PDB-5o70: Structure of the inactive T.maritima PDE (TM1595) D80N D154N muta...

ID or keywords:

Entry

Database: PDB / ID: 5o70

Title

Structure of the inactive T.maritima PDE (TM1595) D80N D154N mutant with reaction products 2 AMP

Components

phosphodiesterase

Keywords

HYDROLASE / phosphodiesterase

Function / homology

Function and homology information

nucleic acid binding / nucleotide binding / metal ion binding
Similarity search - Function

Biological species

Thermotoga maritima (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.55 Å

Authors

Witte, G. / Drexler, D.

Funding support

Germany, 2items

Citation

Journal: Structure / Year: 2017
Title: Structural and Biophysical Analysis of the Soluble DHH/DHHA1-Type Phosphodiesterase TM1595 from Thermotoga maritima.
Authors: Drexler, D.J. / Muller, M. / Rojas-Cordova, C.A. / Bandera, A.M. / Witte, G.

History

Deposition	Jun 7, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 25, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2017	Group: Database references / Category: citation / citation_author Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed ..._citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2	Dec 6, 2017	Group: Database references / Category: pdbx_database_related
Revision 1.3	Dec 13, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4	Jan 17, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5o70.cif.gz	157.1 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5o70_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	5o70_full_validation.pdf.gz	1.1 MB	Display
Data in XML	5o70_validation.xml.gz	17.8 KB	Display
Data in CIF	5o70_validation.cif.gz	26.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o7/5o70 ftp://data.pdbj.org/pub/pdb/validation_reports/o7/5o70	HTTPS FTP

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Related structure data

Related structure data	5o1uC 5o25C 5o4zSC 5o58C 5o7fC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5o4z-1 6asu-d 2gq3-2 1d8c-d 5dx7-d 4bga-1 6c7b-d 5jhh-2 3t06-1 3ht3-1 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #24 - Dec 2001 Glycogen Phosphorylase similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1)

Deposited unit

A: phosphodiesterase

hetero molecules

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

1

A: phosphodiesterase

hetero molecules

A: phosphodiesterase

hetero molecules

defined by software
Evidence: light scattering, SECMALS clearly shows the dimer molecular weight. No detectable monomers, SAXS, SAXS curve is only compatible with the dimeric assembly
79.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	71.410, 87.590, 121.870
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-634- HOH
2	1	A-674- HOH
3	1	A-754- HOH
4	1	A-786- HOH
5	1	A-789- HOH

#1: Protein	phosphodiesterase Mass: 37868.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria) Gene: TM_1595 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1T1
#2: Chemical	ChemComp-AMP / ADENOSINE MONOPHOSPHATE Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₇P / Comment: AMP*YM
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.52 Å³/Da / Density % sol: 51.12 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.2M ammonium sulfate, 0.1M sodium citrate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.1999 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 1, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.1999 Å / Relative weight: 1
Reflection	Resolution: 1.55→50 Å / Num. obs: 106665 / % possible obs: 99.5 % / Redundancy: 6.6 % / CC_1/2: 1 / R_rim(I) all: 0.045 / Net I/σ(I): 19.74
Reflection shell	Resolution: 1.55→1.59 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 1.67 / Num. unique obs: 7778 / CC_1/2: 0.76 / R_rim(I) all: 1.21 / % possible all: 98.3

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Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5O4Z

5o4z

Resolution: 1.55→41.215 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.26 / Phase error: 25.95 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1945	5191	4.87 %
R_work	0.1677	-	-
obs	0.169	106661	99.47 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.55→41.215 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2568	0	108	295	2971

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	2810
X-RAY DIFFRACTION	f_angle_d	0.849	3834
X-RAY DIFFRACTION	f_dihedral_angle_d	7.169	2253
X-RAY DIFFRACTION	f_chiral_restr	0.055	415
X-RAY DIFFRACTION	f_plane_restr	0.005	486

