PDB-5a11: The crystal structure of Ta-TFP, a thiocyanate-forming protein in...

ID or keywords:

Entry

Database: PDB / ID: 5a11

Title

The crystal structure of Ta-TFP, a thiocyanate-forming protein involved in glucosinolate breakdown (space group P21)

Components

THIOCYANATE FORMING PROTEIN

Keywords

IMMUNE SYSTEM / SPECIFIER PROTEIN / KELCH PROTEIN / FIELD-PENNY CRESS / FE(II) DEPENDENT

Function / homology

Function and homology information

N-(sulfonatooxy)prop-2-enimidothioate sulfolyase / glucosinolate metabolic process / nitrile biosynthetic process / enzyme regulator activity / lyase activity / protein homodimerization activity / identical protein binding / nucleus / metal ion binding / cytosol
Similarity search - Function

Biological species

THLASPI ARVENSE (plant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.47 Å

Authors

Krausze, J. / Gumz, F. / Wittstock, U.

Citation

Journal: Plant Mol.Biol. / Year: 2015
Title: The Crystal Structure of the Thiocyanate-Forming Protein from Thlaspi Arvense, a Kelch Protein Involved in Glucosinolate Breakdown.
Authors: Gumz, F. / Krausze, J. / Eisenschmidt, D. / Backenkohler, A. / Barleben, L. / Brandt, W. / Wittstock, U.

History

Deposition	Apr 27, 2015	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 26, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 30, 2015	Group: Database references
Revision 1.2	Jan 10, 2024	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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5a11.cif.gz	274 KB	Display	PDBx/mmCIF format
PDB format	pdb5a11.ent.gz	223.8 KB	Display	PDB format
PDBx/mmJSON format	5a11.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5a11_validation.pdf.gz	446.7 KB	Display	wwPDB validaton report
Full document	5a11_full_validation.pdf.gz	457.8 KB	Display
Data in XML	5a11_validation.xml.gz	25.3 KB	Display
Data in CIF	5a11_validation.cif.gz	34 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/a1/5a11 ftp://data.pdbj.org/pub/pdb/validation_reports/a1/5a11	HTTPS FTP

-
Related structure data

Related structure data	5a10SC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3wqo-d 6khk-d 4kal-d 3a3w-1 2ffi-d 4agt-d 6khm-11 6aqj-d 6d0v-d 6xrh-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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: THIOCYANATE FORMING PROTEIN

B: THIOCYANATE FORMING PROTEIN

hetero molecules

80.4 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)	48.367, 89.613, 83.842
Angle α, β, γ (deg.)	90.00, 101.08, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS oper: (Code: generate
Matrix: (-0.99998, 0.00667, 5.0E-5), (0.00626, 0.94176, -0.33622), (-0.00229, -0.33621, -0.94178)
Vector: 13.74419, 35.56956, 205.34927)

#1: Protein	THIOCYANATE FORMING PROTEIN Mass: 39750.363 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THLASPI ARVENSE (plant) / Plasmid: PGEX6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: G1FNI6
#2: Chemical	ChemComp-IOD / IODIDE ION Mass: 126.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: I
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.25 Å³/Da / Density % sol: 45 % / Description: NONE
Crystal grow	pH: 5.6 Details: 0.1 M SODIUM CITRATE PH 5.6, 20% (W/V) PEG 3350, 0.2 M KI

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 23, 2014 / Details: MIRRORS
Radiation	Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.918409 Å / Relative weight: 1
Reflection	Resolution: 2.47→45.03 Å / Num. obs: 24907 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / B_iso Wilson estimate: 24.55 Å² / R_merge(I) obs: 0.16 / Net I/σ(I): 6.94
Reflection shell	Resolution: 2.47→2.56 Å / Redundancy: 3.1 % / R_merge(I) obs: 0.58 / Mean I/σ(I) obs: 2.02 / % possible all: 97.5

-
Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5A10

5a10

Resolution: 2.47→45.031 Å / SU ML: 0.34 / σ(F): 1.37 / Phase error: 28.7 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2876	1246	5 %
R_work	0.2601	-	-
obs	0.2615	24904	98.48 %

Solvent computation

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

Displacement parameters

B_iso mean: 28.7 Å²

Refinement step

Cycle: LAST / Resolution: 2.47→45.031 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5411	0	7	30	5448

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	5565
X-RAY DIFFRACTION	f_angle_d	1.078	7554
X-RAY DIFFRACTION	f_dihedral_angle_d	13.503	1984
X-RAY DIFFRACTION	f_chiral_restr	0.042	778
X-RAY DIFFRACTION	f_plane_restr	0.006	995

