PDB-1xfi: X-ray structure of gene product from Arabidopsis thaliana At2g17340

ID or keywords:

Entry

Database: PDB / ID: 1xfi

Title

X-ray structure of gene product from Arabidopsis thaliana At2g17340

Components

unknown protein

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PROTEIN STRUCTURE INITIATIVE / PSI / CESG / AT2G17340 / Center for Eukaryotic Structural Genomics

Function / homology

Function and homology information

pantothenate kinase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / coenzyme A biosynthetic process / hydrolase activity / mitochondrion / ATP binding / metal ion binding / cytosol
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD /

SAD / Resolution: 1.7 Å

Authors

Wesenberg, G.E. / Smith, D.W. / Phillips Jr., G.N. / Bitto, E. / Bingman, C.A. / Allard, S.T.M. / Center for Eukaryotic Structural Genomics (CESG)

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: The structure at 1.7 A resolution of the protein product of the At2g17340 gene from Arabidopsis thaliana.
Authors: Bitto, E. / Bingman, C.A. / Allard, S.T. / Wesenberg, G.E. / Phillips, G.N.

History

Deposition	Sep 14, 2004	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 28, 2004	Provider: repository / Type: Initial release
Revision 1.1	Feb 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Oct 11, 2017	Group: Refinement description / Category: software
Revision 1.4	Feb 14, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	1xfi.cif.gz	91.8 KB	Display	PDBx/mmCIF format
PDB format	pdb1xfi.ent.gz	67.2 KB	Display	PDB format
PDBx/mmJSON format	1xfi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	1xfi_validation.pdf.gz	427.2 KB	Display	wwPDB validaton report
Full document	1xfi_full_validation.pdf.gz	427.8 KB	Display
Data in XML	1xfi_validation.xml.gz	17.7 KB	Display
Data in CIF	1xfi_validation.cif.gz	27.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xf/1xfi ftp://data.pdbj.org/pub/pdb/validation_reports/xf/1xfi	HTTPS FTP

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Related structure data

Similar structure data	2qd1-3 1civ-d 2q40-d 4gjb-1 5ybh-1 2a3e-2 2zc5-1 2y0a-d 2bi0-d 5wcx-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: GO.8195

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: unknown protein

hetero molecules

40.9 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)	40.174, 43.280, 52.644
Angle α, β, γ (deg.)	74.57, 74.60, 84.04
Int Tables number	1
Space group name H-M	P1

#1: Protein	unknown protein Mass: 40856.418 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At2g17340 / Plasmid details: pQE derivative / Plasmid: pVP13-GW / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta, B834-DE3 pLacI+RARE / References: UniProt: Q949P3
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal	Density Matthews: 2.08 Å³/Da / Density % sol: 40.89 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 10 MG/ML PROTEIN, 0.100M HEPPS, 0.020M MAGNESIUM CHLORIDE, 22 PERCENT PEG 8000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	110	1
2	100	1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	APS	19-BM	1	0.96411
SYNCHROTRON	APS	14-ID-B	2	0.9793, 0.9789, 0.9637

Detector

Type	ID	Detector	Date	Details
APS-1	1	CCD	Aug 1, 2004	Rosenbaum-Rock vertical focusing mirror
MAR CCD 165 mm	2	CCD	Aug 9, 2004	Bent cylindrical Si-mirror (Rh coating)

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	Rosenbaum-Rock double-crystal monochromator: water cooled, sagitally focusing 2nd crystal	SINGLE WAVELENGTH	M	x-ray	1
2	Diamond (111) double-crystal monochromator	MAD	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.96411	1
2	0.9793	1
3	0.9789	1
4	0.9637	1

Reflection

Resolution: 1.7→50 Å / Num. obs: 35346 / % possible obs: 97 % / Redundancy: 4.3 % / R_merge(I) obs: 0.039 / Χ²: 1.055 / Net I/σ(I): 23.3

