PDB-5m86: Crystal Structure of the Thermoplasma acidophilum Protein Ta1207

ID or keywords:

Entry

Database: PDB / ID: 5m86

Title

Crystal Structure of the Thermoplasma acidophilum Protein Ta1207

Components

Ta1207

Keywords

UNKNOWN FUNCTION / pentamer

Function / homology

Ta1207 family / Ta1207 family / Uncharacterized protein

Function and homology information

Biological species

Thermoplasma acidophilum DSM 1728 (acidophilic)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.4 Å

Authors

Pathare, G.R. / Nagy, I. / Bracher, A.

Citation

Journal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Crystal structure of the Thermoplasma acidophilum protein Ta1207.
Authors: Pathare, G.R. / Nagy, I. / Hubert, A. / Thomas, D.R. / Bracher, A.

History

Deposition	Oct 28, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 14, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jun 21, 2017	Group: Database references / Structure summary / Category: citation / entity Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _entity.pdbx_description

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5m86.cif.gz	1.8 MB	Display	PDBx/mmCIF format
PDB format	pdb5m86.ent.gz	1.6 MB	Display	PDB format
PDBx/mmJSON format	5m86.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5m86_validation.pdf.gz	524.8 KB	Display	wwPDB validaton report
Full document	5m86_full_validation.pdf.gz	544.2 KB	Display
Data in XML	5m86_validation.xml.gz	112.7 KB	Display
Data in CIF	5m86_validation.cif.gz	155.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/m8/5m86 ftp://data.pdbj.org/pub/pdb/validation_reports/m8/5m86	HTTPS FTP

-
Related structure data

Similar structure data	4fd3-d 5kdx-d 6k5p-d 30022 6t9h-1 5g1u-d 1022 5fvb-1 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 - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Ta1207

B: Ta1207

C: Ta1207

D: Ta1207

E: Ta1207

F: Ta1207

G: Ta1207

H: Ta1207

I: Ta1207

J: Ta1207

hetero molecules

396 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Ta1207

B: Ta1207

C: Ta1207

D: Ta1207

F: Ta1207

hetero molecules

defined by author&software
198 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: Ta1207

G: Ta1207

H: Ta1207

I: Ta1207

J: Ta1207

hetero molecules

defined by author&software
198 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	228.639, 112.821, 221.328
Angle α, β, γ (deg.)	90.000, 118.700, 90.000
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	chain A
2	1	chain B
3	1	chain C
4	1	chain D
5	1	chain E
6	1	chain F
7	1	chain G
8	1	chain H
9	1	chain I
10	1	chain J

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details	Auth asym-ID	Auth seq-ID
1	1	1	chain A	A	5 - 501
2	1	1	chain B	B	5 - 501
3	1	1	chain C	C	5 - 501
4	1	1	chain D	D	5 - 501
5	1	1	chain E	E	5 - 501
6	1	1	chain F	F	5 - 501
7	1	1	chain G	G	5 - 501
8	1	1	chain H	H	5 - 501
9	1	1	chain I	I	5 - 501
10	1	1	chain J	J	5 - 501

#1: Protein	Ta1207 Mass: 39401.246 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoplasma acidophilum DSM 1728 (acidophilic) Gene: Ta1207 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HIW9
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 753 / 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: 3.18 Å³/Da / Density % sol: 61.29 % / Mosaicity: 0.08 °
Crystal grow	Temperature: 291 K / Method: vapor diffusion / pH: 6 Details: 50 mM MES pH 6.0, 200 mM Ca-diacetate and 20%(w/v) PEG3350

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID29 / Wavelength: 0.97901,0.97916,0.97670

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2014

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9767	1
2	0.97901	1
3	0.97916	1
4	0.9767	1

Reflection

Resolution: 2.39→49.17 Å / Num. obs: 191535 / % possible obs: 98.7 % / Redundancy: 3.5 % / B_iso Wilson estimate: 46.17 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.077 / R_pim(I) all: 0.048 / R_rim(I) all: 0.09 / Net I/σ(I): 13.6 / Num. measured all: 663454

Reflection shell

Resolution: 2.39→2.43 Å / Redundancy: 3.2 % / R_merge(I) obs: 0.703 / Mean I/σ(I) obs: 2.1 / Num. unique all: 8492 / CC_1/2: 0.621 / % possible all: 88.4

-
Phasing

Phasing

Method:

MAD

Phasing dm

FOM : 0.85 / FOM acentric: 0.85 / FOM centric: 0.77 / Reflection: 81633 / Reflection acentric: 78313 / Reflection centric: 4283

