PDB-5ft4: Crystal structure of the cysteine desulfurase CsdA from Escherich...

ID or keywords:

Entry

Database: PDB / ID: 5ft4

Title

Crystal structure of the cysteine desulfurase CsdA from Escherichia coli at 1.996 Angstroem resolution

Components

CYSTEINE DESULFURASE CSDA

Keywords

TRANSFERASE / L-CYSTEINE DESULFURASE / SULFUR ACCEPTOR / TRANSPERSULFURATION / SULFUR TRAFFICKING

Function / homology

Function and homology information

sulfur compound transport / selenocysteine catabolic process / sulfur amino acid metabolic process / Hydrolases; Acting on carbon-sulfur bonds; Acting on carbon-sulfur bonds / cysteine sulfinate desulfinase activity / selenocysteine lyase / selenocysteine lyase activity / L-cysteine desulfurase complex / sulfurtransferase activity / cysteine desulfurase ...
Similarity search - Function

Biological species

ESCHERICHIA COLI (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.996 Å

Authors

Fernandez, F.J. / Arda, A. / Lopez-Estepa, M. / Aranda, J. / Penya-Soler, E. / Garces, F. / Quintana, J.F. / Round, A. / Campos-Oliva, R. / Bruix, M. ...

Citation

Journal: Acs Catalysis / Year: 2016
Title: The Mechanism of Sulfur Transfer Across Protein- Protein Interfaces: The Csd Model
Authors: Fernandez, F.J. / Arda, A. / Lopez-Estepa, M. / Aranda, J. / Penya-Soler, E. / Garces, F. / Round, A. / Campos-Oliva, R. / Bruix, M. / Coll, M. / Tunon, I. / Jimenez-Barbero, J. / Vega, M.C.

History

Deposition	Jan 11, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 21, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jul 12, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.2	Jan 2, 2019	Group: Data collection / Database references / Structure summary Category: pdbx_database_related / struct / Item: _pdbx_database_related.details / _struct.title

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5ft4.cif.gz	324.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5ft4.ent.gz	275.8 KB	Display	PDB format
PDBx/mmJSON format	5ft4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5ft4_validation.pdf.gz	476.5 KB	Display	wwPDB validaton report
Full document	5ft4_full_validation.pdf.gz	481.9 KB	Display
Data in XML	5ft4_validation.xml.gz	36 KB	Display
Data in CIF	5ft4_validation.cif.gz	53.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ft/5ft4 ftp://data.pdbj.org/pub/pdb/validation_reports/ft/5ft4	HTTPS FTP

-
Related structure data

Related structure data	5ft5 5ft6 5ft7 PDB Unreleased entry 5ft8
Similar structure data	5ft6-d 4lw2-1 4lw2-2 5vlb-2 6mri-1 3n5h-1 5i90-d 6c9e-d 5cg5-1 4gl2-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: CYSTEINE DESULFURASE CSDA

B: CYSTEINE DESULFURASE CSDA

hetero molecules

88.4 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)	64.095, 102.561, 71.258
Angle α, β, γ (deg.)	90.00, 114.45, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS oper: (Code: given
Matrix: (0.1865, 0.9378, -0.2928), (0.9423, -0.2551, -0.2169), (-0.2781, -0.2355, -0.9313)
Vector: 23.8765, -18.1414, 39.6307)

#1: Protein	CYSTEINE DESULFURASE CSDA / CYSTEINE SULFINATE DESULFINASE / CSD / SELENOCYSTEINE LYASE / L-CYSTEINE DESULFURASE CSDA Mass: 43273.980 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q46925, cysteine desulfurase, Lyases; Carbon-sulfur lyases, selenocysteine lyase
#2: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₈O₇
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 584 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.47 Å³/Da / Density % sol: 50.23 % / Description: NONE