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 (%)
2.4701-2.569	0.3221	136	0.2984	2587	X-RAY DIFFRACTION	98
2.569-2.6859	0.3153	140	0.3001	2652	X-RAY DIFFRACTION	99
2.6859-2.8274	0.2918	137	0.2812	2608	X-RAY DIFFRACTION	99
2.8274-3.0046	0.3374	140	0.2939	2650	X-RAY DIFFRACTION	99
3.0046-3.2365	0.3272	137	0.2904	2612	X-RAY DIFFRACTION	99
3.2365-3.5621	0.2696	137	0.262	2609	X-RAY DIFFRACTION	99
3.5621-4.0772	0.2538	139	0.2507	2638	X-RAY DIFFRACTION	98
4.0772-5.1357	0.2898	138	0.2143	2614	X-RAY DIFFRACTION	98
5.1357-45.0388	0.2527	142	0.2399	2688	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	0.0084	-0.0049	0.0215	0.0906	-0.1017	0.1671	0.0585	0.0024	-0.002	0.0063	0.0602	0.0185	0.1	0.0131	0.1787	0.0837	-0.0247	-0.0076	0.0785	-0.0386	0.3477	-7.3717	-28.0597	96.0878
2	0.1837	-0.0281	0.0347	0.0722	-0.0777	0.142	-0.1203	-0.0638	-0.0264	-0.1433	0.0983	-0.0738	-0.0219	-0.1394	0.0152	0.0702	-0.023	0.0108	0.0618	-0.0231	0.1569	-0.6485	-32.6401	85.0029
3	0.2948	0.0589	-0.1456	0.391	-0.0472	0.0781	-0.1579	-0.0884	0.0637	-0.1628	0.0562	-0.1836	0.0727	0.0077	-0.0753	0.1907	-0.08	0.0008	0.1553	-0.0253	0.1415	5.9429	-25.267	76.8977
4	0.0261	0.0396	0.0342	0.0989	-0.0496	0.3258	-0.0183	0.0159	-0.0269	-0.0364	-0.1206	0.0191	0.0247	-0.0387	-0.1773	0.2017	-0.086	-0.1032	0.1509	-0.0165	0.0991	3.9725	-14.9354	80.2139
5	0.0362	0.0142	-0.0205	0.2016	-0.0814	0.0365	-0.0113	-0.0069	-0.0256	-0.1319	0.0035	0.0927	0.076	-0.0798	-0.0844	0.0534	-0.0769	-0.0552	0.1198	-0.1365	0.1459	11.9333	-15.21	77.9795
6	0.0338	-0.0378	0.0011	0.0998	-0.0007	0.0501	0.0685	-0.0044	-0.0145	-0.1662	0.0982	-0.0278	-0.0967	-0.1083	0.3675	0.1287	-0.0021	-0.0154	-0.2172	0.2042	0.0885	9.2969	-6.4577	89.6496
7	0.1478	0.1476	-0.047	0.1595	-0.0807	0.0551	-0.0308	0.0835	-0.0572	-0.0975	0.0733	-0.0132	0.0898	-0.0658	0.0404	0.0519	0.0037	0.0001	0.0875	0.0114	0.0534	-1.9277	-16.831	99.0787
8	0.0144	0.0123	0.0488	0.0137	0.0362	0.1439	-0.0298	0.0236	0.0833	0.1047	0.0751	-0.1343	0.078	0.0276	0.0233	0.1337	0.0795	0.0031	0.1783	0.0162	0.137	20.9943	-23.2102	124.224
9	0.0009	0.0027	-0.0051	0.0294	-0.0335	0.0409	-0.0401	-0.0319	-0.145	0.008	-0.0621	0.0741	0.001	-0.0114	-0.1767	0.2003	-0.2159	0.1028	-0.0338	0.0785	0.0945	12.0034	-23.0418	133.7926
10	0.2068	-0.0141	0.0093	0.1395	-0.1006	0.2019	-0.1401	-0.0423	-0.1339	-0.1621	0.1254	0.1416	0.0218	-0.0689	-0.011	0.1944	-0.0494	-0.0288	0.1639	0.0468	0.174	11.8674	-20.4313	138.4732
11	0.0079	-0.0004	0.0321	0.119	0.0563	0.2122	0.1458	-0.2004	0	0.1281	-0.1306	-0.0387	-0.0271	-0.0709	0.0402	0.1157	-0.0156	0.086	0.1387	0.1014	0.0366	9.3914	-11.2511	142.1321
12	0.0424	-0.1175	0.087	0.302	-0.2228	0.1578	0.1525	0.07	-0.101	-0.0328	0.0395	0.1653	-0.0631	-0.0602	0.1127	0.1527	0.0378	0.0247	0.2585	-0.0522	0.1975	2.9534	-5.0947	136.2718
13	0.0008	-0.0059	0.0027	0.1814	-0.1466	0.1185	0.0293	-0.0131	0.0676	-0.0235	0.1421	0.1676	-0.1879	0.055	0.0265	0.134	0.011	0.0241	0.1528	-0.0232	0.1928	7.7873	-1.1075	125.4566
14	0.2437	-0.2236	0.033	0.2205	-0.0804	0.2478	0.1143	0.0841	-0.0209	-0.0233	0.074	0.1017	-0.0598	0.0246	0.6217	0.1522	0.0344	0.0751	0.0828	-0.0211	0.1262	1.6143	-0.1251	120.9077
15	0.1926	0.0101	-0.1383	0.3199	-0.071	0.1063	0.002	-0.1725	0.0216	0.0997	0.0669	0.0958	-0.0182	0.0742	0.0757	0.0733	0.0096	-0.01	0.1042	0.004	0.0755	13.2231	-11.129	115.2581
16	0.1094	-0.1118	-0.025	0.3713	0.0891	0.1943	-0.0141	-0.0305	0.0184	-0.0538	-0.0183	-0.1006	0.1504	-0.1396	-0.113	0.1091	0.0057	0.0012	0.1073	0.0116	0.0316	20.1828	-18.5062	122.596

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 4 THROUGH 26 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 27 THROUGH 79 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 80 THROUGH 131 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 132 THROUGH 148 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 149 THROUGH 173 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 174 THROUGH 236 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 237 THROUGH 348 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 4 THROUGH 26 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 27 THROUGH 52 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 53 THROUGH 102 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 103 THROUGH 138 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 139 THROUGH 173 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 174 THROUGH 203 )
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESID 204 THROUGH 236 )
15	X-RAY DIFFRACTION	15	CHAIN 'B' AND (RESID 237 THROUGH 310 )
16	X-RAY DIFFRACTION	16	CHAIN 'B' AND (RESID 311 THROUGH 348 )

-
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://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