PDB-2o55: Crystal Structure of a putative glycerophosphodiester phosphodies...

ID or keywords:

Entry

Database: PDB / ID: 2o55

Title

Crystal Structure of a putative glycerophosphodiester phosphodiesterase from Galdieria sulphuraria

Components

putative glycerophosphodiester phosphodiesterase

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / beta barrel / Protein Structure Initiative / PSI-2 / Center for Eukaryotic Structural Genomics / CESG

Function / homology

Phosphatidylinositol (PI) phosphodiesterase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta

Function and homology information

Biological species

Galdieria sulphuraria (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.806 Å

Authors

Mccoy, J.G. / Wesenberg, G.E. / Phillips Jr., G.N. / Bitto, E. / Bingman, C.A. / Center for Eukaryotic Structural Genomics (CESG)

Citation

Journal: To be Published
Title: Crystal Structure of a putative glycerophosphodiester phosphodiesterase from Galdieria sulphuraria
Authors: Mccoy, J.G. / Wesenberg, G.E. / Phillips Jr., G.N. / Bitto, E. / Bingman, C.A.

History

Deposition	Dec 5, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 19, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4	Dec 27, 2023	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 999

SEQUENCE The sequence of the protein is not available at the UNP database at the time of processing.

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2o55.cif.gz	66.1 KB	Display	PDBx/mmCIF format
PDB format	pdb2o55.ent.gz	48.2 KB	Display	PDB format
PDBx/mmJSON format	2o55.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2o55_validation.pdf.gz	441.2 KB	Display	wwPDB validaton report
Full document	2o55_full_validation.pdf.gz	447.2 KB	Display
Data in XML	2o55_validation.xml.gz	11.8 KB	Display
Data in CIF	2o55_validation.cif.gz	14.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o5/2o55 ftp://data.pdbj.org/pub/pdb/validation_reports/o5/2o55	HTTPS FTP

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Related structure data

Similar structure data	6iez-d 2bof-d 5f2t-2 2bog-d 3azy-4 3ks6-3 6b2v-d 6m88-d 1fxu-d 2g2z-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: GO.80034

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: putative glycerophosphodiester phosphodiesterase

hetero molecules

30.1 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)	102.427, 102.427, 51.709
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	putative glycerophosphodiester phosphodiesterase Mass: 29833.285 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Galdieria sulphuraria (eukaryote) / Gene: c454_101305g29.t1 (MSU_Galdi) / Plasmid: PVP 16 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2)
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.7 Å³/Da / Density % sol: 53.5 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Protein Solution (10 MG/ML protein, 0.050 M sodium chloride, 0.0031 M sodium azide, 0.0003 M TCEP, 0.005 M Bis Tris pH 7.0) mixed in a 1:1 ratio with the Well Solution (0.90 M lithium ...Details: Protein Solution (10 MG/ML protein, 0.050 M sodium chloride, 0.0031 M sodium azide, 0.0003 M TCEP, 0.005 M Bis Tris pH 7.0) mixed in a 1:1 ratio with the Well Solution (0.90 M lithium sulfate, 0.10 M sodium succinate pH 4), Cryoprotected with: well solution supplemented with up to 20% glycerol, vapor diffusion, hanging drop, temperature 293K

Crystal

Density Matthews: 2.7 Å³/Da / Density % sol: 53.5 %

Crystal grow

Temperature: 293 K / Method: vapor diffusion, hanging drop
Details: Protein Solution (10 MG/ML protein, 0.050 M sodium chloride, 0.0031 M sodium azide, 0.0003 M TCEP, 0.005 M Bis Tris pH 7.0) mixed in a 1:1 ratio with the Well Solution (0.90 M lithium ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-D / Wavelength: 0.97923, 0.96400

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 8, 2006 / Details: Adjustable focusing mirrors in K-B geometry

Radiation

Monochromator: Si(111) Double Crystal Monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97923	1
2	0.964	1

Reflection

Resolution: 2.8→36.387 Å / Num. obs: 7690 / % possible obs: 97.4 % / Redundancy: 12.7 % / R_merge(I) obs: 0.099 / Χ²: 1.429 / Net I/σ(I): 15.064

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	Χ²	% possible all
2.8-2.9	4.6	0.197	4.527	631	1.207	82.5
2.9-3.02	6.2	0.212		739	1.123	93.1
3.02-3.15	8.5	0.197		757	1.099	99.2
3.15-3.32	11.2	0.167		769	1.215	99.4
3.32-3.53	13.9	0.141		782	1.107	100
3.53-3.8	15.5	0.109		789	1.152	100
3.8-4.18	16.3	0.089		776	1.264	100
4.18-4.79	16.3	0.087		805	1.301	100
4.79-6.03	16.2	0.094		804	1.65	100
6.03-36.387	15.2	0.076		838	2.484	99.6

