PDB-5a5y: Crystal structure of AtTTM3 in complex with tripolyphosphate and ...

ID or keywords:

Entry

Database: PDB / ID: 5a5y

Title

Crystal structure of AtTTM3 in complex with tripolyphosphate and magnesium ion (form A)

Components

TRIPHOSPHATE TUNEL METALLOENZYME 3

Keywords

HYDROLASE / INORGANIC POLYPHOSPHATE / TRIPOLYPHOSPHATE / TRIPHOSPHATE TUNNEL METALLOENZYME

Function / homology

Function and homology information

triphosphatase / inorganic triphosphate phosphatase activity / root development / anaphase-promoting complex / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / ATP hydrolysis activity / ATP binding / nucleus / cytoplasm
Similarity search - Function

Biological species

ARABIDOPSIS THALIANA (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SIRAS / Resolution: 1.92 Å

Authors

Martinez, J. / Truffault, V. / Hothorn, M.

Citation

Journal: J.Biol.Chem. / Year: 2015
Title: Structural Determinants for Substrate Binding and Catalysis in Triphosphate Tunnel Metalloenzymes.
Authors: Martinez, J. / Truffault, V. / Hothorn, M.

History

Deposition	Jun 23, 2015	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 5, 2015	Provider: repository / Type: Initial release
Revision 1.1	Aug 12, 2015	Group: Database references
Revision 1.2	Oct 7, 2015	Group: Database references
Revision 1.3	Aug 23, 2017	Group: Data collection / Refinement description / Category: diffrn_detector / software / Item: _diffrn_detector.type / _software.name
Revision 1.4	May 8, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_sheet / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 700

SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5a5y.cif.gz	199.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5a5y.ent.gz	162.8 KB	Display	PDB format
PDBx/mmJSON format	5a5y.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5a5y_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	5a5y_full_validation.pdf.gz	1.1 MB	Display
Data in XML	5a5y_validation.xml.gz	19.7 KB	Display
Data in CIF	5a5y_validation.cif.gz	28.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/a5/5a5y ftp://data.pdbj.org/pub/pdb/validation_reports/a5/5a5y	HTTPS FTP

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Related structure data

Related structure data	5a60C 5a61C 5a64C 5a65C 5a66C 5a67C 5a68C C: citing same article (ref.)
Similar structure data	3bde-1 6mli-d 2pzf-2 1iuj-d 3zzy-d 1r6y-1 5zz4-6 5jrs-2 1j6t-d 6mla-d 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 - 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	#58 - Oct 2004 G Proteins similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #145 - Jan 2012 Messenger RNA Capping similarity (1)

Deposited unit

A: TRIPHOSPHATE TUNEL METALLOENZYME 3

B: TRIPHOSPHATE TUNEL METALLOENZYME 3

hetero molecules

50 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: TRIPHOSPHATE TUNEL METALLOENZYME 3

hetero molecules

defined by author&software
25 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: TRIPHOSPHATE TUNEL METALLOENZYME 3

hetero molecules

defined by author&software
24.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	136.334, 136.334, 144.202
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	97
Space group name H-M	I422

#1: Protein	TRIPHOSPHATE TUNEL METALLOENZYME 3 / ADENOSINETRIPHOSPHATASE / ATPASE / TRIPHOSPHATASE / PPPASE / INORGANIC TRIPHOSPHATASE Mass: 24323.764 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Strain: COL0 / Plasmid: PETM11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q9SIY3, EC: 3.6.1.3, triphosphatase
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-3PO / TRIPHOSPHATE Mass: 257.955 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H₅O₁₀P₃
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 238 / 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: 3.44 Å³/Da / Density % sol: 64.28 % / Description: NONE
Crystal grow	pH: 5 / Details: 2.2 M NACL, 0.1 M CITRIC ACID/NAOH PH 5.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99998
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99998 Å / Relative weight: 1
Reflection	Resolution: 1.92→45.33 Å / Num. obs: 49737 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 10.59 % / R_merge(I) obs: 0.08 / Net I/σ(I): 20.06
Reflection shell	Resolution: 1.92→2.04 Å / Redundancy: 8.35 % / R_merge(I) obs: 1.21 / Mean I/σ(I) obs: 2.18 / % possible all: 90.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0123	refinement
XDS		data reduction
XDS		data scaling
SHELXD		phasing
SHARP		phasing
RESOLVE		phasing

Refinement

Method to determine structure:

