PDB-2uuv: alkyldihydroxyacetonephosphate synthase in P1

ID or keywords:

Entry

Database: PDB / ID: 2uuv

Title

alkyldihydroxyacetonephosphate synthase in P1

Components

ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE

Alkylglycerone phosphate synthase

Keywords

TRANSFERASE / RHIZOMELIC CHONDRODYSPLASIA PUNCTATA / BIOSYNTHESIS OF PHOSPHOLIPIDS /

FLAVOPROTEIN /

LIPID SYNTHESIS / PEROXISOMAL DISORDER / FAD / FLAVIN /

PEROXISOME / PLASMALOGENS

Function / homology

Function and homology information

alcohol binding /

alkylglycerone-phosphate synthase /

alkylglycerone-phosphate synthase activity / ether lipid biosynthetic process / FAD binding /

peroxisome /

flavin adenine dinucleotide binding / identical protein binding
Similarity search - Function

Biological species

DICTYOSTELIUM DISCOIDEUM (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.99 Å

Authors

Razeto, A. / Mattiroli, F. / Carpanelli, E. / Aliverti, A. / Pandini, V. / Coda, A. / Mattevi, A.

Citation

Journal: Structure / Year: 2007
Title: The Crucial Step in Ether Phospholipid Biosynthesis: Structural Basis of a Noncanonical Reaction Associated with a Peroxisomal Disorder.
Authors: Razeto, A. / Mattiroli, F. / Carpanelli, E. / Aliverti, A. / Pandini, V. / Coda, A. / Mattevi, A.

History

Deposition	Mar 7, 2007	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 26, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2uuv.cif.gz	441.4 KB	Display	PDBx/mmCIF format
PDB format	pdb2uuv.ent.gz	373.4 KB	Display	PDB format
PDBx/mmJSON format	2uuv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uu/2uuv ftp://data.pdbj.org/pub/pdb/validation_reports/uu/2uuv	HTTPS FTP

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Related structure data

Related structure data	2uuuC C: citing same article (ref.)
Similar structure data	2uuu-1 4bby-2 5i17-d 4lz7-d 2uuu-2 3il1-d 3t93-d 3d45-d 3t9u-d 4x2d-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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
Related items in Molecule of the Month	#117 - Sep 2009 Xanthine Oxidoreductase similarity (4)

Deposited unit

A: ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE

B: ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE

C: ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE

D: ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE

hetero molecules

268 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE

B: ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE

hetero molecules

defined by author&software
134 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE

D: ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE

hetero molecules

defined by author&software
134 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	77.800, 98.000, 107.000
Angle α, β, γ (deg.)	114.00, 93.00, 103.00
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.444, -0.807, 0.39), (-0.813, -0.546, -0.203), (0.377, -0.227, -0.898)	36.42632, 104.92245, 83.61928
2	given	(0.28262, -0.87511, 0.39283), (0.40034, 0.26455, 0.87735), (-0.8717, 0.40522, 0.27557)	75.39948, 57.13317, -11.05769
3	given	(-0.78132, -0.46603, -0.41516), (0.18214, 0.46598, -0.86584), (0.59697, -0.75211, -0.2792)	21.53529, 15.7892, 109.62514

#1: Protein	ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE / Alkylglycerone phosphate synthase / ALKYL-DHAP SYNTHASE / ALKYLGLYCERONE-PHOSPHATE SYNTHASE Mass: 66104.734 Da / Num. of mol.: 4 / Fragment: RESIDUES 9-587 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DICTYOSTELIUM DISCOIDEUM (eukaryote) / Strain: KASSX-3 Description: ACADEMIA DNA SEQUENCING CENTER IN COLLABORATION WITH DICTYOSTELIUM CDNA PROJECT Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYS References: UniProt: O96759, alkylglycerone-phosphate synthase
#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#3: Chemical	ChemComp-PL3 / HEXADECAN-1-OL / Cetyl alcohol Mass: 242.441 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₆H₃₄O
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1134 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	THE SEQUENCE GIVEN CORRESPONDS TO THE CONSTRUCT (9-587) WITH THE ADDITIONAL AA AT THE N-TERM GAMGS ...THE SEQUENCE GIVEN CORRESPONDS TO THE CONSTRUCT (9-587) WITH THE ADDITIONAL AA AT THE N-TERM GAMGS (COMING FROM THE VECTOR)