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Phasing

Phasing

Method:

MAD

Phasing MAD set

Highest resolution: 2.81 Å / Lowest resolution: 36.39 Å

ID	R cullis acentric	R cullis centric	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	0	0	0	0	6798	881
ISO_2	0.876	0.902	0.672	0.549	6795	881
ANO_1	0.587	0	2.032	0	6490	0
ANO_2	0.77	0	1.282	0	6793	0

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	11.89-36.39	0	0	0	0	77	44
ISO_1	8.65-11.89	0	0	0	0	133	41
ISO_1	7.13-8.65	0	0	0	0	175	51
ISO_1	6.2-7.13	0	0	0	0	218	42
ISO_1	5.56-6.2	0	0	0	0	237	46
ISO_1	5.09-5.56	0	0	0	0	278	48
ISO_1	4.72-5.09	0	0	0	0	293	35
ISO_1	4.42-4.72	0	0	0	0	314	50
ISO_1	4.17-4.42	0	0	0	0	345	48
ISO_1	3.96-4.17	0	0	0	0	348	41
ISO_1	3.77-3.96	0	0	0	0	384	49
ISO_1	3.62-3.77	0	0	0	0	404	45
ISO_1	3.47-3.62	0	0	0	0	409	43
ISO_1	3.35-3.47	0	0	0	0	443	48
ISO_1	3.24-3.35	0	0	0	0	448	37
ISO_1	3.13-3.24	0	0	0	0	468	45
ISO_1	3.04-3.13	0	0	0	0	475	39
ISO_1	2.96-3.04	0	0	0	0	470	50
ISO_1	2.88-2.96	0	0	0	0	459	38
ISO_1	2.81-2.88	0	0	0	0	420	41
ANO_1	11.89-36.39	0.207	0	6.552	0	77	0
ANO_1	8.65-11.89	0.285	0	5.32	0	133	0
ANO_1	7.13-8.65	0.202	0	7.18	0	175	0
ANO_1	6.2-7.13	0.248	0	6.084	0	218	0
ANO_1	5.56-6.2	0.259	0	5.402	0	237	0
ANO_1	5.09-5.56	0.3	0	4.85	0	278	0
ANO_1	4.72-5.09	0.361	0	4.081	0	293	0
ANO_1	4.42-4.72	0.394	0	3.284	0	314	0
ANO_1	4.17-4.42	0.405	0	3.291	0	345	0
ANO_1	3.96-4.17	0.475	0	2.902	0	348	0
ANO_1	3.77-3.96	0.497	0	2.605	0	384	0
ANO_1	3.62-3.77	0.557	0	2.185	0	404	0
ANO_1	3.47-3.62	0.617	0	1.657	0	409	0
ANO_1	3.35-3.47	0.704	0	1.51	0	443	0
ANO_1	3.24-3.35	0.778	0	1.161	0	446	0
ANO_1	3.13-3.24	0.795	0	0.988	0	460	0
ANO_1	3.04-3.13	0.873	0	0.774	0	449	0
ANO_1	2.96-3.04	0.897	0	0.657	0	410	0
ANO_1	2.88-2.96	0.937	0	0.596	0	371	0
ANO_1	2.81-2.88	0.94	0	0.5	0	296	0
ISO_2	11.89-36.39	0.679	0.834	1.344	0.919	77	44
ISO_2	8.65-11.89	0.83	0.922	1.161	1.045	133	41
ISO_2	7.13-8.65	0.911	0.94	1.414	0.854	175	51
ISO_2	6.2-7.13	0.852	0.866	1.137	0.97	218	42
ISO_2	5.56-6.2	0.873	0.941	1.048	0.717	237	46
ISO_2	5.09-5.56	0.916	0.878	1.013	0.58	278	48
ISO_2	4.72-5.09	0.912	0.91	0.828	0.323	293	35
ISO_2	4.42-4.72	0.915	0.937	0.664	0.412	314	50
ISO_2	4.17-4.42	0.913	0.892	0.62	0.37	345	48
ISO_2	3.96-4.17	0.953	0.96	0.541	0.499	348	41
ISO_2	3.77-3.96	0.936	0.898	0.535	0.452	384	49
ISO_2	3.62-3.77	0.94	0.879	0.519	0.412	404	45
ISO_2	3.47-3.62	0.935	0.947	0.489	0.321	409	43
ISO_2	3.35-3.47	0.925	0.885	0.447	0.291	443	48
ISO_2	3.24-3.35	0.903	0.92	0.404	0.3	448	37
ISO_2	3.13-3.24	0.912	0.865	0.447	0.213	468	45
ISO_2	3.04-3.13	0.878	0.961	0.399	0.285	475	39
ISO_2	2.96-3.04	0.832	0.884	0.34	0.22	470	50
ISO_2	2.88-2.96	0.663	0.846	0.313	0.194	457	38
ISO_2	2.81-2.88	0.813	0.894	0.271	0.21	419	41
ANO_2	11.89-36.39	0.208	0	6.152	0	76	0
ANO_2	8.65-11.89	0.293	0	4.761	0	133	0
ANO_2	7.13-8.65	0.234	0	6.112	0	175	0
ANO_2	6.2-7.13	0.323	0	4.633	0	218	0
ANO_2	5.56-6.2	0.328	0	4.22	0	237	0
ANO_2	5.09-5.56	0.384	0	3.912	0	278	0
ANO_2	4.72-5.09	0.47	0	3.252	0	293	0
ANO_2	4.42-4.72	0.534	0	2.575	0	314	0
ANO_2	4.17-4.42	0.562	0	2.409	0	345	0
ANO_2	3.96-4.17	0.606	0	2.119	0	348	0
ANO_2	3.77-3.96	0.695	0	1.699	0	384	0
ANO_2	3.62-3.77	0.73	0	1.394	0	404	0
ANO_2	3.47-3.62	0.823	0	1.017	0	409	0
ANO_2	3.35-3.47	0.875	0	0.896	0	443	0
ANO_2	3.24-3.35	0.916	0	0.706	0	448	0
ANO_2	3.13-3.24	0.934	0	0.599	0	468	0
ANO_2	3.04-3.13	0.963	0	0.52	0	475	0
ANO_2	2.96-3.04	0.97	0	0.403	0	470	0
ANO_2	2.88-2.96	0.986	0	0.364	0	457	0
ANO_2	2.81-2.88	0.979	0	0.275	0	418	0