SIRAS
Starting model: NONE

Resolution: 1.92→45.37 Å / Cor.coef. F_o:F_c: 0.973 / Cor.coef. F_o:F_c free: 0.958 / SU B: 6.344 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19827	4713	9.3 %	RANDOM
R_work	0.15314	-	-	-
obs	0.15734	46150	98.46 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 39.118 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.35 Å²	0 Å²	0 Å²
2-	-	0.35 Å²	0 Å²
3-	-	-	-0.71 Å²

Refinement step

Cycle: LAST / Resolution: 1.92→45.37 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3404	0	76	238	3718

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.019	3589
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.268	1.989	4836
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.933	5	436
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.771	23.295	173
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.919	15	656
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.897	15	35
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	530
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	2667
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.873	3.329	1702
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.569	4.993	2128
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	3.179	3.902	1887
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr	0.988	3	3589
X-RAY DIFFRACTION	r_sphericity_free	29.515	5	106
X-RAY DIFFRACTION	r_sphericity_bonded	18.709	5	3663

LS refinement shell

Resolution: 1.923→1.973 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.325	280	-
R_work	0.277	2746	-
obs	-	-	80.05 %

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	0.0852	-0.0309	-0.0447	0.0173	0.0461	0.1739	-0.0032	0.001	-0.0012	0.0006	-0.0017	0.0025	0.0039	-0.006	0.0049	0.0083	-0.0009	-0.0003	0.0053	0.0009	0.0394	40.1324	50.4498	18.5941
2	0.335	0.0534	-0.041	0.0095	-0.0004	0.0604	-0.0117	0.0296	0.0097	-0.0003	0.0063	0.0027	0.0107	-0.0016	0.0053	0.0051	-0.0009	-0.0004	0.0069	0.0023	0.0432	54.9589	41.3708	18.0663
3	0.5363	-0.1264	-0.6149	0.9756	-0.4652	1.1733	-0.0285	0.0009	-0.0373	0.0162	0.0235	0.019	0.0397	-0.0284	0.005	0.0052	-0.0033	-0.0013	0.0044	0.0005	0.0371	47.6352	31.7258	35.1937
4	0.2694	-0.1436	0.233	0.0909	-0.0766	0.44	0.0011	0.0309	-0.0023	0.0023	-0.0103	-0.0044	-0.0062	0.0271	0.0091	0.006	0.0003	0.0002	0.0115	-0.0032	0.0406	50.4946	40.9012	9.5008
5	1.1106	-1.1232	2.6163	1.4192	-2.9047	7.1711	0.0146	-0.0035	-0.0407	-0.0407	0.0155	0.0296	0.1345	-0.0531	-0.0301	0.0107	-0.004	0.002	0.0025	-0.0063	0.0316	54.4333	30.7138	15.3
6	0.1844	0.0271	-0.1617	0.0688	-0.1215	0.2896	-0.0105	0.0118	-0.009	-0.0094	0.0008	-0.003	0.0227	-0.0077	0.0097	0.0046	0.0003	-0.0016	0.006	-0.0021	0.0393	64.4499	30.791	17.2018
7	0.4581	-0.1013	-0.0858	0.0236	0.0186	0.0165	-0.0021	0.0308	-0.0143	0.0024	-0.0039	0.0031	0.0007	-0.0073	0.006	0.0058	-0.0007	-0.0004	0.0109	-0.0003	0.0401	58.2391	40.1484	17.1015
8	1.277	0.6747	0.3428	0.4435	0.2256	0.2249	0.0074	-0.0097	0.0027	0.0079	-0.0078	-0.0012	0.0054	0.0012	0.0004	0.006	0.0001	0.0001	0.0029	0.0023	0.0355	43.6879	48.5481	20.4667
