PDB-3wxx: Crystal Structure of a T3SS complex from Aeromonas hydrophila

ID or keywords:

Entry

Database: PDB / ID: 3wxx

Title

Crystal Structure of a T3SS complex from Aeromonas hydrophila

Components

AcrH
AopB

Keywords

Membrane protein/Chaperone / Translocator / Membrane protein-Chaperone complex

Function / homology

Function and homology information

host cell membrane / metal ion binding
Similarity search - Function

Biological species

Aeromonas hydrophila (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.7 Å

Authors

Nguyen, V.S. / Jobichen, C. / Sivaraman, J. / Henry, Y.K.M.

Citation

Journal: Structure / Year: 2015
Title: Structure of AcrH-AopB Chaperone-Translocator Complex Reveals a Role for Membrane Hairpins in Type III Secretion System Translocon Assembly
Authors: Nguyen, V.S. / Jobichen, C. / Tan, K.W. / Tan, Y.W. / Chan, S.L. / Ramesh, K. / Yuan, Y. / Hong, Y. / Seetharaman, J. / Leung, K.Y. / Sivaraman, J. / Mok, Y.K.

History

Deposition	Aug 12, 2014	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 14, 2015	Provider: repository / Type: Initial release
Revision 1.1	Nov 11, 2015	Group: Database references
Revision 1.2	Nov 20, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / 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_ncs_dom_lim / struct_ref_seq_dif / 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_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 / _struct_ref_seq_dif.details / _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	3wxx.cif.gz	254.8 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3wxx_validation.pdf.gz	479 KB	Display	wwPDB validaton report
Full document	3wxx_full_validation.pdf.gz	500.9 KB	Display
Data in XML	3wxx_validation.xml.gz	53.1 KB	Display
Data in CIF	3wxx_validation.cif.gz	69.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wx/3wxx ftp://data.pdbj.org/pub/pdb/validation_reports/wx/3wxx	HTTPS FTP

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Related structure data

Similar structure data	2rj6-d 5t0n-4 5lt4-2 2b7a-1 6n0m-5 5dj4-5 5t0n-2 1pca-d 4tsd-d 3igx-2 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) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: AcrH

B: AopB

C: AcrH

D: AopB

E: AcrH

F: AopB

G: AcrH

H: AopB

hetero molecules

161 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: AcrH

B: AopB

defined by author&software
40.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: AcrH

D: AopB

defined by author&software
40.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: AcrH

F: AopB

defined by author&software
40.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: AcrH

H: AopB

hetero molecules

defined by author&software
40.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	124.662, 151.942, 106.253
Angle α, β, γ (deg.)	90.00, 104.95, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-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	GLU	GLU	GLU	GLU	A	A	10 - 159	2 - 151
2	1	GLU	GLU	GLU	GLU	C	C	10 - 159	2 - 151
1	2	GLU	GLU	MSE	MSE	A	A	10 - 158	2 - 150
2	2	GLU	GLU	MSE	MSE	E	E	10 - 158	2 - 150
1	3	GLU	GLU	MSE	MSE	A	A	10 - 158	2 - 150
2	3	GLU	GLU	MSE	MSE	G	G	10 - 158	2 - 150
1	4	GLY	GLY	ASP	ASP	B	B	45 - 263	1 - 219
2	4	GLY	GLY	ASP	ASP	D	D	45 - 263	1 - 219
1	5	GLY	GLY	ASP	ASP	B	B	45 - 263	1 - 219
2	5	GLY	GLY	ASP	ASP	F	F	45 - 263	1 - 219
1	6	GLY	GLY	ASP	ASP	B	B	45 - 263	1 - 219
2	6	GLY	GLY	ASP	ASP	H	H	45 - 263	1 - 219
1	7	GLU	GLU	MSE	MSE	C	C	10 - 158	2 - 150
2	7	GLU	GLU	MSE	MSE	E	E	10 - 158	2 - 150
1	8	GLU	GLU	MSE	MSE	C	C	10 - 158	2 - 150
2	8	GLU	GLU	MSE	MSE	G	G	10 - 158	2 - 150
1	9	GLY	GLY	ASP	ASP	D	D	45 - 263	1 - 219
2	9	GLY	GLY	ASP	ASP	F	F	45 - 263	1 - 219
1	10	GLY	GLY	ASP	ASP	D	D	45 - 263	1 - 219
2	10	GLY	GLY	ASP	ASP	H	H	45 - 263	1 - 219
1	11	ASN	ASN	GLU	GLU	E	E	9 - 159	1 - 151
2	11	ASN	ASN	GLU	GLU	G	G	9 - 159	1 - 151
1	12	GLY	GLY	ASP	ASP	F	F	45 - 263	1 - 219
2	12	GLY	GLY	ASP	ASP	H	H	45 - 263	1 - 219

