PDB-6ll8: Type II inorganic pyrophosphatase (PPase) from the psychrophilic ...

ID or keywords:

Entry

Database: PDB / ID: 6ll8

Title

Type II inorganic pyrophosphatase (PPase) from the psychrophilic bacterium Shewanella sp. AS-11, Mg-PNP form

Components

Inorganic pyrophosphatase

Keywords

METAL BINDING PROTEIN / Manganese-dependent inorganic pyrophosphatase

Function / homology

Function and homology information

inorganic diphosphatase / inorganic diphosphate phosphatase activity / metal ion binding / cytoplasm
Similarity search - Function

Biological species

Shewanella sp. AS-11 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.3 Å

Model details

Inorganic pyrophosphatase

Authors

Horitani, M. / Kusubayashi, K. / Oshima, K. / Yato, A. / Sugimoto, H. / Watanabe, K.

Funding support

Japan, 2items

Citation

Journal: Sci Rep / Year: 2020
Title: X-ray Crystallography and Electron Paramagnetic Resonance Spectroscopy Reveal Active Site Rearrangement of Cold-Adapted Inorganic Pyrophosphatase.
Authors: Horitani, M. / Kusubayashi, K. / Oshima, K. / Yato, A. / Sugimoto, H. / Watanabe, K.

History

Deposition	Dec 21, 2019	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 25, 2020	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6ll8.cif.gz	279.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6ll8.ent.gz	219.2 KB	Display	PDB format
PDBx/mmJSON format	6ll8.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6ll8_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	6ll8_full_validation.pdf.gz	1.1 MB	Display
Data in XML	6ll8_validation.xml.gz	34.3 KB	Display
Data in CIF	6ll8_validation.cif.gz	54.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ll/6ll8 ftp://data.pdbj.org/pub/pdb/validation_reports/ll/6ll8	HTTPS FTP

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Related structure data

Related structure data	6ll7C 2hawS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1rjb-d 1c9y-d 6ove-2 1oth-d 6st1-1 6l46-d 2j0i-d 1fb5-d 7c7m-d 6dgp-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 - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Inorganic pyrophosphatase

B: Inorganic pyrophosphatase

hetero molecules

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

1

A: Inorganic pyrophosphatase

hetero molecules

defined by author
Evidence: gel filtration
34.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Inorganic pyrophosphatase

hetero molecules

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

Unit cell

Length a, b, c (Å)	53.490, 78.980, 75.300
Angle α, β, γ (deg.)	90.000, 98.593, 90.000
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 2 molecules AB

#1: Protein	Inorganic pyrophosphatase Mass: 33749.828 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella sp. AS-11 (bacteria) / Gene: ppia / Plasmid: pET-16b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: L8AXY8

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Non-polymers , 7 types, 992 molecules

#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical	ChemComp-2PN / IMIDODIPHOSPHORIC ACID Mass: 176.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H₅NO₆P₂ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Chemical	ChemComp-F / FLUORIDE ION Mass: 18.998 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: F
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 971 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Sequence details	The cDNA sequence had a sequence coding Ser at the amino acid position of 116, which is different ...The cDNA sequence had a sequence coding Ser at the amino acid position of 116, which is different from R116 in the database entry (Uniprot L8AXY8). This conflict may be possibly derived from natural mutation or the presence of isoform.

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.33 Å³/Da / Density % sol: 47.21 %
Crystal grow	Temperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 24%(w/v) PEG3350, 10 mM ammonium phosphate dibasic and 0.2 M NaCl., 0.1 M HEPES

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SPring-8

/ Beamline: BL41XU / Wavelength: 1 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 8, 2019 / Details: mirrors

Radiation

Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.3→46.6 Å / Num. obs: 149178 / % possible obs: 96.6 % / Redundancy: 4.644 % / B_iso Wilson estimate: 17.793 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.045 / R_rim(I) all: 0.051 / Χ²: 1.124 / Net I/σ(I): 18.21

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.3-1.34	2.617	0.3	3.05	18810	0.906	0.366	72.3
1.34-1.4	3.119	0.243	4.28	31147	0.942	0.287	92.4
1.4-1.5	4.419	0.174	7.57	44582	0.977	0.197	99.4
1.5-1.7	5.166	0.111	12.99	61126	0.992	0.124	100
1.7-1.9	5.107	0.072	19.59	38033	0.996	0.081	99.9
1.9-2.1	5.225	0.054	26.71	24843	0.997	0.06	99.9
2.1-2.5	4.999	0.044	31.54	28949	0.998	0.049	99.8
2.5-4	5.146	0.034	37.66	31849	0.999	0.038	99.9
4-10	5.178	0.028	41.73	9627	0.999	0.032	99.8
10-46.6	5.037	0.03	42.57	652	0.998	0.033	98.6

