PDB-8jgw: Crystal structure of Klebsiella pneumoniae exopolyphosphatase

ID or keywords:

Entry

Database: PDB / ID: 8jgw

Title

Crystal structure of Klebsiella pneumoniae exopolyphosphatase

Components

Exopolyphosphatase

Keywords

HYDROLASE / Polyphosphate / exopolyphosphatase

Function / homology

Function and homology information

phosphorus metabolic process / exopolyphosphatase / exopolyphosphatase activity / plasma membrane
Similarity search - Function

Biological species

Klebsiella pneumoniae subsp. pneumoniae 1158 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Zhao, Y. / Dai, S.

Funding support

China, 1items

Citation

Journal: Adv Sci / Year: 2024
Title: Structural Evolution of Bacterial Polyphosphate Degradation Enzyme for Phosphorus Cycling.
Authors: Dai, S. / Wang, B. / Ye, R. / Zhang, D. / Xie, Z. / Yu, N. / Cai, C. / Huang, C. / Zhao, J. / Zhang, F. / Hua, Y. / Zhao, Y. / Zhou, R. / Tian, B.

History

Deposition	May 21, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	May 15, 2024	Provider: repository / Type: Initial release
Revision 1.1	Jul 24, 2024	Group: 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	Jul 31, 2024	Group: Database references / Category: citation / citation_author Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8jgw.cif.gz	417.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8jgw.ent.gz	338.3 KB	Display	PDB format
PDBx/mmJSON format	8jgw.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8jgw_validation.pdf.gz	4.4 MB	Display	wwPDB validaton report
Full document	8jgw_full_validation.pdf.gz	4.5 MB	Display
Data in XML	8jgw_validation.xml.gz	39.3 KB	Display
Data in CIF	8jgw_validation.cif.gz	57.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jg/8jgw ftp://data.pdbj.org/pub/pdb/validation_reports/jg/8jgw	HTTPS FTP

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Related structure data

Related structure data	8jgoC 8jgpC 8jgqC 8jgrC 8jgtC 8jguC 8jgxC C: citing same article (ref.)
Similar structure data	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: Exopolyphosphatase

B: Exopolyphosphatase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	86.800, 97.080, 144.110
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Exopolyphosphatase Mass: 59908.477 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae 1158 (bacteria) Gene: RJA_06760 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Y0PUF6
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 482 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.53 Å³/Da / Density % sol: 51.46 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: KCl, HEPES, Pentaerythritol propoxylate

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Data collection

Diffraction

Mean temperature: 95 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL17U1 / Wavelength: 0.979 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 11, 2019

Radiation

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

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 1.8→30 Å / Num. obs: 113613 / % possible obs: 99.5 % / Redundancy: 6.64 % / CC_1/2: 0.999 / R_merge(I) obs: 0.055 / R_rim(I) all: 0.06 / Net I/σ(I): 16.48

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
1.8-1.84	0.541	7878	0.953	0.585	1
1.84-1.89	0.397	8139	0.974	0.43	1
1.89-1.95	0.304	7936	0.984	0.33	1
1.95-2.01	0.241	7693	0.989	0.262	1
2.01-2.07	0.19	7466	0.992	0.206	1
2.07-2.15	0.152	7208	0.995	0.164	1
2.15-2.23	0.124	7002	0.996	0.135	1
2.23-2.32	0.104	6742	0.996	0.113	1
2.32-2.42	0.088	6460	0.997	0.096	1
2.42-2.54	0.075	6165	0.998	0.081	1
2.54-2.68	0.069	5897	0.997	0.075	1
2.68-2.84	0.061	5590	0.998	0.066	1
2.84-3.03	0.055	5273	0.998	0.06	1
3.03-3.28	0.052	4889	0.998	0.056	1
3.28-3.59	0.047	4546	0.998	0.051	1
3.59-4.01	0.044	4120	0.998	0.047	1
4.01-4.63	0.042	3649	0.998	0.046	1
4.63-5.68	0.041	3112	0.998	0.045	1
5.68-8.03	0.042	2462	0.998	0.046	1
8.03-30	0.035	1386	0.997	0.039	1

