PDB-2uuu: alkyldihydroxyacetonephosphate synthase in P212121

ID or keywords:

Entry

Database: PDB / ID: 2uuu

Title

alkyldihydroxyacetonephosphate synthase in P212121

Components

ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE

Keywords

TRANSFERASE / LAVOPROTEIN / LIPID SYNTHESIS / PEROXISOMAL DISORDER

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 /

MOLECULAR REPLACEMENT / Resolution: 1.95 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
Revision 1.2	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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	2uuu.cif.gz	473.1 KB	Display	PDBx/mmCIF format
PDB format	pdb2uuu.ent.gz	386.5 KB	Display	PDB format
PDBx/mmJSON format	2uuu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2uuu_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	2uuu_full_validation.pdf.gz	1.7 MB	Display
Data in XML	2uuu_validation.xml.gz	94.8 KB	Display
Data in CIF	2uuu_validation.cif.gz	137.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uu/2uuu ftp://data.pdbj.org/pub/pdb/validation_reports/uu/2uuu	HTTPS FTP

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Related structure data

Related structure data	2uuvSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2uuv-1 4bby-2 5i17-d 3cnd-d 4lz7-d 1oik-1 3r1j-1 1vz4-1 6d0o-d 2uuv-2 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

269 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)	103.499, 108.913, 216.492
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.994, -0.028, -0.109), (-0.028, -1, 0.002), (-0.109, 0.001, -0.994)	0.25732, 6.11773, 3.76899
2	given	(0.166, 0.986, -0.035), (0.986, -0.166, 0.014), (0.008, -0.037, -0.999)	25.2735, 31.53071, -54.21891
3	given	(0.157, 0.983, 0.09), (-0.987, 0.159, -0.013), (-0.028, -0.087, 0.996)	31.95517, -26.13771, 55.09605

#1: Protein	ALKYLDIHYDROXYACETONEPHOSPHATE 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 Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#3: Chemical	ChemComp-PL3 / HEXADECAN-1-OL Mass: 242.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₆H₃₄O
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1550 / 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: 3.08 Å³/Da / Density % sol: 40 %
Crystal grow	Details: 12% PEG4K, 200 MM LI2SO4, 100 MM TRISCL PH=8.5

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Data collection

Diffraction	Mean temperature: 273 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979078
Detector	Type: ADSC CCD / Detector: CCD / Date: Nov 29, 2006
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979078 Å / Relative weight: 1
Reflection	Resolution: 1.95→29.9 Å / Num. obs: 177635 / % possible obs: 99.8 % / Redundancy: 5.1 % / R_merge(I) obs: 0.01 / Net I/σ(I): 12.5
Reflection shell	Resolution: 1.95→2.06 Å / Redundancy: 5.2 % / R_merge(I) obs: 0.42 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2UUV

2uuv

Resolution: 1.95→29.93 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.917 / SU B: 6.472 / SU ML: 0.113 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.244	8930	5 %	RANDOM
R_work	0.193	-	-	-
obs	0.196	168705	99.8 %	-

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: 26.32 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.22 Å²	0 Å²	0 Å²
2-	-	2.44 Å²	0 Å²
3-	-	-	-1.22 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→29.93 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17325	0	280	1550	19155

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	18080
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.443	1.968	24495
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.941	5	2155
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.717	23.769	788
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.357	15	3103
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.518	15	96
X-RAY DIFFRACTION	r_chiral_restr	0.108	0.2	2683
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	13430
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.204	0.2	8190
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.303	0.2	12168
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.139	0.2	1391
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	0.207	0.2	98
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.114	0.2	37
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	0.888	1.5	11220
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.38	2	17546
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.856	3	8239
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.813	4.5	6945
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: 1.95→2 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.301	677	-
R_work	0.234	12289	-
obs	-	-	100 %