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
Detector	Type: ADSC CCD / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8726 Å / Relative weight: 1
Reflection	Resolution: 2→40 Å / Num. obs: 191504 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / B_iso Wilson estimate: 24.21 Å² / R_merge(I) obs: 0.1 / Net I/σ(I): 11.18
Reflection shell	Resolution: 2→2.07 Å / Redundancy: 3.3 % / R_merge(I) obs: 0.74 / Mean I/σ(I) obs: 1.85 / % possible all: 96.1

-
Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
SCALA		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD
Starting model: NONE

Resolution: 1.996→38.518 Å / SU ML: 0.2 / σ(F): 1.37 / Phase error: 17.87 / Stereochemistry target values: ML / Details: U VALUES WITH TLS ADDED.

	R_factor	Num. reflection	% reflection
R_free	0.1914	2881	5.1 %
R_work	0.1377	-	-
obs	0.1405	56537	99.28 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 25 Å²

Refinement step

Cycle: LAST / Resolution: 1.996→38.518 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6058	0	118	584	6760

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	6423
X-RAY DIFFRACTION	f_angle_d	1.329	8781
X-RAY DIFFRACTION	f_dihedral_angle_d	15.201	2308
X-RAY DIFFRACTION	f_chiral_restr	0.059	983
X-RAY DIFFRACTION	f_plane_restr	0.007	1156

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 (%)
1.9962-2.0289	0.3031	131	0.2247	2348	X-RAY DIFFRACTION	92
2.0289-2.0639	0.2165	132	0.2028	2569	X-RAY DIFFRACTION	100
2.0639-2.1014	0.2632	133	0.1906	2558	X-RAY DIFFRACTION	100
2.1014-2.1419	0.2494	122	0.1812	2587	X-RAY DIFFRACTION	100
2.1419-2.1856	0.2254	147	0.174	2543	X-RAY DIFFRACTION	100
2.1856-2.2331	0.2265	132	0.1607	2601	X-RAY DIFFRACTION	100
2.2331-2.285	0.2183	125	0.1502	2567	X-RAY DIFFRACTION	100
2.285-2.3422	0.2145	146	0.1512	2516	X-RAY DIFFRACTION	100
2.3422-2.4055	0.225	128	0.1433	2598	X-RAY DIFFRACTION	100
2.4055-2.4763	0.2018	164	0.1497	2551	X-RAY DIFFRACTION	100
2.4763-2.5562	0.2222	133	0.1416	2570	X-RAY DIFFRACTION	100
2.5562-2.6475	0.2118	122	0.1371	2568	X-RAY DIFFRACTION	100
2.6475-2.7535	0.184	143	0.1341	2573	X-RAY DIFFRACTION	100
2.7535-2.8788	0.2098	119	0.1323	2571	X-RAY DIFFRACTION	100
2.8788-3.0305	0.1656	135	0.125	2581	X-RAY DIFFRACTION	100
3.0305-3.2203	0.1654	132	0.1249	2574	X-RAY DIFFRACTION	100
3.2203-3.4687	0.1716	135	0.1193	2561	X-RAY DIFFRACTION	100
3.4687-3.8175	0.178	146	0.1133	2573	X-RAY DIFFRACTION	100
3.8175-4.3693	0.1587	143	0.107	2551	X-RAY DIFFRACTION	99
4.3693-5.5023	0.1483	159	0.1181	2534	X-RAY DIFFRACTION	99
5.5023-38.5254	0.2036	154	0.1601	2562	X-RAY DIFFRACTION	98