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.85 Å³/Da / Density % sol: 56.53 %
Crystal grow	Details: 12% PEG4K, 200MM LI2SO4, 100MM TRISCL PH=8.5

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Data collection

Diffraction	Mean temperature: 273 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
Detector	Type: ADSC CCD / Detector: CCD / Date: Jun 27, 2006
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.934 Å / Relative weight: 1
Reflection	Resolution: 2→48.4 Å / Num. obs: 176351 / % possible obs: 95.3 % / Redundancy: 4.6 % / R_merge(I) obs: 0.08 / Net I/σ(I): 12.4
Reflection shell	Resolution: 2→2.1 Å / Redundancy: 3.9 % / R_merge(I) obs: 0.4 / Mean I/σ(I) obs: 3.4 / % possible all: 89

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Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA		data scaling
SHELXD		phasing
SHELXE		phasing
REFMAC	5.2.0019	refinement

Refinement

Method to determine structure:

SAD / Resolution: 1.99→19.98 Å / Cor.coef. F_o:F_c: 0.93 / Cor.coef. F_o:F_c free: 0.9 / SU B: 10.583 / SU ML: 0.165 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.179
Stereochemistry target values: MAXIMUM LIKELIHOODWITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.264	8878	5 %	RANDOM
R_work	0.226	-	-	-
obs	0.228	167473	92.7 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 29.95 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.14 Å²	-0.2 Å²	0.03 Å²
2-	-	-0.12 Å²	-0.32 Å²
3-	-	-	-0.37 Å²

Refinement step

Cycle: LAST / Resolution: 1.99→19.98 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16529	0	263	1134	17926

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.022	17252
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.683	1.967	23389
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.233	5	2051
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.845	23.622	751
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.077	15	2949
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.486	15	95
X-RAY DIFFRACTION	r_chiral_restr	0.128	0.2	2572
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	12806
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.223	0.2	8445
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.311	0.2	11651
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.179	0.2	1177
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.206	0.2	71
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.14	0.2	19
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.026	1.5	10540
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.654	2	16727
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.592	3	7896
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	4.146	4.5	6657
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.99→2.04 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.319	506	-
R_work	0.3	9330	-
obs	-	-	70.46 %

