PDB-1sw5: Crystal structure of ProX from Archeoglobus fulgidus in the ligan...

ID or keywords:

Entry

Database: PDB / ID: 1sw5

Title

Crystal structure of ProX from Archeoglobus fulgidus in the ligand free form

Components

osmoprotection protein (proX)

Keywords

PROTEIN BINDING / binding-protein /

compatible solutes / cation-pi interactions / non-classical hydrogen bonds

Function / homology

Function and homology information

response to stimulus / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex /

metal ion binding
Similarity search - Function

Biological species

Archaeoglobus fulgidus (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Schiefner, A. / Holtmann, G. / Diederichs, K. / Welte, W. / Bremer, E.

Citation

Journal: J.Biol.Chem. / Year: 2004
Title: Structural basis for the binding of compatible solutes by ProX from the hyperthermophilic archaeon Archaeoglobus fulgidus.
Authors: Schiefner, A. / Holtmann, G. / Diederichs, K. / Welte, W. / Bremer, E.

History

Deposition	Mar 30, 2004	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 14, 2004	Provider: repository / Type: Initial release
Revision 1.1	Apr 30, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3	Oct 11, 2017	Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4	Oct 27, 2021	Group: Database references / Derived calculations Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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
Revision 1.5	Aug 23, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	1sw5.cif.gz	227.3 KB	Display	PDBx/mmCIF format
PDB format	pdb1sw5.ent.gz	184.3 KB	Display	PDB format
PDBx/mmJSON format	1sw5.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sw/1sw5 ftp://data.pdbj.org/pub/pdb/validation_reports/sw/1sw5	HTTPS FTP

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Related structure data

Related structure data	1sw1SC 1sw2C 1sw4C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3mam-d 3kyj-d 3ppn-2 4wep-2 4rsm-2 1qw0-d 5nxy-1 6ueo-3 1qn5-1 3tyh-5 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

Related structure data

1sw1SC

1sw2C

1sw4C

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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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: osmoprotection protein (proX)

B: osmoprotection protein (proX)

C: osmoprotection protein (proX)

D: osmoprotection protein (proX)

hetero molecules

125 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: osmoprotection protein (proX)

hetero molecules

defined by author
31.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: osmoprotection protein (proX)

hetero molecules

defined by author
31.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: osmoprotection protein (proX)

hetero molecules

defined by author
31.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: osmoprotection protein (proX)

hetero molecules

defined by author
31.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	161.500, 56.500, 116.100
Angle α, β, γ (deg.)	90.00, 110.60, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
1	2	A
2	2	B
3	2	C
4	2	D
1	3	A
2	3	B
3	3	C
4	3	D

NCS domain segments:

Component-ID: 1

Dom-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	GLU	GLU	ASP	ASP	6	A	A	6 - 110	6 - 110
2	1	GLU	GLU	ASP	ASP	6	B	B	6 - 110	6 - 110
3	1	GLU	GLU	ASP	ASP	6	C	C	6 - 110	6 - 110
4	1	GLU	GLU	ASP	ASP	6	D	D	6 - 110	6 - 110
1	2	TYR	TYR	LEU	LEU	4	A	A	111 - 211	111 - 211
2	2	TYR	TYR	LEU	LEU	4	B	B	111 - 211	111 - 211
3	2	TYR	TYR	LEU	LEU	4	C	C	111 - 211	111 - 211
4	2	TYR	TYR	LEU	LEU	4	D	D	111 - 211	111 - 211
1	3	LEU	LEU	LYS	LYS	6	A	A	211 - 275	211 - 275
2	3	LEU	LEU	LYS	LYS	6	B	B	211 - 275	211 - 275
3	3	LEU	LEU	LYS	LYS	6	C	C	211 - 275	211 - 275
4	3	LEU	LEU	LYS	LYS	6	D	D	211 - 275	211 - 275

NCS ensembles :

ID
1
2
3

#1: Protein	osmoprotection protein (proX) Mass: 31128.305 Da / Num. of mol.: 4 / Mutation: C1G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: proX / Plasmid: pASK-IBA6 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(Codon plus RIL) / References: UniProt: O29280
#2: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#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 / Water Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.99 Å³/Da / Density % sol: 38.22 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: magnesium chloride, Tris, PEG 4000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9778 Å
Detector	Type: MARRESEARCH / Detector: CCD / Date: Jun 11, 2003
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9778 Å / Relative weight: 1
Reflection	Resolution: 1.8→50 Å / Num. all: 90922 / Num. obs: 90922 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / B_iso Wilson estimate: 26.8 Å² / R_sym value: 0.077 / Net I/σ(I): 10.7
Reflection shell	Resolution: 1.8→1.9 Å / Mean I/σ(I) obs: 3.9 / R_sym value: 0.332 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
REFMAC	5.1.25	refinement
MAR345		data collection
XDS		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1SW1

1sw1

Resolution: 1.8→50 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.942 / SU B: 2.832 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21439	4551	5 %	RANDOM
R_work	0.18642	-	-	-
all	0.18785	90922	-	-
obs	0.18785	86386	99.75 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 19.597 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.33 Å²	0 Å²	0.42 Å²
2-	-	0.35 Å²	0 Å²
3-	-	-	0.27 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8644	0	9	327	8980