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12

#1: Protein	AcrH Mass: 16888.354 Da / Num. of mol.: 4 / Fragment: UNP residues 9-159 / Mutation: R107H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Gene: acrH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21De3 / References: UniProt: Q6TLM1
#2: Protein	AopB Mass: 23243.404 Da / Num. of mol.: 4 / Fragment: UNP residues 45-263 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Gene: aopB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q6TLM0
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 56 / 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: 3.03 Å³/Da / Density % sol: 59.38 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.1M Sodium Malonate, 0.1M HEPES, 0.5% Jeffamine, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9798 Å
Detector	Type: ADSC QUANTUM 4r / Detector: CCD / Date: Oct 8, 2013 / Details: Mirrors
Radiation	Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9798 Å / Relative weight: 1
Reflection	Resolution: 2.6→50 Å / Num. obs: 48982 / % possible obs: 96.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.5 % / R_merge(I) obs: 0.026 / Net I/σ(I): 12.9
Reflection shell	Resolution: 2.6→2.64 Å

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
Auto-Rickshaw		phasing
REFMAC	5.8.0073	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.7→15 Å / Cor.coef. F_o:F_c: 0.947 / Cor.coef. F_o:F_c free: 0.921 / SU B: 11.916 / SU ML: 0.245 / Cross valid method: THROUGHOUT / ESU R: 0.685 / ESU R Free: 0.325 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25222	2484	5.1 %	RANDOM
R_work	0.21293	-	-	-
obs	0.21493	46394	93.18 %	-
all	-	49886	-	-

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: 68.348 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.63 Å²	0 Å²	-1.19 Å²
2-	-	-4.25 Å²	-0 Å²
3-	-	-	4.82 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9660	0	1	56	9717

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.019	9806
X-RAY DIFFRACTION	r_bond_other_d	0.006	0.02	9614
X-RAY DIFFRACTION	r_angle_refined_deg	1.649	1.991	13216
X-RAY DIFFRACTION	r_angle_other_deg	1.249	3	22038
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.423	5.008	1323
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.054	25.282	354
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.337	15	1476
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.292	15	32
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	1562
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	11174
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	2050
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	6.073	6.796	5324
X-RAY DIFFRACTION	r_mcbond_other	6.073	6.795	5323
X-RAY DIFFRACTION	r_mcangle_it	9.26	10.162	6622
X-RAY DIFFRACTION	r_mcangle_other	9.151	10.334	6620
X-RAY DIFFRACTION	r_scbond_it	6.707	7.053	4482
X-RAY DIFFRACTION	r_scbond_other	6.509	7.126	4472
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	9.624	10.469	6585
X-RAY DIFFRACTION	r_long_range_B_refined	12.763	53.685	11239
X-RAY DIFFRACTION	r_long_range_B_other	12.764	53.695	11231
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 / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	8574	0.07
1	2	C	8574	0.07
2	1	A	8599	0.05
2	2	E	8599	0.05
3	1	A	8494	0.07
3	2	G	8494	0.07
4	1	B	8435	0.13
4	2	D	8435	0.13
5	1	B	8586	0.13
5	2	F	8586	0.13
6	1	B	8529	0.12
6	2	H	8529	0.12
7	1	C	8566	0.05
7	2	E	8566	0.05
8	1	C	8574	0.05
8	2	G	8574	0.05
9	1	D	8498	0.13
9	2	F	8498	0.13
10	1	D	8622	0.11
10	2	H	8622	0.11
11	1	E	8554	0.06
11	2	G	8554	0.06
12	1	F	8498	0.13
12	2	H	8498	0.13

LS refinement shell

Resolution: 2.7→2.768 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.332	166	-
R_work	0.293	3028	-
obs	-	-	84.86 %

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