PDB-6mt1: Crystal structure of Inorganic Pyrophosphatase from Medicago trun...

ID or keywords:

Entry

Database: PDB / ID: 6mt1

Title

Crystal structure of Inorganic Pyrophosphatase from Medicago truncatula (R3 crystal form)

Components

Soluble inorganic pyrophosphatase

Keywords

HYDROLASE / pyrophosphate / PPA / autoproteolysis

Function / homology

Function and homology information

inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / magnesium ion binding / nucleoplasm / cytosol
Similarity search - Function

Biological species

Medicago truncatula (barrel medic)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.84 Å

Authors

Ruszkowski, M. / Grzechowiak, M. / Dauter, Z.

Citation

Journal: Biochem.J. / Year: 2019
Title: Crystal structures of plant inorganic pyrophosphatase, an enzyme with a moonlighting autoproteolytic activity.
Authors: Grzechowiak, M. / Ruszkowski, M. / Sliwiak, J. / Szpotkowski, K. / Sikorski, M. / Jaskolski, M.

History

Deposition	Oct 18, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 14, 2019	Provider: repository / Type: Initial release
Revision 1.1	Sep 4, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2	Oct 11, 2023	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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Download

PDBx/mmCIF format	6mt1.cif.gz	161.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6mt1.ent.gz	129.2 KB	Display	PDB format
PDBx/mmJSON format	6mt1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6mt1_validation.pdf.gz	429.9 KB	Display	wwPDB validaton report
Full document	6mt1_full_validation.pdf.gz	433.6 KB	Display
Data in XML	6mt1_validation.xml.gz	15.9 KB	Display
Data in CIF	6mt1_validation.cif.gz	22.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mt/6mt1 ftp://data.pdbj.org/pub/pdb/validation_reports/mt/6mt1	HTTPS FTP

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Related structure data

Related structure data	5ls0C 6mt2C 4lugS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6mt2-1 1mjy-1 2auu-1 3q5v-1 3q3l-1 5tea-d 6n1c-d 3r5u-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

Deposited unit

A: Soluble inorganic pyrophosphatase

B: Soluble inorganic pyrophosphatase

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

1

A: Soluble inorganic pyrophosphatase

B: Soluble inorganic pyrophosphatase

A: Soluble inorganic pyrophosphatase

B: Soluble inorganic pyrophosphatase

A: Soluble inorganic pyrophosphatase

B: Soluble inorganic pyrophosphatase

defined by author&software
Evidence: light scattering
148 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	81.784, 81.784, 176.935
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	146
Space group name H-M	H3

Components on special symmetry positions

ID	Model	Components
1	1	A-383- HOH
2	1	B-364- HOH
3	1	B-367- HOH
4	1	B-368- HOH

#1: Protein	Soluble inorganic pyrophosphatase Mass: 24656.223 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: 25500596, MTR_8g024050 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A072TMB0
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.31 Å³/Da / Density % sol: 46.74 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 1.6% Tacsimate pH 5.0, 80 mM Na Citrate tribasic pH 5.6, 12.8% PEG 3350, 20% Glycerol Bromelain 5 ug/ml MtPPA1 7.7 mg/ml

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 6, 2017
Radiation	Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 1.84→50 Å / Num. obs: 37764 / % possible obs: 99.2 % / Redundancy: 5.6 % / CC_1/2: 1 / R_merge(I) obs: 0.045 / R_rim(I) all: 0.049 / Net I/σ(I): 17.22
Reflection shell	Resolution: 1.84→1.95 Å / Redundancy: 5.4 % / R_merge(I) obs: 0.87 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 5879 / CC_1/2: 0.79 / R_rim(I) all: 0.96 / % possible all: 95.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0230	refinement
XDS		data reduction
PHASER		phasing
XDS		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4lug

4lug

Resolution: 1.84→40.89 Å / Cor.coef. F_o:F_c: 0.978 / Cor.coef. F_o:F_c free: 0.968 / SU B: 7.394 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.108 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20108	1020	2.7 %	RANDOM
R_work	0.16449	-	-	-
obs	0.16547	36742	99.17 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 50.482 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.77 Å²	0.39 Å²	-0 Å²
2-	-	0.77 Å²	-0 Å²
3-	-	-	-2.51 Å²

Refinement step

Cycle: 1 / Resolution: 1.84→40.89 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2894	0	0	151	3045