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Χ²	% possible all
1.7-1.73	3.9	0.277	5.23	1638	1.107	89.5
1.73-1.76	3.9	0.258	5.23	1692	1.045	93.3
1.76-1.79	3.9	0.23	5.23	1715	1.076	95.4
1.79-1.83	3.9	0.196	5.23	1772	1.052	96.1
1.83-1.87	3.9	0.16	5.23	1771	1.04	96.4
1.87-1.91	3.9	0.123	5.23	1770	0.986	96.9
1.91-1.96	3.9	0.101	5.23	1733	0.978	97.1
1.96-2.02	3.9	0.082	5.23	1791	0.968	97.2
2.02-2.07	3.9	0.072	5.23	1775	1.049	97.2
2.07-2.14	3.9	0.059	5.23	1767	0.989	97.2
2.14-2.22	3.9	0.051	5.23	1773	1.098	97.6
2.22-2.31	3.9	0.044	5.23	1776	1.106	97.7
2.31-2.41	3.9	0.042	5.23	1789	1.177	98
2.41-2.54	3.9	0.038	5.23	1797	1.244	98
2.54-2.7	3.9	0.034	5.23	1810	1.254	98.4
2.7-2.91	3.9	0.032	5.23	1766	1.03	98.5
2.91-3.2	3.9	0.029	5.23	1788	1.035	98.8
3.2-3.66	3.9	0.029	5.23	1836	1.075	99
3.66-4.61	3.9	0.031	5.23	1780	0.88	99.2
4.61-50	3.9	0.037	5.23	1807	0.91	98.6

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Phasing

Phasing

Method:

SAD

Phasing set

ID
1
2
3

Phasing MAD

D res high: 2.49 Å / D res low: 24.64 Å / FOM : 0.708 / FOM acentric: 0.708 / FOM centric: 0 / Reflection: 22348

Phasing MAD set

R cullis centric: 0 / R kraut centric: 0 / Highest resolution: 2.49 Å / Lowest resolution: 24.64 Å / FOM centric: 0 / Loc centric: 0 / Power centric: 0

ID	R cullis	R cullis acentric	R kraut	R kraut acentric	FOM	FOM acentric	Loc	Loc acentric	Power (kW)	Power acentric
f_peak	0.962	0.962	0.024	0.024	0.126	0.126	6.948	6.948	0.576	0.576
f_peak_FRIED	0.658	0.658	0.023	0.023	0.37	0.37	7.651	7.651	1.732	1.732
f_edge	0.594	0.594	0.014	0.014	0.388	0.388	4.974	4.974	1.971	1.971
f_edge_FRIED	0.539	0.539	0.014	0.014	0.424	0.424	5.122	5.122	2.301	2.301
f_hrem_FRIED	0.631	0.631	0.014	0.014	0.333	0.333	4.76	4.76	1.806	1.806

Phasing MAD set

Clust-ID	Expt-ID	Set-ID	Wavelength (Å)	Atom type	F double prime refined	F prime refined
1	2	1	0.9793	SE	7.66	-3.94
1	2	2	0.9789	SE	2.75	-8.59
1	2	3	0.9637	SE	3.36	-2

Phasing MAD set shell

R cullis centric: 0 / R kraut centric: 0 / FOM centric: 0 / Loc centric: 0 / Power centric: 0

