ub/3ub1 ftp://data.pdbj.org/pub/pdb/validation_reports/ub/3ub1	HTTPS FTP

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Related structure data

Similar structure data	3cih-d 4rxo-2 4rgy-1 6u6x-1 6u6y-2 6dzs-1 5ao0-d 5k7v-d 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 - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: ORF13-like protein

B: ORF13-like protein

C: ORF13-like protein

D: ORF13-like protein

E: ORF13-like protein

F: ORF13-like protein

hetero molecules

183 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ORF13-like protein

C: ORF13-like protein

E: ORF13-like protein

hetero molecules

defined by author&software
91.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: ORF13-like protein

D: ORF13-like protein

F: ORF13-like protein

hetero molecules

defined by author&software
91.5 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	121.495, 121.842, 125.526
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	ORF13-like protein / NTF2-LIKE PROTEIN Mass: 30342.787 Da / Num. of mol.: 6 / Fragment: C-TERMINAL DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: pCW3_0032, tcpC / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: Q1PLH8
#2: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1914 / 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: 2.55 Å³/Da / Density % sol: 51.8 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100MM BIS-TRIS, 50MM CACL2, 28-30%(V/ V) PEG MME 550, 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:

SSRL

/ Beamline: BL11-1 / Wavelength: 0.91837, 0.97860, 0.98133

Detector

Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 21, 2008

Radiation

Monochromator: SIDE SCATTERING BENT CUBE-ROOT I-BEAM SINGLE CRYSTAL, ASYMMETRIC CUT 4.965 DEGS
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.91837	1
2	0.9786	1
3	0.98133	1

Reflection

Resolution: 1.8→70.89 Å / Num. obs: 172185 / % possible obs: 99.9 % / Observed criterion σ(I): 0

Reflection shell

Highest resolution: 1.8 Å / Redundancy: 13.4 % / R_merge(I) obs: 0.48 / Mean I/σ(I) obs: 5.2 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
SOLVE		phasing
REFMAC	5.5.0109	refinement
MOSFLM		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MAD / Resolution: 1.8→62.76 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.946 / SU B: 4.494 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.198	8623	5 %	RANDOM
R_work	0.163	-	-	-
obs	0.165	172095	99.9 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 24.68 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.12 Å²	0 Å²	0 Å²
2-	-	-0.38 Å²	0 Å²
3-	-	-	0.49 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→62.76 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11998	0	27	1914	13939

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	12416
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.327	1.943	16866
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.535	5	1539
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.696	25.462	639
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.183	15	2020
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.191	15	37
X-RAY DIFFRACTION	r_chiral_restr	0.098	0.2	1855
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	9643
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	0.717	1.5	7598
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.333	2	12309
X-RAY DIFFRACTION	r_scbond_it	2.27	3	4818
X-RAY DIFFRACTION	r_scangle_it	3.676	4.5	4541
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.8→1.85 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.238	635	-
R_work	0.199	11914	-
obs	-	-	99.59 %

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	1.0015	0.0354	-0.3528	1.0791	0.2538	1.34	0.0114	-0.0511	-0.0421	0.0854	-0.0125	0.0194	0.1354	0.083	0.0011	0.111	-0.0119	0.0165	0.0964	-0.0163	0.1126	15.4219	68.5573	8.7909
2	1.2895	0.1908	-0.5006	1.1543	0.2106	1.0723	-0.0104	0.109	0.0757	-0.0369	-0.1032	0.3209	0.0042	-0.4133	0.1136	0.0068	-0.0092	0.0004	0.2064	-0.0597	0.1158	-26.9184	64.1205	19.7238
3	1.0176	-0.0655	-0.042	0.8054	-0.2131	0.8277	-0.0466	-0.0082	-0.0166	-0.0293	0.0144	-0.0115	0.0704	-0.0303	0.0322	0.1106	0.0201	0.0132	0.1079	-0.0106	0.1126	44.8794	61.3243	3.6255
4	1.1124	0.1124	0.0787	0.5852	-0.0871	0.6061	-0.0354	0.0451	0.0172	-0.0055	0.0073	-0.1088	-0.0023	0.1184	0.0281	0.0747	0.01	0.0058	0.1223	0.0111	0.1149	84.1845	52.9256	-16.0417
5	0.4923	0.2011	-0.1333	0.6214	0.0766	0.4427	0.0367	-0.0127	0.0041	0.0335	-0.0223	-0.0238	-0.0138	0.0069	-0.0144	0.0909	-0.0048	-0.0045	0.1032	-0.0005	0.0875	3.5918	54.8701	-0.0579
6	0.6602	-0.1681	-0.306	1.5677	-0.1318	1.1581	0.0511	-0.0661	0.146	0.0229	0.003	-0.0615	-0.0849	-0.0091	-0.0542	0.0822	-0.0193	0.0307	0.0632	-0.0328	0.136	18.0329	89.6313	13.5052
7	0.5071	-0.1533	0.0827	0.995	-0.0529	0.4476	-0.0449	-0.0461	-0.0175	0.037	0.0264	0.0126	-0.0399	-0.0195	0.0186	0.1117	0.0134	0.0079	0.1106	0.0056	0.103	55.5987	45.6582	9.3243
8	1.0558	0.1456	0.5198	1.2955	0.5119	2.3178	-0.0607	0.0121	0.2778	-0.0534	-0.0371	-0.0943	-0.3593	0.0422	0.0978	0.0968	0.026	-0.0141	0.034	0.0018	0.1592	44.7367	82.5146	1.8902
9	0.7867	-0.2314	-0.035	0.9636	-0.0781	1.3533	-0.0105	0.0034	0.0167	0.0319	-0.0215	0.0084	-0.0209	-0.037	0.032	0.0901	-0.0152	0.0111	0.1198	-0.0104	0.0837	-6.307	62.7773	20.5957
10	0.8181	0.1264	-0.1156	0.6529	0.1287	1.1167	0.0102	0.1742	-0.0009	-0.1426	0.0053	-0.0113	-0.0269	-0.0583	-0.0155	0.1062	-0.0069	0.0005	0.1151	-0.0017	0.0672	3.0758	48.7123	-20.6305
11	1.0999	0.143	0.1786	0.8961	-0.0554	1.0524	-0.0166	-0.0113	-0.0014	-0.0242	0.0113	0.0292	-0.0221	-0.0852	0.0053	0.091	0.0115	0.0034	0.1214	0.0045	0.1084	63.1668	54.5592	-12.3469
12	0.6661	-0.265	-0.0791	1.3084	-0.4885	1.1334	-0.1463	-0.196	-0.0271	0.3695	0.1165	0.0099	-0.0757	0.047	0.0297	0.1674	0.0793	0.0178	0.1211	0.0319	0.0159	59.0996	37.6129	28.7937

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	104 - 230
2	X-RAY DIFFRACTION	2	A	231 - 354
3	X-RAY DIFFRACTION	3	B	103 - 231
4	X-RAY DIFFRACTION	4	B	232 - 354
5	X-RAY DIFFRACTION	5	C	104 - 251
6	X-RAY DIFFRACTION	6	C	252 - 354
7	X-RAY DIFFRACTION	7	D	104 - 252
8	X-RAY DIFFRACTION	8	D	253 - 356
9	X-RAY DIFFRACTION	9	E	103 - 230
10	X-RAY DIFFRACTION	10	E	231 - 354
11	X-RAY DIFFRACTION	11	F	104 - 230
12	X-RAY DIFFRACTION	12	F	231 - 354

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