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.014	2975
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	2714
X-RAY DIFFRACTION	r_angle_refined_deg	1.519	1.657	4035
X-RAY DIFFRACTION	r_angle_other_deg	0.964	1.636	6377
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.232	5	359
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.202	23.684	152
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.584	15	522
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.494	15	12
X-RAY DIFFRACTION	r_chiral_restr	0.077	0.2	382
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	3281
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	527
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	2.187	3.383	1439
X-RAY DIFFRACTION	r_mcbond_other	2.186	3.379	1438
X-RAY DIFFRACTION	r_mcangle_it	3.207	5.049	1797
X-RAY DIFFRACTION	r_mcangle_other	3.206	5.053	1798
X-RAY DIFFRACTION	r_scbond_it	2.927	3.786	1536
X-RAY DIFFRACTION	r_scbond_other	2.926	3.789	1537
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	4.528	5.531	2239
X-RAY DIFFRACTION	r_long_range_B_refined	6.669	40.187	3193
X-RAY DIFFRACTION	r_long_range_B_other	6.651	39.884	3168
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.843→1.891 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.523	69	-
R_work	0.451	2478	-
obs	-	-	90.51 %

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	1.1466	-1.6078	0.8446	3.6993	-0.4582	1.3061	-0.0461	0.1961	0.1075	-0.2715	-0.0008	-0.1686	-0.073	0.2095	0.047	0.1965	-0.0322	-0.0196	0.1906	-0.0236	0.0888	-1.845	39.7197	16.3184
2	0.7304	-0.6794	-0.3574	0.914	0.8935	1.66	0.0926	-0.0086	-0.0814	-0.0113	0.071	0.0212	0.1428	-0.095	-0.1636	0.1703	-0.031	-0.0493	0.16	0.0058	0.1494	-5.3468	34.7639	29.1071
3	2.2015	-0.0738	-2.0008	0.2093	0.6162	3.8887	0.0748	0.2171	0.0284	-0.1014	0.0063	0.0513	-0.1276	-0.3922	-0.0811	0.166	-0.0289	-0.0668	0.1917	0.0504	0.1297	-12.534	45.762	25.4606
4	0.6374	-0.42	0.0215	0.377	0.3179	1.3632	0.0774	0.0247	-0.081	0.0055	0.0108	0.0214	0.1791	-0.0871	-0.0881	0.1589	-0.0391	-0.0473	0.138	-0.0079	0.1332	-8.6838	34.8249	31.5501
5	2.04	1.3285	-0.3296	0.9779	-0.6891	2.1056	0.0611	0.1338	0.083	-0.0707	0.0374	0.0941	0.4193	0.1744	-0.0985	0.2243	0.0008	-0.0769	0.0773	-0.0442	0.1447	-3.1796	26.3061	30.3306
6	6.4827	-0.615	0.8192	0.272	0.3611	1.0635	0.0147	0.061	-0.0733	0.0615	-0.046	0.0317	0.2321	-0.117	0.0313	0.2002	-0.0833	-0.0432	0.0803	-0.0153	0.1516	-16.3069	27.3622	30.9379
7	3.2788	1.9818	-2.3512	2.5802	-0.4159	3.0666	0.0163	0.0923	-0.2661	0.3097	0.0889	-0.2675	0.4206	0.1644	-0.1052	0.2835	0.0693	-0.099	0.0782	-0.058	0.1481	0.2129	21.8958	38.741
8	3.208	-3.303	2.1297	3.4399	-2.2349	3.109	0.0607	-0.0448	0.0026	-0.0785	0.0626	0.0259	0.4741	-0.3843	-0.1233	0.1824	-0.1093	-0.0453	0.0818	0.0392	0.1448	-14.5055	27.6908	43.4163
