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

ID or keywords:

Entry

Database: PDB / ID: 2wpr

Title

Salmonella enterica SadA 483-523 fused to GCN4 adaptors (SadAK3b-V1, 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: 2.65 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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Download

PDBx/mmCIF format	2wpr.cif.gz	69.1 KB	Display	PDBx/mmCIF format
PDB format	pdb2wpr.ent.gz	52.1 KB	Display	PDB format
PDBx/mmJSON format	2wpr.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/wp/2wpr ftp://data.pdbj.org/pub/pdb/validation_reports/wp/2wpr	HTTPS FTP

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Related structure data

Related structure data	2wpqC 2wpsC 2wpyC 2wpzC 2wq0C 2wq1C 2wq2C 2wq3C 1gcmS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2wps-d 6fia-1 5tfk-d 4qkv-d 4ytd-d 2wpq-d 5uz8-d 4qkw-d 5tfm-d 5wme-d 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)	36.130, 62.530, 172.570
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	ILE	ILE	LYS	LYS	5	A	A	457 - 553	4 - 100
2	1	1	ILE	ILE	LYS	LYS	5	B	B	457 - 553	4 - 100
3	1	1	ILE	ILE	LYS	LYS	5	C	C	457 - 553	4 - 100
1	1	2	ILE	ILE	ASP	ASP	1	A	A	457 - 459	4 - 6
2	1	2	ILE	ILE	ASP	ASP	1	B	B	457 - 459	4 - 6
3	1	2	ILE	ILE	ASP	ASP	1	C	C	457 - 459	4 - 6
1	2	2	ILE	ILE	ASN	ASN	1	A	A	461 - 473	8 - 20
2	2	2	ILE	ILE	ASN	ASN	1	B	B	461 - 473	8 - 20
3	2	2	ILE	ILE	ASN	ASN	1	C	C	461 - 473	8 - 20
1	1	3	ILE	ILE	ALA	ALA	1	A	A	475 - 476	22 - 23
2	1	3	ILE	ILE	ALA	ALA	1	B	B	475 - 476	22 - 23
3	1	3	ILE	ILE	ALA	ALA	1	C	C	475 - 476	22 - 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	VAL	VAL	VAL	VAL	1	A	A	485	32
2	1	4	VAL	VAL	VAL	VAL	1	B	B	485	32
3	1	4	VAL	VAL	VAL	VAL	1	C	C	485	32
1	2	4	ASN	ASN	ASN	ASN	1	A	A	488 - 500	35 - 47
2	2	4	ASN	ASN	ASN	ASN	1	B	B	488 - 500	35 - 47
3	2	4	ASN	ASN	ASN	ASN	1	C	C	488 - 500	35 - 47
1	1	5	ASN	ASN	ILE	ILE	1	A	A	502 - 513	49 - 60
2	1	5	ASN	ASN	ILE	ILE	1	B	B	502 - 513	49 - 60
3	1	5	ASN	ASN	ILE	ILE	1	C	C	502 - 513	49 - 60
1	1	6	ASN	ASN	LYS	LYS	1	A	A	515 - 525	62 - 72
2	1	6	ASN	ASN	LYS	LYS	1	B	B	515 - 525	62 - 72
3	1	6	ASN	ASN	LYS	LYS	1	C	C	515 - 525	62 - 72
1	1	7	ILE	ILE	GLU	GLU	1	A	A	527 - 528	74 - 75
2	1	7	ILE	ILE	GLU	GLU	1	B	B	527 - 528	74 - 75
3	1	7	ILE	ILE	GLU	GLU	1	C	C	527 - 528	74 - 75
1	2	7	ILE	ILE	GLU	GLU	1	A	A	531 - 532	78 - 79
2	2	7	ILE	ILE	GLU	GLU	1	B	B	531 - 532	78 - 79
3	2	7	ILE	ILE	GLU	GLU	1	C	C	531 - 532	78 - 79
1	1	8	ILE	ILE	SER	SER	1	A	A	534 - 536	81 - 83
2	1	8	ILE	ILE	SER	SER	1	B	B	534 - 536	81 - 83
3	1	8	ILE	ILE	SER	SER	1	C	C	534 - 536	81 - 83
1	2	8	ILE	ILE	ILE	ILE	1	A	A	538	85
2	2	8	ILE	ILE	ILE	ILE	1	B	B	538	85
3	2	8	ILE	ILE	ILE	ILE	1	C	C	538	85
1	3	8	HIS	HIS	ILE	ILE	1	A	A	540 - 541	87 - 88
2	3	8	HIS	HIS	ILE	ILE	1	B	B	540 - 541	87 - 88
3	3	8	HIS	HIS	ILE	ILE	1	C	C	540 - 541	87 - 88
1	4	8	ASN	ASN	ASN	ASN	1	A	A	543	90
2	4	8	ASN	ASN	ASN	ASN	1	B	B	543	90
3	4	8	ASN	ASN	ASN	ASN	1	C	C	543	90
1	5	8	ILE	ILE	LYS	LYS	1	A	A	545 - 549	92 - 96
2	5	8	ILE	ILE	LYS	LYS	1	B	B	545 - 549	92 - 96
3	5	8	ILE	ILE	LYS	LYS	1	C	C	545 - 549	92 - 96
1	6	8	LEU	LEU	LYS	LYS	1	A	A	551 - 553	98 - 100
2	6	8	LEU	LEU	LYS	LYS	1	B	B	551 - 553	98 - 100
3	6	8	LEU	LEU	LYS	LYS	1	C	C	551 - 553	98 - 100