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	2.8446	0.3266	-0.0545	2.0526	0.0518	1.287	0.1208	0.1868	-0.1135	-0.4495	0.067	0.4001	0.1995	-0.1882	-0.1877	0.0311	0.0417	-0.1197	-0.1224	-0.0172	-0.0363	-4.703	34.638	5.257
2	0.4315	-0.2883	0.3345	1.1519	-0.1067	0.9887	0.0512	0.0196	-0.0931	-0.0797	-0.0414	-0.0451	0.1485	0.1453	-0.0098	-0.0641	0.079	-0.0089	-0.0538	0.0199	-0.0131	15.831	25.413	30.243
3	0.9272	-0.4325	0.0302	0.896	0.0836	0.5827	-0.0048	-0.0507	0.0467	0.0118	-0.0001	0.0198	-0.0125	0.0037	0.0049	-0.0925	0.0315	-0.0113	-0.0683	0.0279	-0.0219	4.214	44.275	38.881
4	0.7994	-0.3719	0.1126	0.9368	0.543	0.9837	-0.0547	0.0497	0.0487	-0.2138	0.0666	0.0656	-0.0991	0.0506	-0.012	-0.0056	0.0014	-0.055	-0.0992	0.0355	-0.0786	-1.408	55.526	13.42
5	1.1964	0.4868	-0.0388	2.3417	-0.6151	1.2233	0.0756	-0.0168	0.3836	0.206	-0.0395	0.189	0.0183	-0.0122	-0.036	-0.0664	-0.0583	0.0176	-0.0719	-0.045	-0.025	8.696	88.982	68.358
6	1.0493	-0.0237	-0.21	1.0547	0.5625	1.0407	-0.0191	-0.1349	0.0203	0.0669	0.0948	-0.3029	0.016	0.2271	-0.0758	-0.1351	0.0068	-0.0353	0.0238	-0.0118	0.0576	34.8	72.032	56.665
7	1.1318	-0.4707	0.2713	1.0349	0.11	0.8687	0.0369	0.0247	-0.0561	-0.0933	-0.0157	-0.0319	-0.025	0.0227	-0.0212	-0.0944	-0.0037	0.015	-0.0594	0.0032	-0.0111	17.763	69.293	40.172
8	0.6941	0.0302	0.7546	1.1379	0.6723	1.6422	0.054	-0.0419	0.0958	0.1988	-0.2151	0.2175	0.0922	-0.1605	0.161	-0.116	-0.0402	0.0716	-0.0511	-0.0582	0.0005	-3.745	73.26	58.557
9	1.6332	0.4696	1.1784	5.6421	-2.5626	3.9916	0.2119	-0.3758	0.2361	0.9035	0.1111	0.091	-1.3365	-0.1874	-0.3229	0.5927	-0.023	0.2239	-0.0363	-0.0854	-0.1632	-37.629	98.756	24.331
10	0.3576	-0.1337	-0.7963	0.6906	0.7989	2.6808	-0.0067	-0.017	-0.0694	0.2468	-0.0755	0.0785	0.3577	-0.3652	0.0821	0.056	-0.0993	0.058	-0.0198	0.0126	-0.1069	-41.263	66.947	15.983
11	0.9851	0.1732	-0.5092	1.1738	0.5339	2.1358	0.0556	-0.0426	0.0242	0.0386	0.0174	0.0089	-0.0678	0.1955	-0.0729	-0.0234	-0.0356	-0.0153	-0.0577	0.0174	-0.1202	-23.628	74.48	2.05
12	0.6835	0.1467	-0.2142	1.5949	0.3572	1.3193	-0.0065	-0.0876	-0.0025	0.0074	0.0559	0.0732	-0.5949	-0.0166	-0.0494	0.3242	0.0257	0.0959	-0.1931	-0.0353	-0.1639	-31.133	101.513	1.727
13	1.6826	0.3346	0.0832	1.5358	-0.2686	1.7663	0.0933	0.0615	0.0683	-0.0832	-0.0565	-0.0832	-0.2283	0.3711	-0.0367	-0.1132	-0.0281	0.0222	0.0393	0.0356	-0.0694	-0.561	70.3	-46.81
14	0.8269	0.1758	-0.0623	0.4046	0.0941	0.964	-0.0036	0.0694	-0.0855	-0.053	0.0056	-0.0157	0.0034	-0.0757	-0.0019	-0.0965	0.0129	-0.0234	-0.0592	-0.0082	-0.032	-31.747	59.929	-39.389
15	0.8059	0.4018	-0.321	1.137	0.1569	1.1524	0.1101	-0.0533	0.02	0.0309	-0.0426	0.012	-0.2498	-0.0126	-0.0674	-0.0311	0.0118	-0.0065	-0.0787	0.0106	-0.0587	-28.799	78.958	-25.485
16	0.3824	0.0399	-0.6438	1.0389	0.4817	1.7543	0.0821	-0.1961	-0.0093	0.0322	-0.0449	-0.0466	-0.1613	0.5531	-0.0371	-0.1306	-0.1036	-0.0156	0.1429	0.0121	-0.0624	-0.056	76.777	-24.984

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	25 - 79
2	X-RAY DIFFRACTION	2	A	80 - 198
3	X-RAY DIFFRACTION	3	A	199 - 317
4	X-RAY DIFFRACTION	4	A	318 - 514
5	X-RAY DIFFRACTION	5	B	25 - 79
6	X-RAY DIFFRACTION	6	B	80 - 198
7	X-RAY DIFFRACTION	7	B	199 - 317
8	X-RAY DIFFRACTION	8	B	318 - 514
9	X-RAY DIFFRACTION	9	C	25 - 79
10	X-RAY DIFFRACTION	10	C	80 - 198
11	X-RAY DIFFRACTION	11	C	199 - 317
12	X-RAY DIFFRACTION	12	C	318 - 514
13	X-RAY DIFFRACTION	13	D	25 - 79
14	X-RAY DIFFRACTION	14	D	80 - 198
15	X-RAY DIFFRACTION	15	D	199 - 317
16	X-RAY DIFFRACTION	16	D	318 - 514

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