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	2.9467	-2.0566	-0.7392	2.8608	0.776	0.4354	0.1378	0.1994	0.2748	-0.3475	-0.0291	-0.2565	-0.0868	-0.0291	-0.0919	0.1712	-0.0206	0.015	0.1907	0.0257	0.1549	39.6586	4.9611	7.9559
2	1.568	1.9321	1.2577	3.0642	2.7613	3.1444	-0.1099	0.2856	0.166	-0.5649	0.2536	0.0079	-0.2265	0.0457	-0.174	0.2376	0.0668	0.0449	0.3675	0.0642	0.1883	26.5038	7.931	0.2285
3	2.558	0.5395	-1.0741	2.8401	-1.5351	2.7322	0.0868	0.1394	-0.1871	-0.1535	-0.0017	0.3224	0.0601	-0.1828	-0.0772	0.1469	-0.0026	-0.0432	0.1573	-0.0477	0.1757	16.6159	-15.3476	12.2003
4	5.4644	0.0597	-1.6961	3.6135	0.7958	3.7258	-0.2229	0.2761	-0.7959	-0.1942	0.0519	0.1648	0.4147	-0.0636	0.1426	0.2719	-0.0223	-0.0329	0.1762	-0.0726	0.3445	21.0769	-30.8924	9.1879
5	1.1571	-0.2446	-0.2436	0.4775	0.1164	0.3238	0.0757	0.1652	-0.1453	-0.0977	-0.0392	-0.0022	0.0635	-0.0614	-0.0438	0.189	-0.0021	-0.0098	0.1873	-0.0261	0.162	29.9845	-13.0276	8.9946
6	1.1912	0.7994	-0.6868	5.9968	-4.7203	5.7002	-0.1314	0.0634	-0.115	0.0068	-0.0693	-0.4866	0.1207	0.3337	0.2324	0.18	0.0357	-0.0005	0.1698	-0.1102	0.2192	51.6829	-17.1912	16.0227
7	5.7922	0.9422	-1.338	5.5145	1.7933	3.5326	-0.0854	-0.1451	0.2117	0.1745	0.1239	-0.4215	-0.1174	0.2005	-0.0324	0.195	0.0128	-0.0309	0.1074	0.0473	0.1786	26.796	24.5977	20.5659
8	6.2324	-5.723	2.6781	6.62	-2.5573	3.0324	0.0137	0.1909	0.4149	-0.0473	-0.0653	-0.4999	-0.0823	0.4129	0.0136	0.1138	-0.0274	0.0261	0.2044	0.0089	0.2155	42.5325	5.0977	19.033
9	4.0704	-2.198	-5.7921	3.1123	2.9338	8.5419	0.0181	-0.796	-0.0355	-0.0435	0.1359	-0.1943	0.1056	0.7567	-0.0831	0.1707	-0.0087	-0.0733	0.1991	0.0091	0.1837	35.9385	4.8983	30.1964
10	5.0462	0.9017	1.3193	2.1201	0.649	0.9106	0.0535	0.0062	-0.1032	0.0158	-0.0209	0.0623	0.0002	-0.0348	-0.0397	0.1392	0.0108	0.034	0.1269	0.0169	0.0988	8.9361	-1.0462	27.1185
11	3.3617	0.8597	-0.7454	7.781	-0.6727	3.3054	0.0569	-0.2523	0.2997	0.3915	0.0432	0.6163	-0.1125	-0.1994	-0.1019	0.1357	0.0182	0.0648	0.2378	0.0087	0.2	-3.8467	7.7257	32.2156
12	0.6605	-0.0955	-0.0049	1.2697	-0.3782	0.4302	-0.0017	-0.0107	0.0679	0.1309	0.0236	0.044	-0.0712	-0.0486	-0.0309	0.1658	-0.0039	0.0056	0.1539	-0.0028	0.1364	14.1478	14.5515	23.9108

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 2 THROUGH 54 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 55 THROUGH 75 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 76 THROUGH 133 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 134 THROUGH 167 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 168 THROUGH 366 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 367 THROUGH 400 )
7	X-RAY DIFFRACTION	7	CHAIN 'B' AND (RESID 2 THROUGH 32 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 33 THROUGH 54 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 55 THROUGH 75 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 76 THROUGH 133 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 134 THROUGH 167 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 168 THROUGH 400 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi