PDB-2gzq: Phosphatidylethanolamine-binding protein from Plasmodium vivax

ID or keywords:

Entry

Database: PDB / ID: 2gzq

Title

Phosphatidylethanolamine-binding protein from Plasmodium vivax

Components

Phosphatidylethanolamine-binding protein

Keywords

LIPID BINDING PROTEIN / STRUCTURAL GENOMICS / PSI / Protein Structure Initiative / Structural Genomics of Pathogenic Protozoa Consortium / SGPP

Function / homology

Function and homology information

Phosphatidylethanolamine-binding, conserved site / Phosphatidylethanolamine-binding protein family signature. / Phosphatidylethanolamine-binding Protein / PEBP-like / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein, eukaryotic / PEBP-like superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology

Biological species

Plasmodium vivax (malaria parasite P. vivax)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD /

MAD / Resolution: 1.3 Å

Authors

Arakaki, T.L. / Merritt, E.A. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: The structure of Plasmodium vivax phosphatidylethanolamine-binding protein suggests a functional motif containing a left-handed helix
Authors: Arakaki, T. / Neely, H. / Boni, E. / Mueller, N. / Buckner, F.S. / Van Voorhis, W.C. / Lauricella, A. / DeTitta, G. / Luft, J. / Hol, W.G. / Merritt, E.A.

History

Deposition	May 11, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 23, 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	Apr 3, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

Remark 999

SEQUENCE THE SEQUENCE OF THIS PROTEIN IS NOT AVAILABLE AT UNP OR GB SEQUENCE DATABASE AT THE TIME ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

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Validation report

Summary document	2gzq_validation.pdf.gz	425.3 KB	Display	wwPDB validaton report
Full document	2gzq_full_validation.pdf.gz	428.5 KB	Display
Data in XML	2gzq_validation.xml.gz	12.9 KB	Display
Data in CIF	2gzq_validation.cif.gz	19.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gz/2gzq ftp://data.pdbj.org/pub/pdb/validation_reports/gz/2gzq	HTTPS FTP

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Related structure data

Similar structure data	3tfy-1 4lhw-5 2gf0-3 4lhw-3 4phg-d 2psw-1 5usj-2 2w2v-2 1yu9-d 3kko-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: Pviv009166AAA

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Phosphatidylethanolamine-binding protein

23.3 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)	39.309, 54.110, 94.377
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Phosphatidylethanolamine-binding protein Mass: 23298.711 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax) Gene: hPf.PFL0955c / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / References: UniProt: Q4Y719, UniProt: A5K000*PLUS
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.15 Å³/Da / Density % sol: 42.86 %
Crystal grow	Temperature: 273 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.0 ul protein 11 mg/ml 0.4 ul crystallization buffer, 8% PEG8000, 40% PEG 400, 0.04M Hepes, 3.5mM DTT, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 273K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2		1
3		1

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 8.2.2 / Wavelength: 0.9794 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 29, 2005

Radiation

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

Radiation wavelength

Wavelength: 0.9794 Å / Relative weight: 1

Reflection

Χ²: 1.03 / D res high: 1.49 Å

Redundancy (%)	ID	Av σ(I) over netI	Number	R_merge(I) obs	R_sym value	D res low (Å)	Num. obs	% possible obs
3.1	1	9.6	96464	0.04	0.04	15.372	31619	91.1
3	2	9.6	96378	0.039	0.039	15.372	31604	91
3.1	3	8.7	102515	0.041	0.041	14.848	32788	94.5

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	R_sym value	Chi squared	Redundancy
4.71	15.37	96.6	1	0.028	0.028	0.925	3.3
3.33	4.71	100	1	0.034	0.034	0.967	3.5
2.72	3.33	100	1	0.038	0.038	1.01	3.6
2.36	2.72	100	1	0.035	0.035	1.103	3.6
2.11	2.36	100	1	0.051	0.051	1.057	3.6
1.92	2.11	100	1	0.055	0.055	1.036	3.6
1.78	1.92	100	1	0.103	0.103	1.036	3.6
1.67	1.78	98.6	1	0.132	0.132	1.046	2.6
1.57	1.67	83.1	1	0.161	0.161	1.095	1.8
1.49	1.57	56.9	1	0.259	0.259	1.054	1.6
4.71	15.37	96.6	2	0.023	0.023	0.925	3.3
3.33	4.71	100	2	0.032	0.032	0.967	3.5
2.72	3.33	100	2	0.041	0.041	1.01	3.6
2.36	2.72	100	2	0.037	0.037	1.103	3.6
2.11	2.36	100	2	0.048	0.048	1.057	3.6
1.92	2.11	100	2	0.049	0.049	1.036	3.6
1.78	1.92	100	2	0.099	0.099	1.036	3.6
1.67	1.78	98.5	2	0.134	0.134	1.046	2.6
1.57	1.67	83	2	0.186	0.186	1.095	1.8
1.49	1.57	56.8	2	0.31	0.31	1.054	1.6
4.71	15.37	96.3	3	0.022	0.022	0.925	3.4
3.33	4.71	99.9	3	0.03	0.03	0.967	3.5
2.72	3.33	100	3	0.042	0.042	1.01	3.6
2.36	2.72	100	3	0.041	0.041	1.103	3.6
2.11	2.36	100	3	0.054	0.054	1.057	3.6
1.92	2.11	100	3	0.054	0.054	1.036	3.6
1.78	1.92	100	3	0.117	0.117	1.036	3.6
1.67	1.78	99.6	3	0.158	0.158	1.046	3.2
1.57	1.67	93	3	0.232	0.232	1.095	2
1.49	1.57	70.1	3	0.403	0.403	1.054	1.7

Reflection

Resolution: 1.15→50 Å / Num. obs: 69478 / % possible obs: 96.2 % / Redundancy: 3 % / R_merge(I) obs: 0.098 / Χ²: 1.03 / Net I/σ(I): 14.1

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.15-1.19	2	0.233	6040	1.054	1	84.6
1.19-1.24	2.3	0.244	6721	1.095	1	94.7
1.24-1.3	2.8	0.221	7063	1.046	1	99.3
1.3-1.36	3.1	0.196	7129	1.036	1	99.5
1.36-1.45	3.2	0.162	7107	1.036	1	99.4
1.45-1.56	3.2	0.137	7128	1.057	1	99.3
1.56-1.72	3.3	0.122	7142	1.103	1	99.1
1.72-1.97	3.2	0.112	7194	1.01	1	99.2
1.97-2.48	3.2	0.096	7208	0.967	1	98.7
2.48-50	3.1	0.086	6746	0.925	1	88.8

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Phasing

Phasing

Method:

MAD

Phasing set

ID
1
2
3

Phasing MAD set

Clust-ID	Expt-ID	Set-ID	Wavelength (Å)	F double prime refined	F prime refined
1	3 wavelength	1	0.9795	2.62	-9.38
1	3 wavelength	2	0.9793	4.92	-8.81
1	3 wavelength	3	0.9537	2.82	-3.02

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy
1	Se	18.788	0.24	0.219	0.19	0.743
2	Se	28.1	0.464	0.337	0.106	0.72
3	Se	33.97	0.644	0.28	0.056	0.783
4	Se	27.329	0.225	0.947	0.15	0.691
5	Se	21.336	0.235	0.074	0.129	0.486

Phasing dm

FOM : 0.67 / FOM acentric: 0.67 / FOM centric: 0.68 / Reflection: 31886 / Reflection acentric: 28414 / Reflection centric: 3472

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
4.3-15.257	0.97	0.98	0.94	1582	1159	423
2.7-4.3	0.95	0.96	0.92	4708	3968	740
2.1-2.7	0.9	0.91	0.83	5792	5122	670
1.9-2.1	0.78	0.79	0.65	5732	5162	570
1.6-1.9	0.49	0.5	0.4	9941	9117	824
1.5-1.6	0.22	0.22	0.18	4131	3886	245

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SOLVE	2.1	phasing
RESOLVE	2.1	phasing
REFMAC		refinement
PDB_EXTRACT	2	data extraction

Refinement

Method to determine structure:

SAD
Starting model: MAD structure

Resolution: 1.3→20 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.954 / SU B: 1.378 / SU ML: 0.03 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18	2269	5.1 %	random
R_work	0.161	-	-	-
all	0.161	-	-	-
obs	-	44581	88.43 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 7.04 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.81 Å²	0 Å²	0 Å²
2-	-	0.28 Å²	0 Å²
3-	-	-	-1.09 Å²

