PDB-3jqo: Crystal structure of the outer membrane complex of a type IV secr...

ID or keywords:

Entry

Database: PDB / ID: 3jqo

Title

Crystal structure of the outer membrane complex of a type IV secretion system

Components

TraF proteinTNF receptor associated factor
TraN protein
TraO protein

Keywords

TRANSPORT PROTEIN / Helical outer membrane TM / outer membrane protein complex

Function / homology

Function and homology information

plasma membrane
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Chandran, V. / Fronzes, R. / Duquerroy, S. / Cronin, N. / Navaza, J. / Waksman, G.

Citation

Journal: Nature / Year: 2009
Title: Structure of the outer membrane complex of a type IV secretion system
Authors: Chandran, V. / Fronzes, R. / Duquerroy, S. / Cronin, N. / Navaza, J. / Waksman, G.

History

Deposition	Sep 7, 2009	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Dec 1, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Feb 12, 2014	Group: Database references
Revision 1.3	Jul 23, 2014	Group: Other
Revision 1.4	Nov 20, 2019	Group: Database references / Derived calculations / Category: pdbx_database_related / struct_conn Item: _pdbx_database_related.content_type / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5	Apr 3, 2024	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 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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	3jqo.cif.gz	951.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3jqo.ent.gz	786.9 KB	Display	PDB format
PDBx/mmJSON format	3jqo.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/jq/3jqo ftp://data.pdbj.org/pub/pdb/validation_reports/jq/3jqo	HTTPS FTP

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Related structure data

Related structure data	5031 5034 2bhv 2ofq
Similar structure data	3zbi-d 6wpk-d 3w1i-d 21067 1gvh-1 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
Related items in Molecule of the Month	#261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: TraF protein

B: TraO protein

C: TraN protein

D: TraF protein

E: TraO protein

F: TraN protein

G: TraF protein

H: TraO protein

I: TraN protein

J: TraF protein

K: TraO protein

L: TraN protein

M: TraF protein

N: TraO protein

O: TraN protein

P: TraF protein

Q: TraO protein

R: TraN protein

S: TraF protein

T: TraO protein

U: TraN protein

V: TraF protein

W: TraO protein

X: TraN protein

Y: TraF protein

Z: TraO protein

a: TraN protein

b: TraF protein

c: TraO protein

d: TraN protein

e: TraF protein

f: TraO protein

g: TraN protein

h: TraF protein

i: TraO protein

j: TraN protein

k: TraF protein

l: TraO protein

m: TraN protein

n: TraF protein

o: TraO protein

p: TraN protein

hetero molecules

606 kDa, 42 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)	202.400, 211.630, 203.440
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:
NCS ensembles :

ID
1
2
3

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Protein , 2 types, 28 molecules ADGJMPSVYbehknBEHKNQTWZcfilo

#1: Protein	TraF protein / TNF receptor associated factor Mass: 24293.094 Da / Num. of mol.: 14 / Fragment: TraF C-terminal domain, UNP residues 160-386 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: traF / Plasmid: IBA3C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)star / References: UniProt: Q46705
#2: Protein	TraO protein Mass: 15323.768 Da / Num. of mol.: 14 / Fragment: TraO C-terminal domain, UNP residues 160-294 Source method: isolated from a genetically manipulated source Details: All the three genes were expressed under the control of a single tet promoter. Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: traO / Plasmid: IBA3C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)star / References: UniProt: Q46704

#1: Protein

TraF protein /

TNF receptor associated factor

Mass: 24293.094 Da / Num. of mol.: 14 / Fragment: TraF C-terminal domain, UNP residues 160-386
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli (E. coli) / Strain: K-12 / Gene: traF / Plasmid: IBA3C / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)star / References: UniProt: Q46705

#2: Protein

TraO protein

Mass: 15323.768 Da / Num. of mol.: 14 / Fragment: TraO C-terminal domain, UNP residues 160-294
Source method: isolated from a genetically manipulated source
Details: All the three genes were expressed under the control of a single tet promoter.
Source: (gene. exp.)

Escherichia coli (E. coli) / Strain: K-12 / Gene: traO / Plasmid: IBA3C / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)star / References: UniProt: Q46704

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Protein/peptide , 1 types, 14 molecules CFILORUXadgjmp

#3: Protein/peptide	TraN protein Mass: 3635.925 Da / Num. of mol.: 14 / Fragment: UNP residues 15-48 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: traN / Plasmid: IBA3C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)star / References: UniProt: Q46702

#3: Protein/peptide

TraN protein

Mass: 3635.925 Da / Num. of mol.: 14 / Fragment: UNP residues 15-48
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli (E. coli) / Strain: K-12 / Gene: traN / Plasmid: IBA3C / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)star / References: UniProt: Q46702

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Non-polymers , 3 types, 1294 molecules

#4: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#5: Chemical	ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE / Lauryldimethylamine oxide Mass: 229.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₄H₃₁NO / Comment: LDAO, detergent*YM
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1290 / Source method: isolated from a natural source / Formula: H₂O