9	0.3133	-0.4667	-0.3171	0.8544	0.4405	0.3286	0.0048	0.0234	-0.006	-0.0194	-0.0096	0.0119	-0.0018	-0.032	0.0048	0.0027	-0.0035	-0.0026	0.014	0.0007	0.0412	32.8345	47.6994	11.0547
10	0.4084	-0.0207	-0.0723	0.123	-0.0136	0.0466	-0.0036	0.0025	-0.0033	-0.0049	-0.0037	-0.0054	-0.0149	0.0086	0.0073	0.009	-0.0031	-0.0011	0.0067	0.0013	0.0383	49.5568	54.5758	14.8155
11	1.8824	-1.3375	-1.2362	2.0972	0.9591	0.8182	0.02	0.0334	-0.0085	0.0171	-0.0311	0.0362	-0.0085	-0.0202	0.0111	0.0067	0.0027	-0.0096	0.0092	0.004	0.0302	37.1862	54.8539	53.204
12	0.0039	-0.0088	0.0108	0.113	-0.012	0.0338	0.0023	-0.0004	0.0033	-0.0024	-0.0031	-0.0037	0.0062	-0.0019	0.0007	0.0039	-0.0006	0.0016	0.0052	-0.0002	0.0416	39.601	54.3757	39.834
13	0.1085	0.0549	0.1291	0.0891	0.1159	0.3041	0.0054	-0.0021	0.0106	0.0064	-0.0093	0.006	0.001	-0.0199	0.0039	0.004	-0.0017	-0.0001	0.0036	0.0002	0.0407	34.7258	68.3493	43.6365
14	0.6991	-0.8773	-0.0669	2.2079	-0.1568	0.0606	-0.0167	0.0236	-0.0026	0.133	0.0026	-0.0092	-0.0219	-0.0061	0.0141	0.0153	-0.0029	0.0021	0.0098	0.0049	0.0406	37.9843	58.9078	58.7279
15	1.1894	-0.2669	1.5721	1.9948	-3.0468	6.5653	0.0354	-0.0231	-0.0344	0.0093	0.1093	0.1228	-0.0054	-0.2076	-0.1447	0.0038	0	0.0044	0.0088	-0.0021	0.0417	27.1272	70.8649	45.2085
16	0.2196	0.0514	0.1777	0.0936	-0.018	0.3086	0.001	-0.0148	0.0205	0.009	0.0029	0.0143	-0.0164	-0.0164	-0.0039	0.0054	0.0002	0.0028	0.0017	-0.0012	0.0426	32.2045	78.7178	45.9419
17	0.0205	0.0212	0.0043	0.1774	0.0258	0.0054	0.0049	0.0023	0.0011	0.0133	-0.0019	-0.0003	0.0029	-0.0032	-0.003	0.0061	-0.0014	-0.0004	0.0071	0.0005	0.0402	37.0739	65.1438	46.1824
18	0.676	0.3684	-0.4997	0.3305	-0.2318	0.3871	0.0003	0.0033	0.0252	-0.0032	0.006	0.0087	0.0001	-0.0014	-0.0062	0.0041	-0.0001	-0.0015	0.0035	0.0012	0.0394	40.609	54.4995	44.4828
19	1.1976	-1.0321	-1.2345	1.4003	1.2178	1.3191	-0.0207	-0.0239	-0.026	0.0166	-0.0042	0.0231	0.0215	0.0168	0.0249	0.0043	-0.0028	-0.0035	0.0044	0.0041	0.0406	37.5851	40.9062	51.5998
20	0.1227	0.0182	-0.0169	0.4776	0.0004	0.012	-0.0002	-0.0081	0.0084	-0.0044	-0.0068	-0.0169	-0.0039	0.0022	0.0071	0.0038	-0.0011	-0.0019	0.0032	-0.0006	0.0398	48.4976	55.8954	48.6451

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 22
2	X-RAY DIFFRACTION	2	A	23 - 57
3	X-RAY DIFFRACTION	3	A	58 - 69
4	X-RAY DIFFRACTION	4	A	70 - 88
5	X-RAY DIFFRACTION	5	A	89 - 96
6	X-RAY DIFFRACTION	6	A	97 - 124
7	X-RAY DIFFRACTION	7	A	125 - 147
8	X-RAY DIFFRACTION	8	A	148 - 170
9	X-RAY DIFFRACTION	9	A	171 - 189
10	X-RAY DIFFRACTION	10	A	190 - 210
11	X-RAY DIFFRACTION	11	B	0 - 8
12	X-RAY DIFFRACTION	12	B	9 - 40
13	X-RAY DIFFRACTION	13	B	41 - 76
14	X-RAY DIFFRACTION	14	B	77 - 90
15	X-RAY DIFFRACTION	15	B	91 - 96
16	X-RAY DIFFRACTION	16	B	97 - 124
17	X-RAY DIFFRACTION	17	B	125 - 151
18	X-RAY DIFFRACTION	18	B	152 - 174
19	X-RAY DIFFRACTION	19	B	175 - 189
20	X-RAY DIFFRACTION	20	B	190 - 210

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