Refinement step

Cycle: LAST / Resolution: 1.3→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1531	0	0	282	1813

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	1712
X-RAY DIFFRACTION	r_bond_other_d	0	0.02	1585
X-RAY DIFFRACTION	r_angle_refined_deg	1.462	1.978	2349
X-RAY DIFFRACTION	r_angle_other_deg	0.725	3	3739
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.286	5	236
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.83	23.553	76
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.881	15	323
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.367	15	13
X-RAY DIFFRACTION	r_chiral_restr	0.108	0.2	252
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	1924
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	343
X-RAY DIFFRACTION	r_nbd_refined	0.267	0.2	319
X-RAY DIFFRACTION	r_nbd_other	0.242	0.2	1667
X-RAY DIFFRACTION	r_nbtor_refined	0.184	0.2	845
X-RAY DIFFRACTION	r_nbtor_other	0.093	0.2	961
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.188	0.2	160
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.433	0.2	16
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.348	0.2	71
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.204	0.2	37
X-RAY DIFFRACTION	r_mcbond_it	2.797	2	1227
X-RAY DIFFRACTION	r_mcbond_other	0.665	2	411
X-RAY DIFFRACTION	r_mcangle_it	3.006	3	1720
X-RAY DIFFRACTION	r_scbond_it	4.621	2	761
X-RAY DIFFRACTION	r_scangle_it	5.881	3	609

LS refinement shell

Resolution: 1.3→1.334 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.189	159	-
R_work	0.176	2983	-
obs	-	3142	86.25 %

