PDB-6ll7: Type II inorganic pyrophosphatase (PPase) from the psychrophilic ...

ID or keywords:

Entry

Database: PDB / ID: 6ll7

Title

Type II inorganic pyrophosphatase (PPase) from the psychrophilic bacterium Shewanella sp. AS-11, Mn-activated 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: 2.2 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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_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

-
Download

PDBx/mmCIF format	6ll7.cif.gz	427.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6ll7.ent.gz	344.2 KB	Display	PDB format
PDBx/mmJSON format	6ll7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ll/6ll7 ftp://data.pdbj.org/pub/pdb/validation_reports/ll/6ll7	HTTPS FTP

-
Related structure data

Related structure data	6ll8C 2hawS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5bms-d 4tm5-d 6hm2-1 4yp8-1 5uiq-4 5ack-d 1gxo-d 5vil-3 7k46-d 4y73-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

6ll8C

2hawS

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Inorganic pyrophosphatase

B: Inorganic pyrophosphatase

C: Inorganic pyrophosphatase

D: Inorganic pyrophosphatase

hetero molecules

136 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Inorganic pyrophosphatase

hetero molecules

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

2

B: Inorganic pyrophosphatase

hetero molecules

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

3

C: Inorganic pyrophosphatase

hetero molecules

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

4

D: Inorganic pyrophosphatase

hetero molecules

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

Unit cell

Length a, b, c (Å)	52.530, 75.570, 85.670
Angle α, β, γ (deg.)	107.397, 90.060, 92.169
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	Chains A B
2	2	Chains A C
3	3	Chains A D
4	4	Chains B C
5	5	Chains B D
6	6	Chains C D

NCS ensembles :

ID
1
2
3
4
5
6

#1: Protein	Inorganic pyrophosphatase Mass: 33749.828 Da / Num. of mol.: 4 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
#2: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H₂O
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.

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.4 Å³/Da / Density % sol: 48.79 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 30%(w/v) PEG3350, 0.5 M NaCl, 0.1 M glycine and 0.1 M citrate

-
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: Oct 17, 2018 / 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: 2.2→48 Å / Num. obs: 61908 / % possible obs: 96.8 % / Redundancy: 3.494 % / B_iso Wilson estimate: 37.615 Å² / CC_1/2: 0.992 / R_merge(I) obs: 0.123 / R_rim(I) all: 0.146 / Χ²: 0.879 / Net I/σ(I): 6.88

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
2.2-2.33	3.665	0.637	1.98	9866	0.764	0.747	95.4
2.33-2.49	3.614	0.44	2.76	9445	0.867	0.517	97.4
2.49-2.69	3.469	0.326	3.56	8802	0.92	0.387	97.6
2.69-2.95	3.421	0.218	5.13	8101	0.961	0.259	97
2.95-3.29	3.421	0.132	7.9	7317	0.982	0.157	97.2
3.29-3.8	3.517	0.091	11.42	6452	0.989	0.107	97.8
3.8-4.65	3.387	0.07	13.95	5405	0.991	0.084	96.4
4.65-6.54	3.259	0.067	14.18	4158	0.991	0.08	95.3
6.54-48	3.467	0.055	17.48	2362	0.995	0.065	97.1

-
Processing

Software

Name	Version	Classification
XDS	20180409	data scaling
REFMAC	5.8.0258	refinement
PDB_EXTRACT	3.25	data extraction
PHASER	2.8.2	phasing
XDS	Version January 26, 2018	data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2HAW

2haw

Resolution: 2.2→47.509 Å / Cor.coef. F_o:F_c: 0.916 / Cor.coef. F_o:F_c free: 0.881 / SU B: 23.464 / SU ML: 0.284 / Cross valid method: THROUGHOUT / ESU R: 0.415 / ESU R Free: 0.277
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2972	2985	4.925 %
R_work	0.2561	-	-
all	0.258	-	-
obs	-	60604	94.973 %

Solvent computation

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

Displacement parameters

B_iso mean: 39.534 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.314 Å²	1.854 Å²	-0.157 Å²
2-	-	3.041 Å²	0.448 Å²
3-	-	-	-1.8 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→47.509 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9360	0	10	276	9646

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	9544
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	9108
X-RAY DIFFRACTION	r_ext_dist_refined_d	0	0.01	2
X-RAY DIFFRACTION	r_angle_refined_deg	1.4	1.633	12892
X-RAY DIFFRACTION	r_angle_other_deg	1.208	1.578	21160
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.124	5	1220
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.751	24.151	424
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.76	15	1692
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.04	15	36
X-RAY DIFFRACTION	r_chiral_restr	0.06	0.2	1304
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	10560
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1796
X-RAY DIFFRACTION	r_nbd_refined	0.189	0.2	1793
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.176	0.2	8101
X-RAY DIFFRACTION	r_nbtor_refined	0.152	0.2	4520
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.075	0.2	4136
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.176	0.2	261
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.084	0.2	4
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.341	0.2	29
X-RAY DIFFRACTION	r_nbd_other	0.185	0.2	61
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.128	0.2	13
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.075	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	0.97	3.141	4892
X-RAY DIFFRACTION	r_mcbond_other	0.97	3.14	4891
X-RAY DIFFRACTION	r_mcangle_it	1.631	4.706	6108
X-RAY DIFFRACTION	r_mcangle_other	1.631	4.707	6109
X-RAY DIFFRACTION	r_scbond_it	0.894	3.232	4652
X-RAY DIFFRACTION	r_scbond_other	0.89	3.233	4652
X-RAY DIFFRACTION	r_scangle_it	1.516	4.813	6784
X-RAY DIFFRACTION	r_scangle_other	1.516	4.814	6785
X-RAY DIFFRACTION	r_lrange_it	3.045	35.746	10058
X-RAY DIFFRACTION	r_lrange_other	3.025	35.753	10055
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.039	0.05	9694
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.038	0.05	9649
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.027	0.05	9716
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.039	0.05	9692
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.037	0.05	9684
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.033	0.05	9649

