PDB-2wps: Salmonella enterica SadA 483-523 fused to GCN4 adaptors (SadAK3b-...

ID or keywords:

Entry

Database: PDB / ID: 2wps

Title

Salmonella enterica SadA 483-523 fused to GCN4 adaptors (SadAK3b-V2, out-of-register fusion)

Components

TRIMERIC AUTOTRANSPORTER ADHESIN FRAGMENT

Keywords

MEMBRANE PROTEIN / ION COORDINATION / HYDROPHOBIC CORE / TRIMERIC AUTOTRANSPORTER ADHESIN / TAA / STUTTER / STAMMER / COILED COIL / PROTEIN EXPORT / POLAR CORE RESIDUES

Function / homology

Function and homology information

cell outer membrane / protein transport / cell surface
Similarity search - Function

Biological species

SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Hartmann, M.D. / Ridderbusch, O. / Lupas, A.N. / Hernandez Alvarez, B.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: A Coiled-Coil Motif that Sequesters Ions to the Hydrophobic Core.
Authors: Hartmann, M.D. / Ridderbusch, O. / Zeth, K. / Albrecht, R. / Testa, O. / Woolfson, D.N. / Sauer, G. / Dunin-Horkawicz, S. / Lupas, A.N. / Alvarez, B.H.

History

Deposition	Aug 9, 2009	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 3, 2009	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 650

HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2wps.cif.gz	72.1 KB	Display	PDBx/mmCIF format
PDB format	pdb2wps.ent.gz	54.7 KB	Display	PDB format
PDBx/mmJSON format	2wps.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	2wps_validation.pdf.gz	443.5 KB	Display	wwPDB validaton report
Full document	2wps_full_validation.pdf.gz	445.4 KB	Display
Data in XML	2wps_validation.xml.gz	12.3 KB	Display
Data in CIF	2wps_validation.cif.gz	16.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wp/2wps ftp://data.pdbj.org/pub/pdb/validation_reports/wp/2wps	HTTPS FTP

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Related structure data

Related structure data	2wpqC 2wprC 2wpyC 2wpzC 2wq0C 2wq1C 2wq2C 2wq3C 1gcmS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2wpr-d 6fia-1 5tfk-d 2wpq-d 5tfm-d 4ytd-d 4qkw-d 5wme-d 5uz8-d 5w4t-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