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	8792
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	8068
X-RAY DIFFRACTION	r_angle_refined_deg	1.364	1.98	11884
X-RAY DIFFRACTION	r_angle_other_deg	0.825	3	18860
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.047	5	1076
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	1324
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	9732
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1660
X-RAY DIFFRACTION	r_nbd_refined	0.204	0.2	1644
X-RAY DIFFRACTION	r_nbd_other	0.229	0.2	8812
X-RAY DIFFRACTION	r_nbtor_other	0.083	0.2	5233
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.146	0.2	248
X-RAY DIFFRACTION	r_metal_ion_refined	0.089	0.2	1
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.179	0.2	42
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.243	0.2	154
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.286	0.2	21
X-RAY DIFFRACTION	r_mcbond_it	0.822	1.5	5372
X-RAY DIFFRACTION	r_mcangle_it	1.534	2	8660
X-RAY DIFFRACTION	r_scbond_it	2.393	3	3420
X-RAY DIFFRACTION	r_scangle_it	4.049	4.5	3224

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	1545	medium positional	0.39	0.5
2	2	B	1545	medium positional	0.37	0.5
2	3	C	1545	medium positional	0.35	0.5
2	4	D	1545	medium positional	0.4	0.5
1	1	A	1627	loose positional	0.59	5
1	2	B	1627	loose positional	0.45	5
1	3	C	1627	loose positional	0.49	5
1	4	D	1627	loose positional	0.52	5
3	1	A	1025	loose positional	0.47	5
3	2	B	1025	loose positional	0.53	5
3	3	C	1025	loose positional	0.44	5
3	4	D	1025	loose positional	0.48	5
2	1	A	1545	medium thermal	14.02	2
2	2	B	1545	medium thermal	13.64	2
2	3	C	1545	medium thermal	14.85	2
2	4	D	1545	medium thermal	12.96	2
1	1	A	1627	loose thermal	3.16	10
1	2	B	1627	loose thermal	1.82	10
1	3	C	1627	loose thermal	2.38	10
1	4	D	1627	loose thermal	2.54	10
3	1	A	1025	loose thermal	4.43	10
3	2	B	1025	loose thermal	3.36	10
3	3	C	1025	loose thermal	4.48	10
3	4	D	1025	loose thermal	3.49	10

LS refinement shell

Resolution: 1.8→1.847 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.261	333
R_work	0.216	6332

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	0.1392	-0.0222	0.064	0.193	0.0329	0.1694	0.0207	-0.0029	-0.0132	-0.0072	-0.0175	0.0088	-0.0206	0.0095	-0.0032	0.0825	-0.0024	-0.0032	0.0813	0.0003	0.0844	85.5182	27.7789	69.7962
2	0.7175	-0.027	0.0738	0.6333	0.1255	0.2608	0.0136	-0.0134	-0.0192	0.0154	-0.0031	0.0101	0.026	0.0042	-0.0105	0.0809	0.0005	-0.0094	0.0542	-0.0014	0.0791	71.5968	4.694	64.2044
3	0.3465	-0.04	0.0119	0.2313	0.0307	0.1744	0.0281	-0.0123	-0.0027	0.0042	-0.0151	-0.0152	0.013	-0.0261	-0.0129	0.0791	-0.0059	-0.0075	0.0726	0.005	0.0781	115.394	-7.8181	68.5555
4	0.7305	-0.1084	0.0393	0.6935	-0.1753	0.239	0.0047	-0.0183	0.008	0.023	0.0172	0.0029	-0.04	-0.0196	-0.0219	0.084	0.0051	0.0004	0.0541	0.0056	0.076	129.572	15.0483	63.8838
5	0.3596	0.1924	-0.2392	0.4951	-0.2364	0.6763	0.0005	-0.0313	0.0163	-0.0041	-0.0314	-0.0072	-0.0252	0.0299	0.0308	0.0739	-0.0042	-0.0091	0.068	0.0068	0.062	95.4947	0.4963	93.4533
6	0.0705	-0.2512	0.7604	0.7376	0.426	0.2823	0.0814	0.0473	0.1243	-0.0764	-0.1445	-0.1268	0.2832	0.1106	0.0631	0.1277	0.0523	0.0706	0.0939	0.0913	0.0927	108.8845	-22.9332	98.8378
7	0.4285	0.0594	0.105	0.3953	0.091	0.5497	0.0477	-0.0076	-0.0162	-0.0085	-0.038	0.0008	0.0053	-0.0062	-0.0098	0.0729	0.0025	-0.0055	0.0701	-0.0075	0.0624	65.5783	22.5569	93.6767
8	0.8001	0.1899	-0.689	1.5313	-0.0957	0.6337	0.081	0.0476	0.0444	-0.0674	-0.0773	0.1434	-0.236	-0.1513	-0.0037	0.1181	0.0755	-0.0328	0.074	-0.0542	0.0678	51.7541	45.8143	98.1031

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	6 - 109	6 - 109
2	X-RAY DIFFRACTION	1	A	A	213 - 275	213 - 275
3	X-RAY DIFFRACTION	2	A	A	110 - 212	110 - 212
4	X-RAY DIFFRACTION	3	B	B	6 - 109	6 - 109
5	X-RAY DIFFRACTION	3	B	B	213 - 275	213 - 275
6	X-RAY DIFFRACTION	4	B	B	110 - 212	110 - 212
7	X-RAY DIFFRACTION	5	C	C	6 - 109	6 - 109
8	X-RAY DIFFRACTION	5	C	C	213 - 275	213 - 275
9	X-RAY DIFFRACTION	6	C	C	110 - 212	110 - 212
10	X-RAY DIFFRACTION	7	D	D	6 - 109	6 - 109
11	X-RAY DIFFRACTION	7	D	D	213 - 275	213 - 275
12	X-RAY DIFFRACTION	8	D	D	110 - 212	110 - 212

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