ID	Resolution (Å)	R cullis	R cullis acentric	R kraut	R kraut acentric	FOM	FOM acentric	Loc	Loc acentric	Power (kW)	Power acentric
f_peak	4.97-24.64	0.879	0.879	0.021	0.021	0.176	0.176	7.834	7.834	0.87	0.87
f_peak	3.95-4.97	0.957	0.957	0.018	0.018	0.145	0.145	7.871	7.871	0.65	0.65
f_peak	3.45-3.95	0.983	0.983	0.02	0.02	0.137	0.137	7.677	7.677	0.552	0.552
f_peak	3.14-3.45	0.991	0.991	0.022	0.022	0.125	0.125	6.97	6.97	0.493	0.493
f_peak	2.91-3.14	1.002	1.002	0.028	0.028	0.114	0.114	6.834	6.834	0.443	0.443
f_peak	2.74-2.91	0.986	0.986	0.03	0.03	0.111	0.111	6.336	6.336	0.434	0.434
f_peak	2.6-2.74	0.98	0.98	0.033	0.033	0.104	0.104	6.068	6.068	0.409	0.409
f_peak	2.49-2.6	0.955	0.955	0.037	0.037	0.098	0.098	5.927	5.927	0.378	0.378
f_peak_FRIED	4.97-24.64	0.569	0.569	0.023	0.023	0.396	0.396	9.132	9.132	2.156	2.156
f_peak_FRIED	3.95-4.97	0.651	0.651	0.019	0.019	0.367	0.367	9.065	9.065	1.778	1.778
f_peak_FRIED	3.45-3.95	0.692	0.692	0.02	0.02	0.37	0.37	8.696	8.696	1.645	1.645
f_peak_FRIED	3.14-3.45	0.679	0.679	0.021	0.021	0.377	0.377	7.557	7.557	1.618	1.618
f_peak_FRIED	2.91-3.14	0.706	0.706	0.027	0.027	0.36	0.36	7.444	7.444	1.535	1.535
f_peak_FRIED	2.74-2.91	0.683	0.683	0.028	0.028	0.373	0.373	6.789	6.789	1.592	1.592
f_peak_FRIED	2.6-2.74	0.691	0.691	0.03	0.03	0.36	0.36	6.353	6.353	1.595	1.595
f_peak_FRIED	2.49-2.6	0.686	0.686	0.032	0.032	0.355	0.355	6.109	6.109	1.555	1.555
f_edge	4.97-24.64	0.508	0.508	0.013	0.013	0.419	0.419	5.578	5.578	2.432	2.432
f_edge	3.95-4.97	0.562	0.562	0.01	0.01	0.412	0.412	5.59	5.59	2.061	2.061
f_edge	3.45-3.95	0.585	0.585	0.011	0.011	0.417	0.417	5.285	5.285	1.979	1.979
f_edge	3.14-3.45	0.621	0.621	0.014	0.014	0.387	0.387	5.082	5.082	1.792	1.792
f_edge	2.91-3.14	0.615	0.615	0.016	0.016	0.391	0.391	4.678	4.678	1.867	1.867
f_edge	2.74-2.91	0.637	0.637	0.018	0.018	0.38	0.38	4.522	4.522	1.847	1.847
f_edge	2.6-2.74	0.674	0.674	0.021	0.021	0.354	0.354	4.55	4.55	1.742	1.742
f_edge	2.49-2.6	0.692	0.692	0.022	0.022	0.338	0.338	4.464	4.464	1.685	1.685
f_edge_FRIED	4.97-24.64	0.455	0.455	0.013	0.013	0.454	0.454	5.787	5.787	2.843	2.843
f_edge_FRIED	3.95-4.97	0.508	0.508	0.01	0.01	0.447	0.447	5.709	5.709	2.431	2.431
f_edge_FRIED	3.45-3.95	0.526	0.526	0.011	0.011	0.453	0.453	5.369	5.369	2.346	2.346
f_edge_FRIED	3.14-3.45	0.567	0.567	0.014	0.014	0.425	0.425	5.235	5.235	2.086	2.086
f_edge_FRIED	2.91-3.14	0.569	0.569	0.017	0.017	0.423	0.423	4.893	4.893	2.134	2.134
f_edge_FRIED	2.74-2.91	0.581	0.581	0.018	0.018	0.413	0.413	4.674	4.674	2.134	2.134
f_edge_FRIED	2.6-2.74	0.612	0.612	0.021	0.021	0.39	0.39	4.641	4.641	2.036	2.036
f_edge_FRIED	2.49-2.6	0.634	0.634	0.024	0.024	0.378	0.378	4.64	4.64	1.934	1.934
f_hrem_FRIED	4.97-24.64	0.563	0.563	0.013	0.013	0.349	0.349	5.751	5.751	2.107	2.107
f_hrem_FRIED	3.95-4.97	0.601	0.601	0.01	0.01	0.338	0.338	5.271	5.271	1.928	1.928
f_hrem_FRIED	3.45-3.95	0.609	0.609	0.01	0.01	0.36	0.36	4.771	4.771	1.93	1.93
f_hrem_FRIED	3.14-3.45	0.619	0.619	0.012	0.012	0.351	0.351	4.42	4.42	1.8	1.8
f_hrem_FRIED	2.91-3.14	0.669	0.669	0.015	0.015	0.335	0.335	4.512	4.512	1.673	1.673
f_hrem_FRIED	2.74-2.91	0.679	0.679	0.018	0.018	0.327	0.327	4.458	4.458	1.62	1.62
f_hrem_FRIED	2.6-2.74	0.704	0.704	0.021	0.021	0.307	0.307	4.406	4.406	1.555	1.555
f_hrem_FRIED	2.49-2.6	0.729	0.729	0.022	0.022	0.294	0.294	4.513	4.513	1.432	1.432