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Processing

Software

Name	Version	Classification
XDS	20190315	data scaling
REFMAC	5.8.0258	refinement
PDB_EXTRACT	3.25	data extraction
PHASER	2.8.2	phasing
Coot	0.8	model building
XDS	20190315	data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2HAW

2haw

Resolution: 1.3→46.568 Å / Cor.coef. F_o:F_c: 0.986 / Cor.coef. F_o:F_c free: 0.98 / SU B: 0.921 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.033
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1216	7540	5.054 %
R_work	0.0965	-	-
all	0.098	-	-
obs	-	149178	98.271 %

Solvent computation

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

Displacement parameters

B_iso mean: 14.123 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.469 Å²	0 Å²	0.148 Å²
2-	-	-0.022 Å²	0 Å²
3-	-	-	-0.47 Å²

Refinement step

Cycle: LAST / Resolution: 1.3→46.568 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4680	0	85	971	5736

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.013	5137
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	4956
X-RAY DIFFRACTION	r_angle_refined_deg	1.796	1.648	7026
X-RAY DIFFRACTION	r_angle_other_deg	1.562	1.587	11577
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.599	5	700
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.083	23.644	236
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.608	15	941
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.566	15	24
X-RAY DIFFRACTION	r_chiral_restr	0.108	0.2	711
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	5730
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	982
X-RAY DIFFRACTION	r_nbd_refined	0.23	0.2	1089
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.179	0.2	4634
X-RAY DIFFRACTION	r_nbtor_refined	0.173	0.2	2490
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.086	0.2	2293
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.163	0.2	675
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.047	0.2	2
X-RAY DIFFRACTION	r_metal_ion_refined	0.015	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.143	0.2	10
X-RAY DIFFRACTION	r_nbd_other	0.162	0.2	50
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.177	0.2	46
X-RAY DIFFRACTION	r_mcbond_it	1.023	1.169	2552
X-RAY DIFFRACTION	r_mcbond_other	1.014	1.167	2551
X-RAY DIFFRACTION	r_mcangle_it	1.305	1.764	3215
X-RAY DIFFRACTION	r_mcangle_other	1.307	1.766	3216
X-RAY DIFFRACTION	r_scbond_it	1.98	1.453	2585
X-RAY DIFFRACTION	r_scbond_other	1.98	1.454	2586
X-RAY DIFFRACTION	r_scangle_it	2.37	2.075	3768
X-RAY DIFFRACTION	r_scangle_other	2.37	2.076	3769
X-RAY DIFFRACTION	r_lrange_it	2.925	16.755	6207
X-RAY DIFFRACTION	r_lrange_other	2.691	16.083	6057
X-RAY DIFFRACTION	r_rigid_bond_restr	2.249	3	10093

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 (%)
1.3-1.334	0.209	430	0.183	8611	X-RAY DIFFRACTION	81.1871
1.334-1.37	0.163	525	0.134	9988	X-RAY DIFFRACTION	95.8865
1.37-1.41	0.134	548	0.099	10020	X-RAY DIFFRACTION	99.83
1.41-1.453	0.114	498	0.077	9800	X-RAY DIFFRACTION	99.9903
1.453-1.501	0.104	519	0.068	9455	X-RAY DIFFRACTION	100
1.501-1.554	0.092	515	0.062	9154	X-RAY DIFFRACTION	100
1.554-1.612	0.105	469	0.065	8858	X-RAY DIFFRACTION	100
1.612-1.678	0.102	460	0.065	8558	X-RAY DIFFRACTION	100
1.678-1.753	0.104	400	0.069	8172	X-RAY DIFFRACTION	99.9883
1.753-1.838	0.108	426	0.07	7852	X-RAY DIFFRACTION	100
1.838-1.938	0.108	415	0.078	7384	X-RAY DIFFRACTION	100
1.938-2.055	0.102	383	0.083	7086	X-RAY DIFFRACTION	99.9866
2.055-2.197	0.113	340	0.084	6604	X-RAY DIFFRACTION	100
2.197-2.373	0.107	346	0.086	6146	X-RAY DIFFRACTION	99.9846
2.373-2.599	0.113	297	0.092	5706	X-RAY DIFFRACTION	100
2.599-2.905	0.131	273	0.105	5138	X-RAY DIFFRACTION	99.9815
2.905-3.354	0.139	242	0.113	4549	X-RAY DIFFRACTION	100
3.354-4.105	0.132	192	0.11	3877	X-RAY DIFFRACTION	99.9754
4.105-5.797	0.142	168	0.127	2998	X-RAY DIFFRACTION	99.9369
5.797-46.568	0.163	94	0.184	1682	X-RAY DIFFRACTION	99.8314

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