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
8-49.165	0.97	0.98	0.93	5356	4827	529
5-8	0.94	0.95	0.9	16304	15462	842
4-5	0.93	0.93	0.87	20349	19562	787
3.5-4	0.85	0.85	0.79	20505	19867	638
3-3.5	0.69	0.69	0.65	36438	35478	960
2.8-3	0.48	0.48	0.46	22492	21965	527

-
Processing

Software

Name	Version	Classification
Aimless	0.1.27	data scaling
RESOLVE	2.13	phasing
PHENIX		refinement
PDB_EXTRACT	3.2	data extraction
XSCALE		data scaling
SHELXD		phasing
XDS		data reduction

Refinement

Method to determine structure:

MAD / Resolution: 2.4→29.658 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 20.79

	R_factor	Num. reflection	% reflection
R_free	0.2026	9569	5.02 %
R_work	0.1765	-	-
obs	0.1778	190646	98.99 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 240.53 Å² / B_iso mean: 62.5588 Å² / B_iso min: 25.48 Å²

Refinement step

Cycle: final / Resolution: 2.4→29.658 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	26350	0	160	753	27263
B_iso mean	-	-	87.18	53.85	-
Num. residues	-	-	-	-	3210

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	27098
X-RAY DIFFRACTION	f_angle_d	0.915	36570
X-RAY DIFFRACTION	f_chiral_restr	0.034	3980
X-RAY DIFFRACTION	f_plane_restr	0.005	4630
X-RAY DIFFRACTION	f_dihedral_angle_d	12.462	9970