Deposited unit

A: TRIMERIC AUTOTRANSPORTER ADHESIN FRAGMENT

B: TRIMERIC AUTOTRANSPORTER ADHESIN FRAGMENT

C: TRIMERIC AUTOTRANSPORTER ADHESIN FRAGMENT

hetero molecules

37.8 kDa, 3 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)	36.660, 55.850, 168.950
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	GLN	GLN	LYS	LYS	5	A	A	456 - 553	3 - 100
2	1	1	GLN	GLN	LYS	LYS	5	B	B	456 - 553	3 - 100
3	1	1	GLN	GLN	LYS	LYS	5	C	C	456 - 553	3 - 100
1	1	2	ILE	ILE	ILE	ILE	1	A	A	457 - 461	4 - 8
2	1	2	ILE	ILE	ILE	ILE	1	B	B	457 - 461	4 - 8
3	1	2	ILE	ILE	ILE	ILE	1	C	C	457 - 461	4 - 8
1	2	2	ILE	ILE	LEU	LEU	1	A	A	464 - 465	11 - 12
2	2	2	ILE	ILE	LEU	LEU	1	B	B	464 - 465	11 - 12
3	2	2	ILE	ILE	LEU	LEU	1	C	C	464 - 465	11 - 12
1	3	2	LYS	LYS	ILE	ILE	1	A	A	467 - 468	14 - 15
2	3	2	LYS	LYS	ILE	ILE	1	B	B	467 - 468	14 - 15
3	3	2	LYS	LYS	ILE	ILE	1	C	C	467 - 468	14 - 15
1	1	3	ILE	ILE	ALA	ALA	1	A	A	471 - 476	18 - 23
2	1	3	ILE	ILE	ALA	ALA	1	B	B	471 - 476	18 - 23
3	1	3	ILE	ILE	ALA	ALA	1	C	C	471 - 476	18 - 23
1	2	3	ILE	ILE	ILE	ILE	1	A	A	478	25
2	2	3	ILE	ILE	ILE	ILE	1	B	B	478	25
3	2	3	ILE	ILE	ILE	ILE	1	C	C	478	25
1	3	3	LEU	LEU	ILE	ILE	1	A	A	481 - 482	28 - 29
2	3	3	LEU	LEU	ILE	ILE	1	B	B	481 - 482	28 - 29
3	3	3	LEU	LEU	ILE	ILE	1	C	C	481 - 482	28 - 29
1	1	4	LYS	LYS	VAL	VAL	1	A	A	484 - 485	31 - 32
2	1	4	LYS	LYS	VAL	VAL	1	B	B	484 - 485	31 - 32
3	1	4	LYS	LYS	VAL	VAL	1	C	C	484 - 485	31 - 32
1	2	4	GLN	GLN	ASN	ASN	1	A	A	487 - 500	34 - 47
2	2	4	GLN	GLN	ASN	ASN	1	B	B	487 - 500	34 - 47
3	2	4	GLN	GLN	ASN	ASN	1	C	C	487 - 500	34 - 47
1	1	5	ASN	ASN	MET	MET	1	A	A	502 - 524	49 - 71
2	1	5	ASN	ASN	MET	MET	1	B	B	502 - 524	49 - 71
3	1	5	ASN	ASN	MET	MET	1	C	C	502 - 524	49 - 71
1	1	6	GLN	GLN	ILE	ILE	1	A	A	526 - 527	73 - 74
2	1	6	GLN	GLN	ILE	ILE	1	B	B	526 - 527	73 - 74
3	1	6	GLN	GLN	ILE	ILE	1	C	C	526 - 527	73 - 74
1	2	6	ASP	ASP	ASP	ASP	1	A	A	529	76
2	2	6	ASP	ASP	ASP	ASP	1	B	B	529	76
3	2	6	ASP	ASP	ASP	ASP	1	C	C	529	76
1	3	6	ILE	ILE	ILE	ILE	1	A	A	531	78
2	3	6	ILE	ILE	ILE	ILE	1	B	B	531	78
3	3	6	ILE	ILE	ILE	ILE	1	C	C	531	78
1	1	7	GLU	GLU	ILE	ILE	1	A	A	533 - 538	80 - 85
2	1	7	GLU	GLU	ILE	ILE	1	B	B	533 - 538	80 - 85
3	1	7	GLU	GLU	ILE	ILE	1	C	C	533 - 538	80 - 85
1	2	7	ILE	ILE	ILE	ILE	1	A	A	541	88
2	2	7	ILE	ILE	ILE	ILE	1	B	B	541	88
3	2	7	ILE	ILE	ILE	ILE	1	C	C	541	88
1	3	7	ASN	ASN	ALA	ALA	1	A	A	543 - 546	90 - 93
2	3	7	ASN	ASN	ALA	ALA	1	B	B	543 - 546	90 - 93
3	3	7	ASN	ASN	ALA	ALA	1	C	C	543 - 546	90 - 93
1	4	7	ILE	ILE	LYS	LYS	1	A	A	548 - 549	95 - 96
2	4	7	ILE	ILE	LYS	LYS	1	B	B	548 - 549	95 - 96
3	4	7	ILE	ILE	LYS	LYS	1	C	C	548 - 549	95 - 96
1	5	7	LEU	LEU	ILE	ILE	1	A	A	551 - 552	98 - 99
2	5	7	LEU	LEU	ILE	ILE	1	B	B	551 - 552	98 - 99
3	5	7	LEU	LEU	ILE	ILE	1	C	C	551 - 552	98 - 99

NCS ensembles :

ID
1
2
3
4
5
6
7

#1: Protein	TRIMERIC AUTOTRANSPORTER ADHESIN FRAGMENT Mass: 12554.290 Da / Num. of mol.: 3 / Fragment: RESIDUES 483-523 FUSED TO GCN4 ADAPTORS Source method: isolated from a genetically manipulated source Details: N- AND C-TERMINAL IN-REGISTER FUSION TO GCN4 ADAPTORS Source: (gene. exp.) SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8ZL64
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	N- AND C-TERMINAL OUT-OF-REGISTER FUSION TO GCN4 ADAPTORS (UNIPROT: P03069)

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.4 Å³/Da / Density % sol: 49 % / Description: NONE
Crystal grow	Details: 10% (W/V) PEG 4000, 10% (V/V) ISOPOPANOL, 3% (W/V) 1,5-DIAMINOPENTANE DIHYDROCHLORIDE, 100 MM NA-CITRATE PH 5.6

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.992
Detector	Type: MARRESEARCH / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.992 Å / Relative weight: 1
Reflection	Resolution: 2.6→36 Å / Num. obs: 11193 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 3.47 % / B_iso Wilson estimate: 35.9 Å² / R_merge(I) obs: 0.13 / Net I/σ(I): 7.61
Reflection shell	Resolution: 2.6→2.75 Å / Redundancy: 3.05 % / R_merge(I) obs: 0.55 / Mean I/σ(I) obs: 2.01 / % possible all: 97.1

