PDB-3tx3: CysZ, a putative sulfate permease

ID or keywords:

Entry

Database: PDB / ID: 3tx3

Title

CysZ, a putative sulfate permease

Components

Uncharacterized protein involved in cysteine biosynthesis

Keywords

TRANSPORT PROTEIN /

Structural Genomics / PSI-Biology / New York Consortium on Membrane Protein Structure / NYCOMPS /

membrane protein /

anion channel

Function / homology

Sulfate transporter CysZ / Etoposide-induced protein 2.4 (EI24) / sulfate transmembrane transporter activity / sulfate assimilation / cysteine biosynthetic process / plasma membrane => GO:0005886 / Sulfate transporter CysZ

Function and homology information

Biological species

Idiomarina loihiensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Native SAD / Resolution: 2.3 Å

Authors

Assur, Z. / Liu, Q. / Hendrickson, W.A. / Mancia, F. / New York Consortium on Membrane Protein Structure (NYCOMPS)

Citation

Journal: To be Published
Title: CysZ, a putative sulfate permease
Authors: Assur, Z. / Liu, Q. / Hendrickson, W.A. / Mancia, F.

History

Deposition	Sep 22, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 9, 2011	Provider: repository / Type: Initial release
Revision 1.1	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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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Download

PDBx/mmCIF format	3tx3.cif.gz	202.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3tx3.ent.gz	165.5 KB	Display	PDB format
PDBx/mmJSON format	3tx3.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/tx/3tx3 ftp://data.pdbj.org/pub/pdb/validation_reports/tx/3tx3	HTTPS FTP

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Related structure data

Similar structure data	2ohg-1 5ha7-d 2oho-d 3mmu-12 4y9p-d 4nna-d 2qum-1 3plz-d 6j3f-d 5xr2-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: GO.7980

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Uncharacterized protein involved in cysteine biosynthesis

B: Uncharacterized protein involved in cysteine biosynthesis

hetero molecules

61.6 kDa, 2 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)	128.853, 81.986, 100.375
Angle α, β, γ (deg.)	90.00, 125.12, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Uncharacterized protein involved in cysteine biosynthesis Mass: 28968.293 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Idiomarina loihiensis (bacteria) / Gene: cysZ, IL1703 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 PLysS / References: UniProt: Q5QUJ8
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE / Lauryldimethylamine oxide Mass: 229.402 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C₁₄H₃₁NO / Comment: LDAO, detergent*YM
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 7

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Sample preparation

Crystal	Density Matthews: 3.74 Å³/Da / Density % sol: 67.13 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100 mM MES, pH 6.0, 30% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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	NSLS	X4A	1	1.7432
SYNCHROTRON	NSLS	X4C	2	0.97912

Detector

Type	ID	Detector	Date	Details
ADSC QUANTUM 4r	1	CCD	Jul 20, 2010	mirror
MAR CCD 165 mm	2	CCD	Jul 20, 2010	mirror

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	DCM	SINGLE WAVELENGTH	M	x-ray	1
2	DCM	SINGLE WAVELENGTH	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.7432	1
2	0.97912	1

Reflection

Resolution: 2.3→30 Å / Num. all: 38075 / Num. obs: 38075 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / B_iso Wilson estimate: 34.2 Å²

Reflection shell

Resolution: 2.3→2.36 Å / % possible all: 100

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.7_650)	refinement
XDS		data reduction
SCALA		data scaling

Refinement

Method to determine structure: Native SAD / Resolution: 2.3→29.172 Å / SU ML: 0.31 / σ(F): 0 / Phase error: 22.54 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2376	3719	5.13 %	RANDOM
R_work	0.1995	-	-	-
all	0.2015	72433	-	-
obs	0.2015	72433	97.04 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 53.167 Å² / k_sol: 0.321 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.3042 Å²	0 Å²	-1.4099 Å²
2-	-	13.4327 Å²	0 Å²
3-	-	-	-10.1284 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→29.172 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3677	0	249	152	4078

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	4007
X-RAY DIFFRACTION	f_angle_d	0.894	5387
X-RAY DIFFRACTION	f_dihedral_angle_d	14.043	1519
X-RAY DIFFRACTION	f_chiral_restr	0.062	581
X-RAY DIFFRACTION	f_plane_restr	0.004	621