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 (%)
2.2-2.257	0.383	221	0.36	4194	X-RAY DIFFRACTION	93.5778
2.257-2.319	0.397	216	0.339	4169	X-RAY DIFFRACTION	95.7842
2.319-2.386	0.368	216	0.32	4139	X-RAY DIFFRACTION	96.2431
2.386-2.459	0.352	184	0.312	3979	X-RAY DIFFRACTION	96.6117
2.459-2.54	0.323	198	0.303	3829	X-RAY DIFFRACTION	96.5476
2.54-2.628	0.329	179	0.297	3775	X-RAY DIFFRACTION	96.2044
2.628-2.727	0.351	195	0.295	3554	X-RAY DIFFRACTION	96.1036
2.727-2.838	0.327	191	0.271	3442	X-RAY DIFFRACTION	96.1874
2.838-2.964	0.322	164	0.261	3296	X-RAY DIFFRACTION	95.9512
2.964-3.108	0.341	157	0.283	3188	X-RAY DIFFRACTION	96.0931
3.108-3.276	0.352	147	0.28	3018	X-RAY DIFFRACTION	95.3888
3.276-3.473	0.333	151	0.28	2784	X-RAY DIFFRACTION	94.4945
3.473-3.712	0.254	135	0.245	2588	X-RAY DIFFRACTION	93.5417
3.712-4.008	0.242	141	0.222	2400	X-RAY DIFFRACTION	92.5683
4.008-4.387	0.2	132	0.192	2189	X-RAY DIFFRACTION	92.4333
4.387-4.9	0.26	98	0.197	2000	X-RAY DIFFRACTION	93.1203
4.9-5.649	0.284	92	0.203	1802	X-RAY DIFFRACTION	93.8088
5.649-6.897	0.291	71	0.216	1507	X-RAY DIFFRACTION	93.2073
6.897-9.663	0.218	65	0.184	1121	X-RAY DIFFRACTION	90.7422
9.663-47.509	0.244	32	0.227	645	X-RAY DIFFRACTION	89.6689

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	0.678	-0.0455	-0.0042	0.2021	0.0776	0.6431	-0.0136	0.0375	0.016	-0.0139	0.009	-0.0034	-0.0175	-0.0808	0.0046	0.0761	0.0655	0.0137	0.0722	0.0107	0.0487	8.2	21.89	12.3276
2	2.1411	0.165	-0.2231	3.3881	0.9601	1.6412	0.3227	0.3881	0.3753	-0.1666	-0.1475	-0.6754	-0.2856	-0.17	-0.1752	0.1846	0.1129	0.1035	0.1069	0.1246	0.2447	14.7628	42.4771	0.2066
3	0.449	0.045	-0.0123	0.1835	-0.0801	0.7726	0.0027	0.0046	-0.0215	0.0168	-0.0266	0.0174	-0.0062	0.0639	0.0239	0.1146	0.07	0.0141	0.0536	0.0107	0.0764	32.8831	15.0649	31.6311
4	1.8169	0.3155	-0.2046	1.8985	0.3356	1.3514	0.3028	-0.2793	0.2484	0.1983	-0.3479	0.2742	-0.0719	-0.0892	0.0451	0.2074	0.012	0.1022	0.1383	-0.0524	0.0771	26.8179	26.1406	52.9976
5	0.449	-0.0726	0.1129	0.3097	-0.2339	0.5708	-0.0752	0.0297	0.033	0.0255	0.0052	0.0411	0.0121	0.0392	0.0699	0.1078	0.0409	0.0232	0.0252	0.0234	0.0838	56.2279	67.6307	48.4937
6	1.3937	0.3221	-0.3151	2.8489	-0.1756	0.6156	0.1033	0.1249	-0.1694	-0.4222	-0.1203	0.4633	-0.0279	0.0279	0.0169	0.1999	0.1165	-0.0854	0.0849	-0.0387	0.1184	49.9772	56.1402	27.5115
7	0.4993	-0.008	-0.1888	0.0744	0.0803	0.8874	-0.0363	-0.0248	-0.0052	0.0278	0.0205	-0.0032	0.0127	-0.0031	0.0158	0.0985	0.0757	0.0331	0.0588	0.0204	0.0699	31.5333	61.0937	67.8796
8	2.7526	-0.294	-0.3587	1.9525	0.1942	1.6694	-0.1025	-0.4291	-0.3763	-0.1097	0.1259	-0.2381	0.2257	0.0846	-0.0234	0.1872	0.0858	0.0746	0.105	0.0713	0.1107	38.2648	40.5763	80.4438

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	2 - 200
2	X-RAY DIFFRACTION	2	ALL	A	201 - 307
3	X-RAY DIFFRACTION	3	ALL	B	2 - 200
4	X-RAY DIFFRACTION	4	ALL	B	201 - 307
5	X-RAY DIFFRACTION	5	ALL	C	2 - 200
6	X-RAY DIFFRACTION	6	ALL	C	201 - 307
7	X-RAY DIFFRACTION	7	ALL	D	2 - 200
8	X-RAY DIFFRACTION	8	ALL	D	201 - 307

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi