PDB-5a66: Crystal structure of AtTTM3 in complex with tripolyphosphate and ...

ID or keywords:

Entry

Database: PDB / ID: 5a66

Title

Crystal structure of AtTTM3 in complex with tripolyphosphate and manganese 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 / OTHER / Resolution: 2.05 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 24, 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	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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PDBx/mmCIF format	5a66.cif.gz	195.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5a66.ent.gz	159 KB	Display	PDB format
PDBx/mmJSON format	5a66.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5a66_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	5a66_full_validation.pdf.gz	1.2 MB	Display
Data in XML	5a66_validation.xml.gz	19.5 KB	Display
Data in CIF	5a66_validation.cif.gz	27.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/a6/5a66 ftp://data.pdbj.org/pub/pdb/validation_reports/a6/5a66	HTTPS FTP

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Related structure data

Related structure data	5a5yC 5a60C 5a61C 5a64C 5a65C 5a67C 5a68C C: citing same article (ref.)
Similar structure data	4wml-d 4huf-2 1opr-d 1c8y-d 4ehc-d 2pry-d 5ufa-3 2qhl-1 3ecv-2 3s0p-3 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

49.7 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
24.9 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
24.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	136.273, 136.273, 145.485
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-3PO / TRIPHOSPHATE Mass: 257.955 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H₅O₁₀P₃
#3: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 227 / 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: 3.47 Å³/Da / Density % sol: 64.56 % / Description: NONE
Crystal grow	pH: 5 / Details: 2.5 M NACL, 0.1 M SODIUM CITRATE PH 5.0

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X10SA / Wavelength: 1.000000, 1.802090

Detector

Type: DECTRIS PILATUS / Detector: PIXEL / Date: Mar 20, 2013

Radiation

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

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1	1
2	1.80209	1

Reflection

Resolution: 2.05→48.18 Å / Num. obs: 42478 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 11.73 % / R_merge(I) obs: 0.09 / Net I/σ(I): 19.13

Reflection shell

Resolution: 2.05→2.17 Å / Redundancy: 6.47 % / R_merge(I) obs: 0.74 / Mean I/σ(I) obs: 2.2 / % possible all: 88.1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0123	refinement
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure: OTHER
Starting model: NONE

Resolution: 2.05→48.18 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.941 / SU B: 8.593 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.342 / ESU R Free: 0.146 / 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	0.21963	3927	9.3 %	RANDOM
R_work	0.18199	-	-	-
obs	0.18549	38451	98.35 %	-

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: 35.766 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.64 Å²	0 Å²	0 Å²
2-	-	-0.64 Å²	0 Å²
3-	-	-	1.28 Å²

Refinement step

Cycle: LAST / Resolution: 2.05→48.18 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3408	0	56	227	3691

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.019	3574
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	3446
X-RAY DIFFRACTION	r_angle_refined_deg	1.136	1.987	4826
X-RAY DIFFRACTION	r_angle_other_deg	0.818	3	7952
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.599	5	436
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.982	23.372	172
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.326	15	658
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.683	15	34
X-RAY DIFFRACTION	r_chiral_restr	0.058	0.2	531
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.021	3936
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	806
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	1.235	2.236	1702
X-RAY DIFFRACTION	r_mcbond_other	1.233	2.235	1701
X-RAY DIFFRACTION	r_mcangle_it	1.588	3.345	2128
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.395	2.434	1872
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	0.924	3	7019
X-RAY DIFFRACTION	r_sphericity_free	23.288	5	67
X-RAY DIFFRACTION	r_sphericity_bonded	4.633	5	7117

LS refinement shell

Resolution: 2.05→2.103 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.301	251	-
R_work	0.265	2417	-
obs	-	-	85.35 %