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
XSCALE		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.8→29.67 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.67 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2073	5734	5.05 %
R_work	0.1831	-	-
obs	0.1843	113503	99.47 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.8→29.67 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7943	0	27	482	8452

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006
X-RAY DIFFRACTION	f_angle_d	0.803
X-RAY DIFFRACTION	f_dihedral_angle_d	14.055	3044
X-RAY DIFFRACTION	f_chiral_restr	0.053	1219
X-RAY DIFFRACTION	f_plane_restr	0.008	1432

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 (%)
1.8-1.82	0.3573	162	0.348	3130	X-RAY DIFFRACTION	88
1.82-1.84	0.3547	206	0.2905	3542	X-RAY DIFFRACTION	100
1.84-1.86	0.3175	210	0.2681	3531	X-RAY DIFFRACTION	100
1.86-1.88	0.2685	169	0.2413	3585	X-RAY DIFFRACTION	100
1.88-1.91	0.255	190	0.236	3555	X-RAY DIFFRACTION	100
1.91-1.93	0.2364	231	0.2273	3586	X-RAY DIFFRACTION	100
1.93-1.96	0.2465	183	0.225	3530	X-RAY DIFFRACTION	100
1.96-1.99	0.2308	205	0.2137	3543	X-RAY DIFFRACTION	100
1.99-2.02	0.2365	168	0.2037	3631	X-RAY DIFFRACTION	100
2.02-2.05	0.2646	181	0.2031	3567	X-RAY DIFFRACTION	100
2.05-2.09	0.2466	215	0.2024	3539	X-RAY DIFFRACTION	100
2.09-2.13	0.2328	188	0.1976	3608	X-RAY DIFFRACTION	100
2.13-2.17	0.2794	198	0.1988	3566	X-RAY DIFFRACTION	100
2.17-2.21	0.2245	180	0.1932	3609	X-RAY DIFFRACTION	100
2.21-2.26	0.2296	187	0.1852	3570	X-RAY DIFFRACTION	100
2.26-2.31	0.2113	202	0.1819	3575	X-RAY DIFFRACTION	100
2.31-2.37	0.2296	200	0.1796	3601	X-RAY DIFFRACTION	100
2.37-2.44	0.2121	201	0.1887	3553	X-RAY DIFFRACTION	100
2.44-2.51	0.2143	194	0.1853	3600	X-RAY DIFFRACTION	100
2.51-2.59	0.2502	178	0.185	3630	X-RAY DIFFRACTION	100
2.59-2.68	0.255	172	0.2022	3602	X-RAY DIFFRACTION	100
2.68-2.79	0.2281	164	0.2017	3646	X-RAY DIFFRACTION	100
2.79-2.91	0.2329	186	0.1924	3622	X-RAY DIFFRACTION	100
2.91-3.07	0.2021	187	0.1895	3644	X-RAY DIFFRACTION	100
3.07-3.26	0.2017	192	0.2011	3630	X-RAY DIFFRACTION	100
3.26-3.51	0.2045	181	0.1757	3662	X-RAY DIFFRACTION	100
3.51-3.86	0.1913	193	0.1673	3666	X-RAY DIFFRACTION	100
3.86-4.42	0.1483	199	0.1485	3673	X-RAY DIFFRACTION	100
4.42-5.57	0.1727	206	0.1581	3711	X-RAY DIFFRACTION	100
5.57-29.67	0.1863	206	0.1682	3862	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Origin x: -16.1723 Å / Origin y: -24.4391 Å / Origin z: -7.5575 Å

	11	12	13	21	22	23	31	32	33
T	0.2756 Å²	-0.0093 Å²	0.0243 Å²	-	0.2638 Å²	-0.0172 Å²	-	-	0.2786 Å²
L	0.0412 °²	-0.0479 °²	0.0126 °²	-	0.2158 °²	0.0147 °²	-	-	0.5233 °²
S	0.0162 Å °	0.0066 Å °	-0.0001 Å °	-0.0116 Å °	0.0031 Å °	-0.037 Å °	-0.0384 Å °	0.0899 Å °	-0.0216 Å °

Refinement TLS group

Selection details: all

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