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	8.858	45.623	2.581	SE	53.8	0.82
2	37.207	11.253	0.865	SE	58.2	0.91
3	46.367	19.166	3.741	SE	48.67	0.8
4	-17.324	72.118	8.263	SE	58.58	0.86
5	45.572	59.045	5.474	SE	78.02	0.81
6	32.433	57.679	4.402	SE	79.73	0.48

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 7679

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
7.2-100	57.5	0.74	506
5.67-7.2	54.6	0.864	503
4.94-5.67	59.8	0.899	501
4.47-4.94	54.3	0.921	505
4.14-4.47	58.3	0.919	513
3.89-4.14	57.8	0.911	503
3.68-3.89	59.6	0.916	511
3.52-3.68	57.9	0.884	510
3.38-3.52	65	0.867	506
3.26-3.38	64.4	0.855	501
3.16-3.26	70.5	0.832	501
3.07-3.16	72.2	0.826	502
2.98-3.07	74.6	0.786	507
2.9-2.98	75.8	0.752	506
2.8-2.9	83.6	0.712	604

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHARP		phasing
DM	5	phasing
REFMAC	5.2.0005	refinement
PDB_EXTRACT	2	data extraction
HKL-2000		data reduction

Refinement

Method to determine structure:

MAD / Resolution: 2.806→36.387 Å / Cor.coef. F_o:F_c: 0.941 / Cor.coef. F_o:F_c free: 0.893 / WR_factor R_free: 0.257 / WR_factor R_work: 0.191 / SU B: 34.913 / SU ML: 0.3 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0 / ESU R Free: 0.389 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.255	352	4.585 %	RANDOM
R_work	0.192	-	-	-
obs	0.195	7678	97.412 %	-

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: 17.983 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.506 Å²	0.753 Å²	0 Å²
2-	-	1.506 Å²	0 Å²
3-	-	-	-2.258 Å²

Refinement step

Cycle: LAST / Resolution: 2.806→36.387 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2045	0	15	1	2061

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	2115
X-RAY DIFFRACTION	r_angle_refined_deg	1.486	1.974	2862
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.242	5	255
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.546	24.444	99
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.807	15	380
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.714	15	10
X-RAY DIFFRACTION	r_chiral_restr	0.102	0.2	310
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	1582
X-RAY DIFFRACTION	r_nbd_refined	0.235	0.2	1008
X-RAY DIFFRACTION	r_nbtor_refined	0.316	0.2	1405
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.15	0.2	64
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.235	0.2	37
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.171	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	0.46	1.5	1294
X-RAY DIFFRACTION	r_mcangle_it	0.844	2	2045
X-RAY DIFFRACTION	r_scbond_it	1.363	3	925
X-RAY DIFFRACTION	r_scangle_it	2.251	4.5	816