NCS ensembles :

ID
1
2
3
4
5
6
7
8

#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 OUT-OF-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 / Chloride Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.7 Å³/Da / Density % sol: 54 % / 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: 0.9784
Detector	Type: MARRESEARCH / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9784 Å / Relative weight: 1
Reflection	Resolution: 2.65→36 Å / Num. obs: 10608 / % possible obs: 87.8 % / Observed criterion σ(I): 0 / Redundancy: 3.29 % / B_iso Wilson estimate: 41 Å² / R_merge(I) obs: 0.13 / Net I/σ(I): 8
Reflection shell	Resolution: 2.65→2.81 Å / Redundancy: 3.25 % / R_merge(I) obs: 0.65 / Mean I/σ(I) obs: 2.53 / % possible all: 78.3

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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: 2.65→35.36 Å / Cor.coef. F_o:F_c: 0.922 / Cor.coef. F_o:F_c free: 0.854 / Cross valid method: THROUGHOUT / ESU R: 1.189 / ESU R Free: 0.438 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.32729	529	5 %	RANDOM
R_work	0.26704	-	-	-
obs	0.26989	10114	88.54 %	-

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: 36.188 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.89 Å²	0 Å²	0 Å²
2-	-	3.88 Å²	0 Å²
3-	-	-	-4.76 Å²

Refinement step

Cycle: LAST / Resolution: 2.65→35.36 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2277	0	4	19	2300

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.022	2286
X-RAY DIFFRACTION	r_bond_other_d	0	0.02	1458
X-RAY DIFFRACTION	r_angle_refined_deg	1.551	1.957	3093
X-RAY DIFFRACTION	r_angle_other_deg	4.196	3	3669
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.219	5	288
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.402	27.917	96
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.77	15	473
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	30.119	15	4
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	408
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	2440
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	340
X-RAY DIFFRACTION	r_nbd_refined	0.253	0.2	719
X-RAY DIFFRACTION	r_nbd_other	0.205	0.2	1393
X-RAY DIFFRACTION	r_nbtor_refined	0.215	0.2	1192
X-RAY DIFFRACTION	r_nbtor_other	0.104	0.2	1209
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.136	0.2	35
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	0.179	0.2	18
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.225	0.2	29
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.236	0.2	4
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	2.046	4	1452
X-RAY DIFFRACTION	r_mcbond_other	0	4	579
X-RAY DIFFRACTION	r_mcangle_it	3.751	6	2394
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	6.103	8	834
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	9.519	12	699
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	208	tight positional	0.04	0.05
2	2	B	208	tight positional	0.05	0.05
2	3	C	208	tight positional	0.05	0.05
3	1	A	59	tight positional	0.04	0.05
3	2	B	59	tight positional	0.04	0.05
3	3	C	59	tight positional	0.06	0.05
4	1	A	153	tight positional	0.06	0.05
4	2	B	153	tight positional	0.06	0.05
4	3	C	153	tight positional	0.07	0.05
5	1	A	131	tight positional	0.06	0.05
5	2	B	131	tight positional	0.06	0.05
5	3	C	131	tight positional	0.05	0.05
6	1	A	124	tight positional	0.04	0.05
6	2	B	124	tight positional	0.05	0.05
6	3	C	124	tight positional	0.04	0.05
7	1	A	48	tight positional	0.05	0.05
7	2	B	48	tight positional	0.05	0.05
7	3	C	48	tight positional	0.05	0.05
8	1	A	182	tight positional	0.05	0.05
8	2	B	182	tight positional	0.05	0.05
8	3	C	182	tight positional	0.05	0.05
1	1	A	581	medium positional	0.29	0.5
1	2	B	581	medium positional	0.3	0.5
1	3	C	581	medium positional	0.39	0.5
1	1	A	616	loose positional	0.63	5
1	2	B	616	loose positional	0.85	5
1	3	C	616	loose positional	0.76	5
2	1	A	208	tight thermal	0.12	0.5
2	2	B	208	tight thermal	0.11	0.5
2	3	C	208	tight thermal	0.12	0.5
3	1	A	59	tight thermal	0.1	0.5
3	2	B	59	tight thermal	0.12	0.5
3	3	C	59	tight thermal	0.13	0.5
4	1	A	153	tight thermal	0.21	0.5
4	2	B	153	tight thermal	0.2	0.5
4	3	C	153	tight thermal	0.21	0.5
5	1	A	131	tight thermal	0.22	0.5
5	2	B	131	tight thermal	0.18	0.5
5	3	C	131	tight thermal	0.21	0.5
6	1	A	124	tight thermal	0.14	0.5
6	2	B	124	tight thermal	0.13	0.5
6	3	C	124	tight thermal	0.11	0.5
7	1	A	48	tight thermal	0.13	0.5
7	2	B	48	tight thermal	0.13	0.5
7	3	C	48	tight thermal	0.1	0.5
8	1	A	182	tight thermal	0.11	0.5
8	2	B	182	tight thermal	0.12	0.5
8	3	C	182	tight thermal	0.13	0.5
1	1	A	581	medium thermal	0.55	2
1	2	B	581	medium thermal	0.57	2
1	3	C	581	medium thermal	0.54	2
1	1	A	616	loose thermal	2.44	10
1	2	B	616	loose thermal	2.49	10
1	3	C	616	loose thermal	2.03	10

LS refinement shell

Resolution: 2.65→2.718 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.381	34	-
R_work	0.34	677	-
obs	-	-	80.61 %

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