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	1.9727	1.0808	-0.0285	1.9525	-0.1597	1.3998	0.0912	-0.3189	-0.3494	0.2511	-0.1724	-0.3064	0.1106	0.2576	0.0812	0.0076	0.0109	-0.0608	-0.1361	0.0853	-0.0475	51.277	-15.591	22.147
2	2.9039	0.6839	-0.1559	1.8453	0.1478	2.1134	-0.0203	-0.2805	-0.4424	0.0373	-0.1417	0.0575	0.437	-0.0751	0.1621	0.0967	-0.0367	0.0549	-0.2547	0.0762	-0.009	24.834	-34.489	22.078
3	2.2893	-0.1406	-0.0987	0.9667	0.0158	0.9322	0.0238	-0.0914	0.0636	0.0011	-0.0437	0.0299	-0.0818	0.026	0.02	0.0639	-0.0186	-0.0129	-0.1925	-0.0208	-0.0837	35.527	-0.371	13.968
4	0.8443	-0.1932	0.1816	1.2617	-0.5458	1.0806	0.0065	0.0271	-0.104	-0.0326	-0.0864	0.1442	0.1906	-0.1401	0.0798	0.0608	-0.0497	0.0177	-0.2325	-0.0524	-0.0358	18.656	-21.374	4.508
5	1.5609	-0.5454	0.1733	1.9774	0.1655	0.9333	-0.0149	0.3233	0.2498	-0.6194	0.0553	-0.2282	-0.2807	0.226	-0.0405	0.2879	-0.0989	0.1152	-0.1394	0.0483	-0.0781	50.821	19.775	-23.407
6							8.2165	20.3085	-1.982	11.3522	8.2165	-8.0022	18.2318	-8.8373	-16.433	0.3383	-0.168	-0.171	1.0097	0.101	0.5519	23.539	39.277	-21.498
7	2.5519	0.4715	0.0619	1.0272	0.2173	0.9989	-0.0425	0.0629	0.0001	-0.205	0.0022	0.0968	-0.0947	-0.0033	0.0402	0.1427	0.0129	-0.0033	-0.1931	-0.0152	-0.0848	34.085	5.442	-13.91
8	1.5513	0.9179	-0.564	2.0784	-0.7404	1.2286	0.0472	0.058	0.3608	-0.0781	-0.0011	0.3764	-0.2655	-0.1771	-0.0461	0.1252	0.1102	-0.046	-0.2982	-0.0256	0.0875	18.775	26.857	-2.81
9	2.2541	-0.7822	0.3129	1.7748	0.4439	1.4873	-0.2208	-0.2455	0.3563	0.2231	0.1478	-0.34	-0.1618	0.1239	0.073	0.0703	0.0297	-0.0691	-0.1772	-0.0476	-0.0369	-6.837	24.305	-31.265
10	5.7484	-1.7355	-2.2154	3.3455	0.8114	3.7201	-0.2742	-0.4962	-0.5837	0.2824	0.3036	-0.3626	0.7675	0.5654	-0.0294	0.1096	0.2053	-0.1313	-0.1356	-0.0127	0.0662	10.101	-4.502	-34.401
11	1.8637	0.4299	0.4016	2.4895	-0.1653	1.1636	-0.0568	-0.0532	-0.0801	0.0058	0.0381	0.0914	0.035	-0.1011	0.0188	0.0483	0.0011	0.0459	-0.1593	-0.004	-0.1022	-23.832	11.458	-40.868
12	2.9853	0.662	1.2557	1.4477	0.3158	0.8514	-0.0005	0.298	-0.722	0.115	0.1881	-0.2587	0.3133	0.2658	-0.1876	0.0431	0.0874	0.0643	-0.126	-0.1492	0.077	-5.316	-7.396	-51.417
13	1.5445	0.1813	-0.1211	0.7856	-0.3884	1.035	-0.0353	0.1547	0.2194	-0.1206	0.054	0.1007	-0.115	-0.0989	-0.0186	0.0878	-0.086	-0.0315	-0.1676	0.0665	-0.0759	-40.253	32.549	-77.155
14	4.2565	-1.8208	0.05	2.2797	0.7491	3.8004	0.003	0.2434	-0.8212	-0.0691	0.0637	0.4916	0.4134	-0.3317	-0.0667	0.0357	-0.2054	-0.0957	-0.1893	0.0661	0.0527	-64.529	8.931	-77.509
15	1.3985	-0.2504	0.25	1.8276	-0.1667	1.2874	-0.0627	0.0396	-0.1126	-0.0512	0.0298	-0.0212	0.1442	0.0373	0.033	0.09	-0.0692	0.0339	-0.1564	0.0122	-0.1034	-29.007	13.131	-68.944
16	2.1889	-1.2432	1.0792	2.4398	-1.293	1.3471	-0.1356	-0.0388	-0.38	-0.0662	0.3141	0.1838	0.1626	-0.3248	-0.1784	0.0265	-0.1627	-0.0288	-0.1154	0.0512	-0.0398	-52.825	0.374	-59.856

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	9 - 22
2	X-RAY DIFFRACTION	1	A	77 - 195
3	X-RAY DIFFRACTION	2	A	23 - 76
4	X-RAY DIFFRACTION	3	A	196 - 314
5	X-RAY DIFFRACTION	4	A	315 - 511
6	X-RAY DIFFRACTION	5	B	77 - 195
7	X-RAY DIFFRACTION	6	B	23 - 76
8	X-RAY DIFFRACTION	7	B	196 - 314
9	X-RAY DIFFRACTION	8	B	315 - 511
10	X-RAY DIFFRACTION	9	C	12 - 22
11	X-RAY DIFFRACTION	9	C	77 - 195
12	X-RAY DIFFRACTION	10	C	23 - 76
13	X-RAY DIFFRACTION	11	C	196 - 314
14	X-RAY DIFFRACTION	12	C	315 - 511
15	X-RAY DIFFRACTION	13	D	77 - 195
16	X-RAY DIFFRACTION	14	D	23 - 76
17	X-RAY DIFFRACTION	15	D	196 - 314
18	X-RAY DIFFRACTION	16	D	315 - 511

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