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	Num. reflection all	% reflection obs (%)
2.806-2.879	0.491	18	0.253	443	574	80.314
2.879-2.958	0.438	21	0.269	475	548	90.511
2.958-3.043	0.39	22	0.247	506	554	95.307
3.043-3.137	0.28	30	0.256	482	515	99.417
3.137-3.24	0.317	28	0.26	489	520	99.423
3.24-3.353	0.261	25	0.242	459	486	99.588
3.353-3.479	0.307	28	0.249	473	501	100
3.479-3.621	0.422	10	0.201	447	457	100
3.621-3.782	0.3	23	0.184	417	440	100
3.782-3.966	0.176	18	0.167	417	435	100
3.966-4.18	0.176	15	0.157	376	391	100
4.18-4.433	0.17	18	0.152	375	393	100
4.433-4.739	0.16	19	0.145	351	370	100
4.739-5.117	0.185	16	0.143	322	338	100
5.117-5.604	0.308	14	0.168	296	310	100
5.604-6.262	0.188	13	0.172	275	288	100
6.262-7.225	0.204	17	0.199	241	258	100
7.225-8.834	0.228	9	0.171	213	222	100
8.834-12.431	0.322	6	0.157	169	175	100
12.431-36.39	0.286	2	0.246	100	107	95.327

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	3.4788	0.6737	-1.4498	2.1581	0.6748	4.1076	-0.0221	-0.5065	-0.1336	-0.1433	0.1254	0.3823	0.4031	0.0794	-0.1033	0.2844	0.025	-0.0331	0.2444	0.1372	0.2829	31.5396	11.057	12.9083
2	12.9861	2.5989	-3.1747	3.5905	-2.2726	1.6492	0.2549	0.2379	0.9413	0.132	0.1781	0.8331	-1.2842	-0.6426	-0.433	0.2291	0.1812	-0.0385	0.2366	0.129	0.4262	23.9342	27.6854	13.6082
3	5.1231	0.7966	6.1788	5.1428	7.502	15.9776	-0.6936	-0.2796	0.6556	-0.2537	-0.53	1.3061	-0.3848	-1.3397	1.2237	0.3116	0.4163	-0.0281	0.8636	0.2123	0.8753	15.8918	27.1923	10.8328
4	11.7486	1.883	3.4086	5.5504	0.1768	17.1918	-0.0567	-0.9448	-0.4912	1.0573	0.2478	1.4362	0.0371	-0.4411	-0.1911	0.173	0.0706	0.1434	0.3722	0.1001	0.3657	24.2455	16.9317	23.0815
5	4.3338	2.3919	-0.483	10.2399	-1.1003	7.9791	0.0834	-0.1825	0.6124	0.4048	0.0002	0.3096	-0.4018	-0.1647	-0.0835	0.0957	0.1049	0.0378	0.2507	0.0241	0.3055	34.0156	25.6902	21.2533
6	3.7763	1.6512	-1.7145	0.809	0.2016	11.1827	-0.0518	0.2208	0.5957	-0.1227	0.051	0.9561	-0.781	-0.1334	0.0008	0.3005	0.0658	0.0076	0.1979	0.052	0.2594	40.1937	27.3444	14.7416
7	2.0511	-0.4345	-0.2296	2.4198	-0.043	5.8801	-0.0022	-0.0809	0.0713	0.2676	-0.0607	0.176	0.3512	-0.1763	0.0629	0.2166	0.0025	-0.0047	0.1638	0.0184	0.1685	43.8873	25.9706	8.8042
8	2.5331	1.7492	1.4988	6.4844	2.6102	6.9054	-0.187	0.304	-0.0732	-0.5257	0.4573	-0.0256	0.1505	0.6636	-0.2704	0.2778	0.0451	-0.0041	0.3825	0.0408	0.1202	49.841	19.8972	5.14
9	11.9685	0.344	3.3497	1.5676	-1.4793	2.5311	-0.0888	0.3456	-0.2446	-0.557	0.2271	0.41	0.5134	-0.0934	-0.1383	0.4714	0.0067	-0.0309	0.2472	0.0742	0.1646	38.5154	9.988	1.839
10	4.5941	5.3316	1.2892	9.9236	-0.0225	2.0416	0.1226	-0.3918	-0.4343	0.0097	-0.078	0.235	0.273	0.1161	-0.0446	0.3611	0.0567	-0.0628	0.2389	0.1187	0.1778	37.8848	4.6595	6.8679

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

ID	Refine TLS-ID	Auth seq-ID	Label seq-ID
1	1	4 - 48	2 - 46
2	2	49 - 61	47 - 59
3	3	62 - 90	60 - 88
4	4	91 - 107	89 - 105
5	5	108 - 144	106 - 142
6	6	145 - 160	143 - 158
7	7	161 - 181	159 - 179
8	8	182 - 214	180 - 212
9	9	215 - 237	213 - 235
10	10	238 - 257	236 - 255

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