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	13.1074	-6.5507	-1.5297	7.9735	4.1172	2.5703	-0.4246	-0.4216	0.1672	0.5307	0.3071	0.0385	0.02	-0.2454	0.1174	0.0798	0.053	-0.007	0.0357	0.0011	0.0678	17.33	62.755	29.256
2	3.1558	-0.3298	-0.7735	4.8776	-2.2817	4.1263	-0.0508	-0.0713	0.0814	0.1912	-0.0007	-0.1226	-0.0023	0.0846	0.0515	0.0358	0.0051	-0.0228	0.0437	0.0078	0.135	23.584	58.803	23.011
3	8.4303	4.0932	1.3861	3.4007	-0.0583	0.6063	0.0674	-0.3039	-0.0256	0.2081	-0.0166	-0.1303	-0.0955	-0.0027	-0.0507	0.033	0.0152	-0.0127	0.0249	-0.0088	0.1313	15.148	68.739	23.399
4	5.7277	1.4475	1.1684	12.8172	1.2821	3.2993	0.0404	-0.1248	-0.4216	0.1875	-0.0443	0.4027	0.2268	-0.2348	0.0039	0.0222	-0.0244	0.0141	0.051	0.0391	0.1874	1.44	57.251	19.449
5	10.2925	6.1021	1.7097	17.2062	-0.1625	3.677	-0.1473	-0.1376	-0.0404	0.7569	0.2187	0.5029	0.0617	-0.086	-0.0715	0.0905	0.0169	0.0421	0.0602	0.0543	0.1365	9.249	53.472	23.779
6	1.5959	0.0476	0.089	2.5062	0.8125	1.9264	-0.0025	-0.0186	-0.1651	0.0244	0.0377	-0.0042	0.1177	-0.1758	-0.0352	0.0049	-0.0152	0.0077	0.0502	0.0237	0.1693	2.159	59.533	15.723
7	1.1242	-0.0964	-0.183	4.2324	0.7671	3.5756	-0.0282	-0.0615	0.1734	0.1137	-0.0157	0.1335	-0.2834	-0.0634	0.0439	0.0461	0.0035	-0.0177	0.0635	-0.0035	0.1734	9.992	77.436	15.977
8	2.8028	-2.5929	0.786	4.8884	-0.7506	1.3221	0.0327	0.0063	-0.145	-0.0763	-0.0157	-0.0205	0.1065	0.0213	-0.017	0.0108	0.0014	-0.0008	0.0133	0.0058	0.0968	17.471	54.142	11.363
9	8.6871	-5.9008	7.5038	34.1544	-30.553	28.9044	0.277	-0.0456	-0.555	-1.3073	-0.0947	-0.1534	1.4012	0.4038	-0.1823	0.1076	0.068	0.0096	0.0475	0.0158	0.1986	24.898	46.746	10.159
10	2.5556	-1.1712	0.2759	3.1958	0.0659	0.7811	-0.0346	-0.001	-0.0569	-0.0274	-0.0291	0.0349	0.0395	-0.0158	0.0637	0.0136	-0.0014	-0.0029	0.0468	0.0174	0.1026	13.167	62.14	8.45
11	5.1008	2.4833	0.7797	8.4869	4.6831	3.8196	0.1279	-0.2526	0.325	0.5206	0.0522	0.0975	0.1767	-0.0938	-0.1801	0.0478	0.019	-0.0141	0.0592	0.0203	0.186	1.263	72.371	16.149
12	2.477	0.7277	1.3184	0.8323	-0.6152	2.3269	0.0421	-0.154	0.0102	0.0826	-0.1395	0.0249	-0.0596	0.0667	0.0974	-0.0004	0.01	0.0063	0.0794	0.024	0.167	0.112	70.581	8.361
13	2.4464	0.1776	-0.0143	3.6749	-1.1195	2.6784	0.0108	0.0337	-0.1127	-0.1684	-0.0446	0.0299	0.1486	0.0217	0.0338	0.0116	0.0051	-0.0082	0.0574	0.0032	0.1197	8.161	62.625	3.917
14	25.6779	-26.9434	5.9689	33.1094	-8.4084	6.366	0.7962	0.4762	-0.3789	-1.1989	-0.3726	0.4717	0.7161	-0.1696	-0.4236	0.1246	-0.0182	-0.0624	0.014	0.0093	0.1915	12.804	44.716	9.205
15	1.3007	-0.7067	0.3495	3.7659	-0.3186	0.4113	0.0281	-0.0188	-0.1028	-0.0581	-0.0261	0.0489	0.0809	-0.0149	-0.0019	0.0129	0.0006	0.0001	0.0123	0.0071	0.0876	15.037	57.663	15.793
16	6.8971	-1.4654	1.8481	6.501	0.2889	20.3015	-0.0703	0.2868	0.3306	-0.1848	-0.0867	-0.1674	-1.114	0.1589	0.157	0.069	-0.0099	-0.0132	0.0218	0.0262	0.1554	14.193	80.49	8.193
17	3.625	-1.4771	2.113	1.9381	-0.247	2.0656	0.2896	0.2574	0.0665	-0.0378	-0.1905	-0.0511	-0.07	0.1024	-0.0991	0.0066	0.0077	-0.0088	0.0641	0.0514	0.1617	16.703	72.934	1.941
18	1.5343	-0.3701	0.2364	0.6353	-0.6846	0.7577	0.0258	0.2145	-0.0335	-0.0754	-0.0812	-0.0174	0.0471	0.0512	0.0554	0.0174	0.0125	0.0005	0.0678	0.0057	0.1121	15.165	61.776	-2.094
19	3.2532	-0.1612	-1.6372	2.9063	-0.0403	2.9095	0.0004	0.0456	0.0627	0.0484	-0.0518	-0.1486	-0.0179	0.0422	0.0514	0.0123	-0.0049	0.0042	0.0733	0.0278	0.1512	24.141	66.313	8.076
20	1.5149	0.323	-0.5373	3.4482	-1.9792	1.5305	-0.109	0.0824	-0.1086	-0.2482	0.1068	0.0985	0.2609	-0.0111	0.0022	0.0825	0.0013	0.0004	0.0903	-0.0009	0.1462	14.651	59.363	16.772

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	2 - 8	10 - 16
2	2	9 - 23	17 - 31
3	3	24 - 31	32 - 39
4	4	32 - 41	40 - 49
5	5	42 - 47	50 - 55
6	6	48 - 62	56 - 70
7	7	63 - 73	71 - 81
8	8	74 - 83	82 - 91
9	9	84 - 88	92 - 96
10	10	89 - 99	97 - 107
11	11	100 - 105	108 - 113
12	12	106 - 112	114 - 120
13	13	113 - 120	121 - 128
14	14	121 - 126	129 - 134
15	15	127 - 138	135 - 146
16	16	139 - 143	147 - 151
17	17	144 - 151	152 - 159
18	18	152 - 165	160 - 173
19	19	166 - 176	174 - 184
20	20	177 - 192	185 - 200

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