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 (%)
1.55-1.5676	0.3504	155	0.3704	3375	X-RAY DIFFRACTION	97
1.5676-1.586	0.3357	152	0.3308	3346	X-RAY DIFFRACTION	99
1.586-1.6054	0.3617	181	0.3188	3379	X-RAY DIFFRACTION	100
1.6054-1.6257	0.3694	182	0.3142	3346	X-RAY DIFFRACTION	99
1.6257-1.6471	0.3196	156	0.3088	3388	X-RAY DIFFRACTION	99
1.6471-1.6696	0.3443	134	0.2981	3398	X-RAY DIFFRACTION	99
1.6696-1.6935	0.3564	177	0.282	3351	X-RAY DIFFRACTION	99
1.6935-1.7188	0.2803	176	0.2649	3414	X-RAY DIFFRACTION	100
1.7188-1.7456	0.2857	170	0.2526	3385	X-RAY DIFFRACTION	99
1.7456-1.7742	0.2267	165	0.2427	3369	X-RAY DIFFRACTION	100
1.7742-1.8048	0.2568	174	0.2199	3364	X-RAY DIFFRACTION	99
1.8048-1.8377	0.2632	180	0.2174	3419	X-RAY DIFFRACTION	100
1.8377-1.873	0.2358	194	0.2048	3351	X-RAY DIFFRACTION	99
1.873-1.9112	0.2072	181	0.2012	3357	X-RAY DIFFRACTION	99
1.9112-1.9528	0.2262	200	0.1829	3395	X-RAY DIFFRACTION	99
1.9528-1.9982	0.2117	149	0.1789	3375	X-RAY DIFFRACTION	100
1.9982-2.0482	0.2288	164	0.1742	3374	X-RAY DIFFRACTION	100
2.0482-2.1036	0.2245	185	0.1651	3416	X-RAY DIFFRACTION	100
2.1036-2.1655	0.1832	185	0.1614	3386	X-RAY DIFFRACTION	100
2.1655-2.2353	0.1675	173	0.1608	3381	X-RAY DIFFRACTION	100
2.2353-2.3152	0.2191	141	0.1705	3413	X-RAY DIFFRACTION	100
2.3152-2.4079	0.1766	177	0.1673	3388	X-RAY DIFFRACTION	100
2.4079-2.5175	0.2184	194	0.1731	3376	X-RAY DIFFRACTION	100
2.5175-2.6502	0.2307	175	0.181	3390	X-RAY DIFFRACTION	100
2.6502-2.8162	0.2088	159	0.1767	3426	X-RAY DIFFRACTION	100
2.8162-3.0336	0.1935	169	0.1697	3343	X-RAY DIFFRACTION	100
3.0336-3.3387	0.1787	179	0.1617	3425	X-RAY DIFFRACTION	100
3.3387-3.8216	0.187	178	0.1342	3391	X-RAY DIFFRACTION	100
3.8216-4.8136	0.1161	186	0.1114	3385	X-RAY DIFFRACTION	100
4.8136-41.2291	0.1806	200	0.1516	3364	X-RAY DIFFRACTION	100

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	2.508	0.2746	-0.7012	5.3314	-1.2319	3.8136	0.2127	-0.1729	-0.091	0.4267	-0.2376	-0.115	0.0524	-0.0156	0.0433	0.2116	-0.0723	-0.0132	0.2403	0.0005	0.2322	-12.6915	-22.8578	-9.135
2	2.2575	0.5185	-0.5744	5.7737	-1.4577	3.5006	0.1875	0.2102	0.1497	0.2455	0.0044	0.4224	-0.3333	-0.4194	-0.1969	0.1961	0.0133	0.0305	0.2868	-0.0022	0.2612	-18.7745	-13.4875	-15.7198
3	1.554	0.53	-0.6286	1.4791	-0.1171	3.3067	0.1353	-0.1693	-0.0123	0.1892	-0.1079	0.0164	-0.0023	-0.009	-0.0247	0.2184	-0.0469	-0.0223	0.234	0.0042	0.2597	-7.5717	-20.082	-12.4313
4	1.2904	0.8197	0.8462	3.0717	0.5554	1.6714	-0.1568	-0.0138	0.1864	-0.2451	0.073	0.3982	-0.2185	-0.1966	0.0751	0.2158	0.0446	0.0063	0.2722	0.0169	0.2226	-7.81	-1.6457	-27.6958
5	2.5488	-0.4505	0.2553	3.3187	0.437	2.9559	-0.0998	-0.0893	0.0845	0.1428	0.0412	0.1301	-0.2432	-0.0853	0.0804	0.2725	-0.0063	-0.0006	0.217	-0.0331	0.2099	3.209	5.0553	-17.574
6	2.9265	-1.1005	-0.7308	5.571	1.9303	4.5885	-0.0995	-0.0649	-0.1322	0.6184	0.1036	-0.0753	0.3445	0.1721	-0.0481	0.2949	-0.0335	-0.032	0.2147	-0.0007	0.2102	9.7036	-4.2364	-9.7985
7	7.8407	-1.6181	-1.3621	9.4774	1.3867	9.2365	-0.1642	-0.3531	-0.131	0.7678	0.2486	-0.7592	0.4754	0.6145	-0.0961	0.3701	-0.1097	-0.0965	0.2991	0.0174	0.336	16.645	3.1281	-9.629

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -2 through 39 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 40 through 64 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 65 through 176 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 177 through 205 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 206 through 268 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 269 through 298 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 299 through 320 )

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