9	2.7791	-2.8926	-0.8895	6.9549	1.6008	0.8216	-0.0189	-0.022	-0.0969	-0.0326	0.0416	0.2504	0.2336	-0.3084	-0.0226	0.1386	-0.1733	-0.0679	0.2467	0.0385	0.1171	-21.4944	30.3754	36.7976
10	0.8373	-1.3075	1.4717	2.6808	-3.7905	6.5487	-0.0191	0.5022	-0.1333	-0.0311	-0.4962	-0.1522	0.4773	0.1216	0.5154	0.2952	-0.1033	-0.0346	0.4476	-0.2271	0.2416	-10.4018	24.7143	17.1785
11	3.6334	0.2303	-0.6617	3.3248	-3.3857	3.4991	-0.1694	-0.1982	0.0381	0.1459	-0.036	-0.199	-0.1148	0.0655	0.2054	0.1896	0.029	0.0535	0.1695	-0.0009	0.046	-8.2106	49.8242	75.9021
12	0.3412	-0.7121	-0.3854	1.811	0.8574	0.8717	0.0235	-0.0856	0.0134	0.014	0.0998	0.0598	0.0939	-0.1645	-0.1234	0.1235	-0.0289	0.0307	0.2397	0.0429	0.1418	-13.4485	48.5396	63.087
13	0.5677	0.4709	1.2995	1.3157	2.0774	5.4393	0.0485	-0.143	-0.0767	0.1542	0.0472	0.0777	0.2983	-0.1787	-0.0957	0.1672	-0.0167	0.0193	0.1472	0.0527	0.107	-7.6977	37.0978	67.1383
14	0.5282	-0.246	-0.7051	0.3191	0.1879	1.0649	-0.012	0.0305	0.0345	0.0096	0.1404	0.1382	0.0834	-0.1745	-0.1284	0.1546	-0.0472	0.0331	0.2078	0.0616	0.1492	-16.8798	42.927	62.8973
15	0.252	-0.5179	0.1553	2.1316	-0.8172	1.231	0.082	0.0192	-0.0383	-0.0161	-0.0328	-0.0754	-0.1041	-0.1404	-0.0492	0.1162	0.025	0.0374	0.1645	-0.0135	0.1288	-11.8553	51.5166	57.5568
16	1.5402	1.0238	0.1292	0.7407	-0.1989	1.9887	0.0657	-0.056	-0.1123	0.1331	0.0245	-0.0179	-0.3407	-0.2797	-0.0902	0.1412	0.075	0.1086	0.187	0.0128	0.1517	-19.4987	55.0472	62.3673
17	1.3249	2.6657	-0.2623	5.6735	0.07	1.3905	0.0434	0.0299	0.0152	0.089	-0.0704	0.034	0.0058	-0.4638	0.027	0.0202	0.0096	0.0559	0.3029	0.0315	0.1633	-25.3939	43.1268	61.6283
18	4.152	0.8725	1.8391	1.2678	1.6007	2.9363	0.0208	0.1469	0.2592	-0.0348	-0.0364	0.1785	-0.3179	-0.1506	0.0156	0.1442	0.1224	0.0941	0.1689	0.0344	0.1598	-21.6741	60.0883	53.8621
19	1.7471	-1.4811	-0.5209	2.5919	0.0001	0.4278	-0.0264	0.0992	-0.0425	-0.0306	0.0507	0.0654	0.1179	-0.2877	-0.0243	0.0778	-0.1569	0.0066	0.3839	0.0666	0.1	-24.8155	40.6524	52.7432
20	4.0313	-3.668	4.4155	3.7534	-3.7087	6.6423	-0.2184	-0.2553	0.055	0.4409	-0.0174	0.1872	0.021	-0.5168	0.2359	0.1878	-0.0663	0.1693	0.3196	-0.0697	0.1733	-24.388	49.1834	75.7527

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	30 - 39
2	X-RAY DIFFRACTION	2	A	40 - 65
3	X-RAY DIFFRACTION	3	A	66 - 77
4	X-RAY DIFFRACTION	4	A	78 - 116
5	X-RAY DIFFRACTION	5	A	117 - 126
6	X-RAY DIFFRACTION	6	A	127 - 142
7	X-RAY DIFFRACTION	7	A	143 - 158
8	X-RAY DIFFRACTION	8	A	159 - 171
9	X-RAY DIFFRACTION	9	A	172 - 187
10	X-RAY DIFFRACTION	10	A	188 - 209
11	X-RAY DIFFRACTION	11	B	31 - 40
12	X-RAY DIFFRACTION	12	B	41 - 65
13	X-RAY DIFFRACTION	13	B	66 - 77
14	X-RAY DIFFRACTION	14	B	78 - 102
15	X-RAY DIFFRACTION	15	B	103 - 116
16	X-RAY DIFFRACTION	16	B	117 - 126
17	X-RAY DIFFRACTION	17	B	127 - 142
18	X-RAY DIFFRACTION	18	B	143 - 158
19	X-RAY DIFFRACTION	19	B	159 - 187
20	X-RAY DIFFRACTION	20	B	188 - 209

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