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.3-2.3291	0.2618	139	0.2132	2350	X-RAY DIFFRACTION	91
2.3291-2.3597	0.2352	144	0.1969	2418	X-RAY DIFFRACTION	91
2.3597-2.392	0.226	150	0.1811	2440	X-RAY DIFFRACTION	93
2.392-2.4262	0.2694	136	0.1803	2410	X-RAY DIFFRACTION	92
2.4262-2.4624	0.2328	148	0.1819	2446	X-RAY DIFFRACTION	94
2.4624-2.5009	0.2546	146	0.1715	2446	X-RAY DIFFRACTION	96
2.5009-2.5418	0.2029	114	0.1755	2578	X-RAY DIFFRACTION	96
2.5418-2.5856	0.1914	89	0.1567	2506	X-RAY DIFFRACTION	96
2.5856-2.6326	0.2011	145	0.1656	2609	X-RAY DIFFRACTION	96
2.6326-2.6832	0.216	136	0.1731	2471	X-RAY DIFFRACTION	97
2.6832-2.738	0.2221	136	0.1785	2564	X-RAY DIFFRACTION	97
2.738-2.7974	0.2196	130	0.1714	2549	X-RAY DIFFRACTION	98
2.7974-2.8625	0.2073	145	0.1842	2568	X-RAY DIFFRACTION	98
2.8625-2.934	0.2672	130	0.1879	2609	X-RAY DIFFRACTION	98
2.934-3.0132	0.2478	125	0.1896	2531	X-RAY DIFFRACTION	98
3.0132-3.1018	0.2359	136	0.1863	2583	X-RAY DIFFRACTION	98
3.1018-3.2018	0.2013	136	0.1918	2597	X-RAY DIFFRACTION	99
3.2018-3.3161	0.2419	129	0.1822	2628	X-RAY DIFFRACTION	99
3.3161-3.4487	0.2213	154	0.1995	2577	X-RAY DIFFRACTION	99
3.4487-3.6054	0.239	147	0.21	2610	X-RAY DIFFRACTION	100
3.6054-3.7951	0.2797	134	0.1975	2622	X-RAY DIFFRACTION	99
3.7951-4.0323	0.2398	142	0.2157	2612	X-RAY DIFFRACTION	100
4.0323-4.3427	0.2537	162	0.2205	2602	X-RAY DIFFRACTION	100
4.3427-4.778	0.2193	161	0.2044	2621	X-RAY DIFFRACTION	100
4.778-5.4654	0.237	117	0.1975	2620	X-RAY DIFFRACTION	100
5.4654-6.8709	0.2575	153	0.2522	2592	X-RAY DIFFRACTION	100
6.8709-29.1739	0.2481	135	0.2102	2555	X-RAY DIFFRACTION	97

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	0.5754	0.3298	-0.0707	0.7954	-0.0881	0.388	-0.126	0.135	0.3681	-0.1864	0.2673	0.1159	-0.1891	-0.11	-0.0433	0.3522	-0.0453	-0.0575	0.4084	0.0608	0.3919	38.6378	49.0206	8.9195
2	0.2872	-0.0476	0.0434	0.2902	-0.4662	0.6642	-0.2362	-0.0173	-0.4926	-0.0541	-0.1368	-0.4536	0.1247	0.0248	0.1862	0.3135	-0.0454	0.0915	0.3176	0.0524	0.5053	40.7969	18.1987	19.91
3	1.0719	-0.2171	0.0241	1.3792	0.3019	0.5957	-0.1059	0.1798	0.0285	-0.1112	0.0104	0.0354	-0.0627	0.0758	0.0392	0.2676	-0.0755	0.0134	0.2105	0.046	0.2082	48.6081	46.0169	19.5463
4	1.0944	0.3958	-0.0594	0.9407	0.4905	0.5072	-0.1019	0.4153	-0.2427	-0.3169	0.1762	-0.2171	0.2344	0.0084	-0.0226	0.2881	-0.012	0.063	0.3311	0.0021	0.2437	22.1996	16.4332	11.9942
5	1.0009	0.9817	0.6008	0.9082	0.6129	0.3912	-0.1154	-0.0009	0.848	0.1353	-0.1709	0.7383	-0.0336	0.0758	0.2031	0.3607	-0.0478	-0.0207	0.356	-0.0703	0.6061	23.7059	46.5444	22.9675
6	0.7732	-0.1493	0.603	0.9391	-0.2481	0.9762	-0.154	-0.0017	0.1323	-0.0817	0.0595	0.0101	-0.0004	-0.1206	0.0509	0.1592	-0.0485	-0.011	0.1878	-0.0152	0.1918	16.1883	19.5222	25.2307

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A and (resseq 5:34)
2	X-RAY DIFFRACTION	2	chain A and (resseq 35:98)
3	X-RAY DIFFRACTION	3	chain A and (resseq 99:246)
4	X-RAY DIFFRACTION	4	chain B and (resseq 4:34)
5	X-RAY DIFFRACTION	5	chain B and (resseq 35:98)
6	X-RAY DIFFRACTION	6	chain B and (resseq 99:246)

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