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	19833	X-RAY DIFFRACTION	9.032	TORSIONAL
1	2	B	19833	X-RAY DIFFRACTION	9.032	TORSIONAL
1	3	C	19833	X-RAY DIFFRACTION	9.032	TORSIONAL
1	4	D	19833	X-RAY DIFFRACTION	9.032	TORSIONAL
1	5	E	19833	X-RAY DIFFRACTION	9.032	TORSIONAL
1	6	F	19833	X-RAY DIFFRACTION	9.032	TORSIONAL
1	7	G	19833	X-RAY DIFFRACTION	9.032	TORSIONAL
1	8	H	19833	X-RAY DIFFRACTION	9.032	TORSIONAL
1	9	I	19833	X-RAY DIFFRACTION	9.032	TORSIONAL
1	10	J	19833	X-RAY DIFFRACTION	9.032	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.3999-2.4272	0.301	333	0.2816	5885	6218	98
2.4272-2.4557	0.3127	322	0.2656	6066	6388	99
2.4557-2.4857	0.2821	280	0.259	5998	6278	99
2.4857-2.5171	0.2839	330	0.2544	6014	6344	99
2.5171-2.5502	0.2926	309	0.2532	6069	6378	99
2.5502-2.5851	0.2949	323	0.2504	5949	6272	99
2.5851-2.6221	0.2518	341	0.2405	6027	6368	99
2.6221-2.6612	0.2687	317	0.2362	6041	6358	99
2.6612-2.7027	0.2763	316	0.2337	6008	6324	99
2.7027-2.747	0.2437	339	0.2248	5991	6330	99
2.747-2.7943	0.2787	344	0.2268	6008	6352	99
2.7943-2.8451	0.2315	325	0.2185	6059	6384	99
2.8451-2.8998	0.2563	292	0.2137	6066	6358	99
2.8998-2.9589	0.2355	296	0.2132	5913	6209	98
2.9589-3.0232	0.2431	303	0.2186	6071	6374	99
3.0232-3.0935	0.2305	302	0.2124	6058	6360	99
3.0935-3.1707	0.2253	317	0.204	6058	6375	99
3.1707-3.2564	0.2518	342	0.2089	5997	6339	99
3.2564-3.3521	0.2231	318	0.1948	6061	6379	99
3.3521-3.4601	0.2101	374	0.1892	5996	6370	99
3.4601-3.5836	0.2182	323	0.1835	6041	6364	99
3.5836-3.7268	0.2049	323	0.1798	6048	6371	99
3.7268-3.896	0.1879	279	0.1676	6051	6330	98
3.896-4.101	0.1685	296	0.1465	6079	6375	99
4.101-4.3571	0.1634	330	0.1359	6066	6396	99
4.3571-4.6924	0.1503	320	0.1218	6092	6412	99
4.6924-5.1623	0.1384	343	0.1189	6036	6379	99
5.1623-5.9042	0.1749	299	0.1439	6053	6352	98
5.9042-7.4194	0.1926	321	0.1618	6125	6446	99
7.4194-29.6605	0.1503	312	0.1432	6151	6463	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	1.2569	-0.0907	-0.2617	2.2088	0.1341	1.0779	0.0071	-0.2697	-0.06	0.1989	-0.0605	-0.1581	0.1239	0.1199	0.0349	0.3569	0.0042	0.0361	0.6412	0.0725	0.2479	-22.5789	72.7366	90.57
2	1.5985	0.1815	-0.4821	2.0744	-0.8451	1.8267	0.0853	-0.382	0.1291	0.3256	0.0304	0.008	-0.3011	0.1274	-0.0817	0.4356	-0.0599	0.0676	0.6229	-0.0977	0.2818	-23.6289	115.0459	88.5738
3	1.3507	-0.387	-1.026	1.5461	0.3963	2.7262	0.0812	-0.2939	0.1888	0.098	0.0927	-0.1424	-0.368	0.4611	-0.1126	0.3976	-0.1208	0.0706	0.4461	-0.0605	0.3008	0.0617	127.131	55.5698
4	0.8237	0.2847	-0.2524	2.3447	-0.2478	1.6234	0.0235	-0.1868	-0.0406	0.2992	-0.0557	-0.0788	-0.0197	0.4024	0.0518	0.2088	0.0111	-0.0045	0.5708	0.0069	0.2566	15.9116	92.4745	37.1095
5	1.8191	-0.0528	-0.2659	1.5629	-0.2605	1.453	-0.0633	0.129	-0.146	-0.1818	-0.011	0.1144	0.2313	-0.1309	0.0479	0.4673	-0.0753	0.0456	0.4602	-0.0975	0.332	-44.0539	55.177	25.5123
6	1.9507	0.3708	-0.8314	1.1884	0.0559	2.0683	-0.0428	-0.2411	-0.1541	0.1577	-0.0274	-0.0989	0.1596	0.2525	0.0335	0.3801	0.1194	0.0484	0.4408	0.0764	0.3221	2.287	58.6915	58.9308
7	1.5063	-0.2352	-0.5575	2.5588	-0.0034	1.2984	-0.0902	0.2938	0.0037	-0.0161	-0.0015	0.22	0.115	-0.2836	0.0723	0.3394	-0.0546	-0.0683	0.5766	-0.0119	0.166	-30.3031	88.7239	3.4494
8	1.589	0.0032	-0.7506	1.2998	0.3592	2.0522	0.0703	0.2897	0.3238	-0.1215	0.034	0.1746	-0.3017	-0.3698	-0.0512	0.4376	0.1199	-0.0496	0.459	0.0868	0.4274	-46.0479	123.6142	21.5525
9	0.8178	0.4907	-0.2311	2.5848	-0.4885	1.3098	0.0613	-0.0033	0.1404	0.0633	-0.0054	0.3752	-0.1777	-0.27	-0.0374	0.3075	0.1377	0.0288	0.5946	-0.0388	0.4255	-69.776	111.8436	54.803
10	1.099	-0.3523	-0.1271	1.334	0.2794	1.6133	-0.1094	0.0155	-0.0761	0.0083	0.1043	0.0601	0.168	-0.2991	0.0127	0.3187	-0.1161	0.0428	0.6289	-0.002	0.2908	-68.4751	69.4409	56.9854

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 325 )	A	5 - 325
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 5 through 325 )	B	5 - 325
3	X-RAY DIFFRACTION	3	chain 'C' and (resid 5 through 325 )	C	5 - 325
4	X-RAY DIFFRACTION	4	chain 'D' and (resid 5 through 325 )	D	5 - 325
5	X-RAY DIFFRACTION	5	chain 'E' and (resid 5 through 325 )	E	5 - 325
6	X-RAY DIFFRACTION	6	chain 'F' and (resid 5 through 325 )	F	5 - 325
7	X-RAY DIFFRACTION	7	chain 'G' and (resid 5 through 325 )	G	5 - 325
8	X-RAY DIFFRACTION	8	chain 'H' and (resid 5 through 325 )	H	5 - 325
9	X-RAY DIFFRACTION	9	chain 'I' and (resid 5 through 325 )	I	5 - 325
10	X-RAY DIFFRACTION	10	chain 'J' and (resid 5 through 325 )	J	5 - 325

-
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

-
Phasing

-
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

-Phasing

-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

-
Phasing

-
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