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	32.0686	51.6522	37.5716	SE	14.5826	1
2	36.0203	49.5443	45.1732	SE	15.199	1
3	41.2188	16.5846	35.7758	SE	49.0165	1
4	49.753	45.2291	33.687	SE	45.5464	1
5	22.2406	42.8197	47.7376	SE	73.4848	1

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	Reflection
4.97-24.64	0.7362	0.7362	2728
3.95-4.97	0.7265	0.7265	2847
3.45-3.95	0.7481	0.7481	2897
3.14-3.45	0.719	0.719	2847
2.91-3.14	0.703	0.703	2859
2.74-2.91	0.7057	0.7057	2843
2.6-2.74	0.6715	0.6715	2821
2.49-2.6	0.6507	0.6507	2506

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
CNS		phasing
REFMAC	refmac_5.2.0005	refinement
PDB_EXTRACT	1	data extraction
HKL-2000		data reduction
HKL-2000		data scaling
ARP/wARP		model building

Refinement

Method to determine structure:

MAD / Resolution: 1.7→49.386 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.945 / WR_factor R_free: 0.24 / WR_factor R_work: 0.179 / SU B: 2.801 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.117 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2213	1773	5.016 %	RANDOM
R_work	0.1689	-	-	-
all	0.172	-	-	-
obs	0.17156	35346	96.672 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 21.982 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.003 Å²	-0.961 Å²	-1.107 Å²
2-	-	-1.049 Å²	1.297 Å²
3-	-	-	0.143 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→49.386 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2734	0	2	357	3093

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.022	2788
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2594
X-RAY DIFFRACTION	r_angle_refined_deg	1.642	1.981	3771
X-RAY DIFFRACTION	r_angle_other_deg	0.88	3	6066
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.623	5	340
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.63	24.923	130
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.51	15	507
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.869	15	18
X-RAY DIFFRACTION	r_chiral_restr	0.106	0.2	431
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	3044
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	530
X-RAY DIFFRACTION	r_nbd_refined	0.222	0.2	591
X-RAY DIFFRACTION	r_nbd_other	0.183	0.2	2696
X-RAY DIFFRACTION	r_nbtor_refined	0.183	0.2	1381
X-RAY DIFFRACTION	r_nbtor_other	0.087	0.2	1585
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.195	0.2	234
X-RAY DIFFRACTION	r_metal_ion_refined	0.032	0.2	2
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.153	0.2	8
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.185	0.2	47
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.189	0.2	24
X-RAY DIFFRACTION	r_mcbond_it	1.979	2	2233
X-RAY DIFFRACTION	r_mcbond_other	0.324	2	688
X-RAY DIFFRACTION	r_mcangle_it	2.46	4	2803
X-RAY DIFFRACTION	r_mcangle_other	1.18	4	2384
X-RAY DIFFRACTION	r_scbond_it	4.174	6	1209
X-RAY DIFFRACTION	r_scbond_other	1.448	6	2280
X-RAY DIFFRACTION	r_scangle_it	5.736	8	968
X-RAY DIFFRACTION	r_scangle_other	2.402	8	3682

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 (%)
1.695-1.739	0.306	118	0.252	2225	2719	86.171
1.739-1.787	0.315	115	0.242	2363	2617	94.689
1.787-1.838	0.281	102	0.232	2364	2561	96.291
1.838-1.895	0.306	109	0.213	2324	2520	96.548
1.895-1.957	0.286	116	0.202	2186	2375	96.926
1.957-2.026	0.264	123	0.188	2163	2348	97.359
2.026-2.102	0.245	111	0.196	2080	2257	97.076
2.102-2.188	0.239	118	0.179	1994	2168	97.417
2.188-2.285	0.261	90	0.167	1928	2064	97.771
2.285-2.396	0.226	92	0.17	1872	2005	97.955
2.396-2.525	0.223	99	0.164	1739	1876	97.974
2.525-2.678	0.22	109	0.167	1654	1791	98.437
2.678-2.862	0.216	72	0.17	1579	1675	98.567
2.862-3.091	0.248	89	0.162	1478	1587	98.74
3.091-3.384	0.231	84	0.154	1305	1406	98.791
3.384-3.781	0.162	67	0.148	1217	1297	98.998
3.781-4.362	0.148	58	0.134	1096	1162	99.312
4.362-5.332	0.158	45	0.138	911	962	99.376
5.332-7.497	0.236	42	0.182	702	747	99.598
7.497-49.386	0.195	14	0.163	393	426	95.54

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News

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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

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