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Details

Sequence details	AUTHOR INDICATED THE SEQUENCE IN THE DATABASE (UNIPROT Q46705) AT THIS POSITION IS WRONG. ...AUTHOR INDICATED THE SEQUENCE IN THE DATABASE (UNIPROT Q46705) AT THIS POSITION IS WRONG. SEQUENCING RESULTS AND ELECTRON DENSITY FOR A CLEAR ARG SIDECHAIN CONFIRM THAT RESIDUE 308 IN TRAF IS INDEED AN ARG.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.6 Å³/Da / Density % sol: 65.81 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20-40% w/v MPD, 100mM Bis-Tris pH 6.5-7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	ESRF	ID14-4	1	0.9755
SYNCHROTRON	SOLEIL	PROXIMA 1	2	0.979

Detector

Type	ID	Detector	Date	Details
ADSC QUANTUM 315r	1	CCD	Feb 12, 2009	torroidal focussing mirrors
ADSC QUANTUM 315r	2	CCD	Jan 29, 2009	Adjustable focus mirrors

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	Channel cut ESRF monochromator	SINGLE WAVELENGTH	M	x-ray	1
2	Channel cut cryogenically cooled monochromator crystal	SINGLE WAVELENGTH	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9755	1
2	0.979	1

Reflection

Resolution: 2.6→52.91 Å / Num. all: 519405 / Num. obs: 496105 / % possible obs: 95.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.98 % / B_iso Wilson estimate: 42 Å² / R_merge(I) obs: 0.055 / Net I/σ(I): 12.12

Reflection shell

Resolution: 2.6→2.8 Å / Redundancy: 1.98 % / R_merge(I) obs: 0.264 / Mean I/σ(I) obs: 3.11 / Num. unique all: 98005 / % possible all: 94.7

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
AMoRE		phasing
REFMAC	5.5.0072	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: EMDB entry 5034, Cryo-EM structure of trypsin digested core TraF/TraN/TraO complex

Resolution: 2.6→52.91 Å / Cor.coef. F_o:F_c: 0.892 / Cor.coef. F_o:F_c free: 0.869 / SU B: 8.093 / SU ML: 0.18 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.395 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE SF FILE HAS Fplus and Fminus columns for friedel pairs.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25935	12939	5 %	RANDOM
R_work	0.22725	-	-	-
obs	0.22885	496104	95.5 %	-

Solvent computation

Solvent model: BABINET MODEL PARAMETERS FOR MASK CACLULATION

Displacement parameters

B_iso mean: 37.277 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.54 Å²	0 Å²	0 Å²
2-	-	5.12 Å²	0 Å²
3-	-	-	-2.58 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→52.91 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	37512	0	40	1290	38842

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.022	38268
X-RAY DIFFRACTION	r_angle_refined_deg	1.985	1.954	51960
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.146	5	4852
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.873	24.115	1689
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.088	15	6314
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.24	15	308
X-RAY DIFFRACTION	r_chiral_restr	0.138	0.2	5856
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	29090
X-RAY DIFFRACTION	r_mcbond_it	0.865	1.5	24374
X-RAY DIFFRACTION	r_mcangle_it	1.678	2	39387
X-RAY DIFFRACTION	r_scbond_it	3.123	3	13894
X-RAY DIFFRACTION	r_scangle_it	4.962	4.5	12573

