PDB-9f49: Structure of the bacteriophage K gp155 C-terminal domain, seleno-...

ID or keywords:

Entry

Database: PDB / ID: 9f49

Title

Structure of the bacteriophage K gp155 C-terminal domain, seleno-methionine modified version

Components

GP-PDE domain-containing protein

Keywords

VIRAL PROTEIN / glycerophosphoryl diester phosphodiesterase

Function / homology

Glycerophosphodiester phosphodiesterase domain / Glycerophosphoryl diester phosphodiesterase family / GP-PDE domain profile. / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / phosphoric diester hydrolase activity / lipid metabolic process / SN-GLYCEROL-3-PHOSPHATE / PHOSPHATE ION / GP-PDE domain-containing protein

Function and homology information

Biological species

Staphylococcus phage K (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.621 Å

Authors

Pichel, A. / van Raaij, M.J.

Funding support

Spain, 3items

Organization	Grant number	Country
Agencia Estatal de Investigacion (AEI)	BFU2014-53425-P	Spain
Agencia Estatal de Investigacion (AEI)	BFU2017-82207-P	Spain
Agencia Estatal de Investigacion (AEI)	PID2021-125597NB-I00	Spain

Citation

Journal: to be published
Title: Structure of bacteriophage K gp155
Authors: Pichel, A. / van Raaij, M.J.

History

Deposition	Apr 26, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 14, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9f49.cif.gz	70.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9f49.ent.gz		Display	PDB format
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Validation report

Summary document	9f49_validation.pdf.gz	750.1 KB	Display	wwPDB validaton report
Full document	9f49_full_validation.pdf.gz	750.8 KB	Display
Data in XML	9f49_validation.xml.gz	14.8 KB	Display
Data in CIF	9f49_validation.cif.gz	20.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f4/9f49 ftp://data.pdbj.org/pub/pdb/validation_reports/f4/9f49	HTTPS FTP

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Related structure data

Related structure data	9f5mC 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

AAA: GP-PDE domain-containing protein

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	42.397, 42.861, 123.646
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	GP-PDE domain-containing protein Mass: 27019.410 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus phage K (virus) / Gene: 812_115, 812a_115, 812F1_115, K1/420_115, K1_115 / Plasmid: pET28a+ / Production host: Escherichia coli (E. coli) / Strain (production host): B824(DE3) / References: UniProt: A0A0U1WFD7
#2: Chemical	ChemComp-G3P / SN-GLYCEROL-3-PHOSPHATE Mass: 172.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₉O₆P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	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: 2.08 Å³/Da / Density % sol: 40.84 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% (w/v)PEG 1500, 100 mM HEPES-NaOH pH 7.5, 10 mM Tris-HCl

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97872 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 29, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 1.62→123.65 Å / Num. obs: 26390 / % possible obs: 89.4 % / Redundancy: 10.7 % / B_iso Wilson estimate: 17.6 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.089 / R_pim(I) all: 0.027 / R_rim(I) all: 0.093 / Χ²: 0.96 / Net I/σ(I): 20.9
Reflection shell	Resolution: 1.62→1.71 Å / Redundancy: 5 % / R_merge(I) obs: 0.471 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 2360 / CC_1/2: 0.729 / R_pim(I) all: 0.232 / R_rim(I) all: 0.529 / Χ²: 1.06 / % possible all: 56.1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
Aimless	0.6.2	data scaling
CRANK2	2.0.281	phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.621→61.823 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.949 / SU B: 1.722 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.091
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1837	1266	4.808 %
R_work	0.1582	25063	-
all	0.159	-	-
obs	-	26329	89.387 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 18.598 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.426 Å²	-0 Å²	0 Å²
2-	-	-0.102 Å²	-0 Å²
3-	-	-	-0.324 Å²

Refinement step

Cycle: LAST / Resolution: 1.621→61.823 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1862	0	21	210	2093

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.013	1930
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	1806
X-RAY DIFFRACTION	r_angle_refined_deg	1.319	1.655	2611
X-RAY DIFFRACTION	r_angle_other_deg	1.326	1.583	4176
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.731	5	237
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.642	23.789	95
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.73	15	325
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.529	15	7
X-RAY DIFFRACTION	r_chiral_restr	0.059	0.2	261
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	2156
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	426
X-RAY DIFFRACTION	r_nbd_refined	0.194	0.2	356
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.165	0.2	1679
X-RAY DIFFRACTION	r_nbtor_refined	0.163	0.2	938
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.072	0.2	846
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.143	0.2	152
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.096	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.098	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.114	0.2	9
X-RAY DIFFRACTION	r_nbd_other	0.168	0.2	34
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.12	0.2	19
X-RAY DIFFRACTION	r_mcbond_it	1.031	1.763	939
X-RAY DIFFRACTION	r_mcbond_other	1.019	1.759	938
X-RAY DIFFRACTION	r_mcangle_it	1.647	2.638	1173
X-RAY DIFFRACTION	r_mcangle_other	1.65	2.642	1174
X-RAY DIFFRACTION	r_scbond_it	1.691	2.014	991
X-RAY DIFFRACTION	r_scbond_other	1.68	2.001	980
X-RAY DIFFRACTION	r_scangle_it	2.662	2.932	1436
X-RAY DIFFRACTION	r_scangle_other	2.647	2.908	1425
X-RAY DIFFRACTION	r_lrange_it	4.236	21.914	2154
X-RAY DIFFRACTION	r_lrange_other	4.054	21.439	2110

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.621-1.663	0.265	43	0.232	1039	0.233	2135	0.852	0.865	50.6792	0.221
1.663-1.708	0.27	59	0.221	1215	0.223	2091	0.871	0.878	60.9278	0.213
1.708-1.758	0.254	79	0.201	1375	0.204	2017	0.886	0.892	72.0873	0.192
1.758-1.812	0.22	64	0.174	1544	0.176	1977	0.916	0.928	81.3354	0.168
1.812-1.871	0.206	80	0.171	1619	0.173	1928	0.934	0.944	88.1224	0.158
1.871-1.937	0.205	92	0.166	1679	0.168	1858	0.947	0.947	95.3176	0.144
1.937-2.01	0.167	83	0.158	1712	0.159	1795	0.961	0.962	100	0.134
2.01-2.092	0.193	60	0.144	1645	0.146	1705	0.962	0.968	100	0.126
2.092-2.185	0.185	94	0.144	1575	0.146	1670	0.952	0.967	99.9401	0.131
2.185-2.291	0.156	67	0.14	1528	0.14	1595	0.97	0.972	100	0.129
2.291-2.415	0.169	83	0.144	1439	0.145	1522	0.968	0.971	100	0.137
2.415-2.561	0.157	78	0.142	1359	0.143	1437	0.974	0.974	100	0.139
2.561-2.738	0.165	65	0.152	1307	0.153	1374	0.968	0.968	99.8544	0.153
2.738-2.957	0.162	61	0.162	1190	0.162	1251	0.962	0.958	100	0.169
2.957-3.238	0.21	46	0.158	1133	0.16	1181	0.947	0.962	99.8307	0.175
3.238-3.619	0.16	53	0.15	1025	0.151	1079	0.964	0.966	99.9073	0.168
3.619-4.177	0.155	51	0.138	901	0.139	953	0.971	0.976	99.8951	0.164
4.177-5.109	0.201	44	0.151	779	0.154	824	0.97	0.977	99.8786	0.184
5.109-7.201	0.206	40	0.19	626	0.191	666	0.959	0.966	100	0.227
7.201-61.823	0.209	24	0.207	372	0.207	396	0.966	0.966	100	0.245

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