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	1.1914	1.4171	0.1851	3.4212	2.2801	5.613	-0.0523	0.0906	0.0665	-0.0616	0.2506	-0.144	0.1172	0.2315	-0.1983	0.014	-0.0233	-0.0129	0.0861	0.0247	0.0538	39.7681	50.9624	18.5398
2	6.6071	-0.605	-1.923	0.6622	0.593	1.5879	-0.1119	0.0846	-0.0124	0.0551	0.0777	-0.0931	0.1185	0.104	0.0342	0.086	-0.0202	-0.0318	0.0316	0.0083	0.0404	54.6105	41.3663	18.172
3	1.0589	-1.3312	0.6293	2.8699	0.3096	1.7368	0.1553	-0.0308	-0.2009	-0.0857	-0.019	0.1152	0.4828	-0.2028	-0.1363	0.2404	-0.1192	0.0464	0.1245	-0.0045	0.1184	49.2859	38.0074	17.5354
4	5.1606	0.4944	1.4642	1.3963	-0.3697	6.1692	-0.0609	-0.1285	-0.4534	-0.1239	0.0082	0.0108	0.4497	0.0521	0.0527	0.1256	0.0171	0.0097	0.0586	0.0061	0.0933	62.3627	31.8654	21.8996
5	4.5816	4.126	-4.1914	10.5095	-7.4062	12.8223	0.0163	0.458	-0.5747	-0.1706	-0.0683	0.168	0.4018	-0.0548	0.0519	0.1958	-0.0023	-0.0004	0.188	-0.0617	0.2096	61.6768	29.5394	9.2968
6	5.7766	-1.1002	-0.9289	0.8244	0.3504	0.6908	-0.0725	0.0265	0.0257	0.1093	0.0637	0.01	0.0421	0.0027	0.0088	0.0705	-0.0276	-0.0145	0.0504	0.0225	0.0112	49.6947	44.9086	19.7987
7	3.6706	-3.2544	-0.8415	11.2868	5.0879	5.3813	0.0007	0.2485	-0.204	-0.195	-0.1598	0.3962	0.0234	-0.242	0.1591	0.0363	-0.0503	-0.0221	0.1019	0.0209	0.0342	32.5781	48.8082	11.7826
8	5.5477	-2.1922	0.5365	0.9642	-0.5074	1.0892	-0.0102	0.0851	0.4806	0.003	-0.1123	-0.2242	-0.1092	0.2455	0.1226	0.1029	-0.0184	-0.0062	0.064	0.0416	0.0794	50.5412	54.3276	15.0834
9	11.278	-4.3375	-4.7504	5.1206	2.922	5.7576	0.3235	0.0015	0.5907	0.0143	-0.0519	-0.0028	-0.5639	-0.1561	-0.2716	0.1347	-0.0503	0.0076	0.0989	0.05	0.0789	37.1356	54.9769	53.6974
10	0.7127	0.3164	0.2223	4.7025	1.3922	1.258	0.0285	-0.0407	0.1533	0.1355	-0.0714	-0.0341	-0.0368	-0.0581	0.0429	0.0257	-0.0172	0.0012	0.0831	0.0197	0.05	39.5697	60.5188	44.0214
11	1.2909	-0.9409	-1.2886	3.1617	0.0158	1.6483	0.0145	0.0888	0.0132	0.241	0.028	0.1319	-0.0875	-0.1659	-0.0425	0.0653	-0.0587	0.0316	0.1341	-0.0166	0.1075	33.0384	62.7222	46.4129
12	1.5842	0.2202	0.7142	3.1942	-1.0927	6.4001	0.0449	-0.0422	0.1761	0.0633	0.0385	0.5315	-0.2068	-0.4721	-0.0833	0.0946	0.0116	0.0323	0.1324	-0.0171	0.1339	31.5097	77.0794	43.3502
13	0.9798	1.4283	-0.0819	8.3833	2.0466	0.8147	0.1152	-0.1468	0.1469	0.3176	-0.1599	0.3755	-0.0039	-0.0739	0.0447	0.0959	0.0372	-0.0141	0.2062	-0.0002	0.0545	36.8197	74.1089	49.652
14	2.6866	1.2561	-0.736	3.7231	-0.8385	3.1399	0.0842	-0.0401	0.259	0.0904	-0.0208	0.1568	-0.1019	-0.0399	-0.0635	0.0585	-0.0112	-0.0029	0.0379	0.0189	0.0404	37.6563	51.9355	44.9338
15	11.7877	-7.9863	-8.819	7.4172	3.5749	9.4953	-0.1284	0.0884	-0.224	0.175	-0.0604	0.1419	0.0593	-0.0915	0.1887	0.1179	-0.0797	-0.0008	0.0695	0.0245	0.0441	36.8716	41.6651	52.3971
16	0.8161	-0.2537	-0.1432	7.0146	-0.0639	0.9017	-0.0795	-0.0295	0.0941	0.245	0.037	-0.4722	-0.0926	0.2071	0.0424	0.0574	-0.0147	-0.0099	0.1098	0.0392	0.0684	47.9925	55.1102	48.3841

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 - 89
4	X-RAY DIFFRACTION	4	A	90 - 112
5	X-RAY DIFFRACTION	5	A	113 - 126
6	X-RAY DIFFRACTION	6	A	127 - 169
7	X-RAY DIFFRACTION	7	A	170 - 190
8	X-RAY DIFFRACTION	8	A	191 - 210
9	X-RAY DIFFRACTION	9	B	0 - 8
10	X-RAY DIFFRACTION	10	B	9 - 57
11	X-RAY DIFFRACTION	11	B	58 - 89
12	X-RAY DIFFRACTION	12	B	90 - 117
13	X-RAY DIFFRACTION	13	B	118 - 145
14	X-RAY DIFFRACTION	14	B	146 - 175
15	X-RAY DIFFRACTION	15	B	176 - 188
16	X-RAY DIFFRACTION	16	B	189 - 210

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