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	768	tight positional	0.05	0.05
1	1	D	768	tight positional	0.05	0.05
1	1	G	768	tight positional	0.05	0.05
1	1	J	768	tight positional	0.05	0.05
1	1	M	768	tight positional	0.05	0.05
1	1	P	768	tight positional	0.06	0.05
1	1	S	768	tight positional	0.06	0.05
1	1	V	768	tight positional	0.05	0.05
1	1	Y	768	tight positional	0.05	0.05
1	1	b	768	tight positional	0.05	0.05
1	1	e	768	tight positional	0.05	0.05
1	1	h	768	tight positional	0.05	0.05
1	1	k	768	tight positional	0.05	0.05
1	1	n	768	tight positional	0.05	0.05
2	2	B	1033	tight positional	0.06	0.05
2	2	E	1033	tight positional	0.05	0.05
2	2	H	1033	tight positional	0.06	0.05
2	2	K	1033	tight positional	0.06	0.05
2	2	N	1033	tight positional	0.06	0.05
2	2	Q	1033	tight positional	0.06	0.05
2	2	T	1033	tight positional	0.06	0.05
2	2	W	1033	tight positional	0.05	0.05
2	2	Z	1033	tight positional	0.06	0.05
2	2	c	1033	tight positional	0.05	0.05
2	2	f	1033	tight positional	0.06	0.05
2	2	i	1033	tight positional	0.06	0.05
2	2	l	1033	tight positional	0.05	0.05
2	2	o	1033	tight positional	0.07	0.05
3	3	C	181	tight positional	0.08	0.05
3	3	F	181	tight positional	0.05	0.05
3	3	I	181	tight positional	0.05	0.05
3	3	L	181	tight positional	0.06	0.05
3	3	O	181	tight positional	0.05	0.05
3	3	R	181	tight positional	0.05	0.05
3	3	U	181	tight positional	0.09	0.05
3	3	X	181	tight positional	0.05	0.05
3	3	a	181	tight positional	0.04	0.05
3	3	d	181	tight positional	0.05	0.05
3	3	g	181	tight positional	0.06	0.05
3	3	j	181	tight positional	0.06	0.05
3	3	m	181	tight positional	0.05	0.05
3	3	p	181	tight positional	0.08	0.05
1	1	A	656	loose positional	0.1	5
1	1	D	656	loose positional	0.07	5
1	1	G	656	loose positional	0.06	5
1	1	J	656	loose positional	0.06	5
1	1	M	656	loose positional	0.06	5
1	1	P	656	loose positional	0.06	5
1	1	S	656	loose positional	0.07	5
1	1	V	656	loose positional	0.06	5
1	1	Y	656	loose positional	0.06	5
1	1	b	656	loose positional	0.06	5
1	1	e	656	loose positional	0.11	5
1	1	h	656	loose positional	0.06	5
1	1	k	656	loose positional	0.06	5
1	1	n	656	loose positional	0.07	5
1	1	A	768	tight thermal	0.17	0.5
1	1	D	768	tight thermal	0.15	0.5
1	1	G	768	tight thermal	0.15	0.5
1	1	J	768	tight thermal	0.16	0.5
1	1	M	768	tight thermal	0.17	0.5
1	1	P	768	tight thermal	0.16	0.5
1	1	S	768	tight thermal	0.17	0.5
1	1	V	768	tight thermal	0.15	0.5
1	1	Y	768	tight thermal	0.16	0.5
1	1	b	768	tight thermal	0.15	0.5
1	1	e	768	tight thermal	0.16	0.5
1	1	h	768	tight thermal	0.16	0.5
1	1	k	768	tight thermal	0.17	0.5
1	1	n	768	tight thermal	0.17	0.5
2	2	B	1033	tight thermal	0.18	0.5
2	2	E	1033	tight thermal	0.15	0.5
2	2	H	1033	tight thermal	0.15	0.5
2	2	K	1033	tight thermal	0.15	0.5
2	2	N	1033	tight thermal	0.16	0.5
2	2	Q	1033	tight thermal	0.16	0.5
2	2	T	1033	tight thermal	0.16	0.5
2	2	W	1033	tight thermal	0.15	0.5
2	2	Z	1033	tight thermal	0.16	0.5
2	2	c	1033	tight thermal	0.15	0.5
2	2	f	1033	tight thermal	0.17	0.5
2	2	i	1033	tight thermal	0.16	0.5
2	2	l	1033	tight thermal	0.14	0.5
2	2	o	1033	tight thermal	0.16	0.5
3	3	C	181	tight thermal	0.16	0.5
3	3	F	181	tight thermal	0.13	0.5
3	3	I	181	tight thermal	0.15	0.5
3	3	L	181	tight thermal	0.15	0.5
3	3	O	181	tight thermal	0.15	0.5
3	3	R	181	tight thermal	0.14	0.5
3	3	U	181	tight thermal	0.18	0.5
3	3	X	181	tight thermal	0.14	0.5
3	3	a	181	tight thermal	0.14	0.5
3	3	d	181	tight thermal	0.13	0.5
3	3	g	181	tight thermal	0.15	0.5
3	3	j	181	tight thermal	0.14	0.5
3	3	m	181	tight thermal	0.13	0.5
3	3	p	181	tight thermal	0.15	0.5
1	1	A	656	loose thermal	0.18	10
1	1	D	656	loose thermal	0.17	10
1	1	G	656	loose thermal	0.18	10
1	1	J	656	loose thermal	0.18	10
1	1	M	656	loose thermal	0.18	10
1	1	P	656	loose thermal	0.19	10
1	1	S	656	loose thermal	0.19	10
1	1	V	656	loose thermal	0.18	10
1	1	Y	656	loose thermal	0.19	10
1	1	b	656	loose thermal	0.19	10
1	1	e	656	loose thermal	0.18	10
1	1	h	656	loose thermal	0.19	10
1	1	k	656	loose thermal	0.18	10
1	1	n	656	loose thermal	0.19	10

LS refinement shell

Resolution: 2.602→2.67 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.294	911	-
R_work	0.263	17313	-
obs	-	98005	100 %

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Protein , 2 types, 28 molecules ADGJMPSVYbehknBEHKNQTWZcfilo

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Protein/peptide , 1 types, 14 molecules CFILORUXadgjmp

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Non-polymers , 3 types, 1294 molecules

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-Protein/peptide , 1 types, 14 molecules CFILORUXadgjmp

-Non-polymers , 3 types, 1294 molecules

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Protein , 2 types, 28 molecules ADGJMPSVYbehknBEHKNQTWZcfilo

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Protein/peptide , 1 types, 14 molecules CFILORUXadgjmp

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Non-polymers , 3 types, 1294 molecules

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