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GCM

1gcm

Resolution: 2.6→35.83 Å / Cor.coef. F_o:F_c: 0.937 / Cor.coef. F_o:F_c free: 0.857 / SU B: 12.427 / SU ML: 0.261 / Cross valid method: THROUGHOUT / ESU R: 1.072 / ESU R Free: 0.413 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.32443	577	5.2 %	RANDOM
R_work	0.23786	-	-	-
obs	0.24193	10616	98.69 %	-

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: 26.717 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.16 Å²	0 Å²	0 Å²
2-	-	4.53 Å²	0 Å²
3-	-	-	-4.37 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→35.83 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2365	0	4	73	2442

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	2374
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	1548
X-RAY DIFFRACTION	r_angle_refined_deg	1.32	1.962	3204
X-RAY DIFFRACTION	r_angle_other_deg	0.967	3	3885
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.802	5	291
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.205	27.876	113
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.176	15	510
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.72	15	6
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	411
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	2531
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	351
X-RAY DIFFRACTION	r_nbd_refined	0.236	0.2	606
X-RAY DIFFRACTION	r_nbd_other	0.15	0.2	1375
X-RAY DIFFRACTION	r_nbtor_refined	0.193	0.2	1174
X-RAY DIFFRACTION	r_nbtor_other	0.091	0.2	1280
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.161	0.2	75
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	0.156	0.2	24
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.231	0.2	37
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.223	0.2	10
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	2.87	4	1642
X-RAY DIFFRACTION	r_mcbond_other	0.445	4	585
X-RAY DIFFRACTION	r_mcangle_it	3.96	6	2427
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	6.385	8	957
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	9.758	12	777
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
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
2	1	A	130	tight positional	0.04	0.05
2	2	B	130	tight positional	0.03	0.05
2	3	C	130	tight positional	0.04	0.05
3	1	A	114	tight positional	0.05	0.05
3	2	B	114	tight positional	0.04	0.05
3	3	C	114	tight positional	0.04	0.05
4	1	A	187	tight positional	0.04	0.05
4	2	B	187	tight positional	0.06	0.05
4	3	C	187	tight positional	0.05	0.05
5	1	A	260	tight positional	0.04	0.05
5	2	B	260	tight positional	0.04	0.05
5	3	C	260	tight positional	0.04	0.05
6	1	A	53	tight positional	0.04	0.05
6	2	B	53	tight positional	0.04	0.05
6	3	C	53	tight positional	0.05	0.05
7	1	A	201	tight positional	0.04	0.05
7	2	B	201	tight positional	0.04	0.05
7	3	C	201	tight positional	0.04	0.05
1	1	A	587	medium positional	0.24	0.5
1	2	B	587	medium positional	0.25	0.5
1	3	C	587	medium positional	0.26	0.5
1	1	A	695	loose positional	0.7	5
1	2	B	695	loose positional	0.71	5
1	3	C	695	loose positional	0.65	5
2	1	A	130	tight thermal	0.11	0.5
2	2	B	130	tight thermal	0.1	0.5
2	3	C	130	tight thermal	0.09	0.5
3	1	A	114	tight thermal	0.12	0.5
3	2	B	114	tight thermal	0.11	0.5
3	3	C	114	tight thermal	0.11	0.5
4	1	A	187	tight thermal	0.15	0.5
4	2	B	187	tight thermal	0.15	0.5
4	3	C	187	tight thermal	0.13	0.5
5	1	A	260	tight thermal	0.14	0.5
5	2	B	260	tight thermal	0.14	0.5
5	3	C	260	tight thermal	0.14	0.5
6	1	A	53	tight thermal	0.14	0.5
6	2	B	53	tight thermal	0.1	0.5
6	3	C	53	tight thermal	0.12	0.5
7	1	A	201	tight thermal	0.1	0.5
7	2	B	201	tight thermal	0.1	0.5
7	3	C	201	tight thermal	0.12	0.5
1	1	A	587	medium thermal	0.54	2
1	2	B	587	medium thermal	0.45	2
1	3	C	587	medium thermal	0.63	2
1	1	A	695	loose thermal	2.08	10
1	2	B	695	loose thermal	2.06	10
1	3	C	695	loose thermal	2.47	10

LS refinement shell

Resolution: 2.597→2.664 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.363	50	-
R_work	0.317	732	-
obs	-	-	94.9 %

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