PDB-4bby: MAMMALIAN ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE: WILD-TYPE

ID or keywords:

Entry

Database: PDB / ID: 4bby

Title

MAMMALIAN ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE: WILD-TYPE

Components

ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL

Keywords

TRANSFERASE / PLASMALOGEN / FLAVIN / PEROXISOME

Function / homology

Function and homology information

alkylglycerone-phosphate synthase / alkylglycerone-phosphate synthase activity / ether lipid biosynthetic process / peroxisomal membrane / FAD binding / peroxisome
Similarity search - Function

Biological species

CAVIA PORCELLUS (domestic guinea pig)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Nenci, S. / Piano, V. / Rosati, S. / Aliverti, A. / Pandini, V. / Fraaije, M.W. / Heck, A.J.R. / Edmondson, D.E. / Mattevi, A.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Precursor of Ether Phospholipids is Synthesized by a Flavoenzyme Through Covalent Catalysis.
Authors: Nenci, S. / Piano, V. / Rosati, S. / Aliverti, A. / Pandini, V. / Fraaije, M.W. / Heck, A.J.R. / Edmondson, D.E. / Mattevi, A.

History

Deposition	Sep 28, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 7, 2012	Provider: repository / Type: Initial release
Revision 1.1	Nov 28, 2012	Group: Database references
Revision 1.2	Dec 20, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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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PDBx/mmCIF format	4bby.cif.gz	835.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4bby.ent.gz	696.1 KB	Display	PDB format
PDBx/mmJSON format	4bby.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4bby_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	4bby_full_validation.pdf.gz	1.8 MB	Display
Data in XML	4bby_validation.xml.gz	96.1 KB	Display
Data in CIF	4bby_validation.cif.gz	129.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bb/4bby ftp://data.pdbj.org/pub/pdb/validation_reports/bb/4bby	HTTPS FTP

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Related structure data

Related structure data	4bc7C 4bc9C 4bcaC 2uuuS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6gou-2 4bc7-1 5ae1-2 4bc9-2 4bc9-1 6gou-1 5ae1-1 5ae3-2 5ae2-2 5ae2-1 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 (5)

Deposited unit

A: ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL

B: ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL

C: ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL

D: ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL

hetero molecules

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

1

A: ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL

B: ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL

hetero molecules

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

2

C: ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL

D: ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL

hetero molecules

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

Unit cell

Length a, b, c (Å)	61.295, 99.170, 107.835
Angle α, β, γ (deg.)	90.43, 92.18, 94.92
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLY	GLY	LYS	LYS	A	A	81 - 102	81 - 102
2	1	GLY	GLY	LYS	LYS	B	B	81 - 102	81 - 102
3	1	GLY	GLY	LYS	LYS	C	C	81 - 102	81 - 102
4	1	GLY	GLY	LYS	LYS	D	D	81 - 102	81 - 102
1	2	ILE	ILE	HIS	HIS	A	A	159 - 192	159 - 192
2	2	ILE	ILE	HIS	HIS	B	B	159 - 192	159 - 192
3	2	ILE	ILE	HIS	HIS	C	C	159 - 192	159 - 192
4	2	ILE	ILE	HIS	HIS	D	D	159 - 192	159 - 192
1	3	ILE	ILE	ARG	ARG	A	A	205 - 265	205 - 265
2	3	ILE	ILE	ARG	ARG	B	B	205 - 265	205 - 265
3	3	ILE	ILE	ARG	ARG	C	C	205 - 265	205 - 265
4	3	ILE	ILE	ARG	ARG	D	D	205 - 265	205 - 265
1	4	VAL	VAL	PRO	PRO	A	A	278 - 385	278 - 385
2	4	VAL	VAL	PRO	PRO	B	B	278 - 385	278 - 385
3	4	VAL	VAL	PRO	PRO	C	C	278 - 385	278 - 385
4	4	VAL	VAL	PRO	PRO	D	D	278 - 385	278 - 385
1	5	GLN	GLN	GLN	GLN	A	A	400 - 424	400 - 424
2	5	GLN	GLN	GLN	GLN	B	B	400 - 424	400 - 424
3	5	GLN	GLN	GLN	GLN	C	C	400 - 424	400 - 424
4	5	GLN	GLN	GLN	GLN	D	D	400 - 424	400 - 424
1	6	MET	MET	TYR	TYR	A	A	514 - 578	514 - 578
2	6	MET	MET	TYR	TYR	B	B	514 - 578	514 - 578
3	6	MET	MET	TYR	TYR	C	C	514 - 578	514 - 578
4	6	MET	MET	TYR	TYR	D	D	514 - 578	514 - 578
1	7	THR	THR	LEU	LEU	A	A	598 - 658	598 - 658
2	7	THR	THR	LEU	LEU	B	B	598 - 658	598 - 658
3	7	THR	THR	LEU	LEU	C	C	598 - 658	598 - 658
4	7	THR	THR	LEU	LEU	D	D	598 - 658	598 - 658

NCS oper:

ID	Code	Matrix	Vector
1	given	(1), (1), (1)
2	given	(0.977339, 0.206287, -0.047467), (0.206089, -0.978491, -0.009091), (-0.048321, -0.000898, -0.998831)	-7.09205, 92.89027, 109.10454
3	given	(0.975078, -0.000211, 0.221862), (0.206842, 0.362558, -0.908718), (-0.080246, 0.931961, 0.353566)	14.28107, 8.96422, -37.49273
4	given	(0.999277, 0.037881, -0.003309), (0.016538, -0.354583, 0.934878), (0.034241, -0.934257, -0.354953)	9.82189, 85.98566, 146.07585

#1: Protein	ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL / ALKYL-DHAP SYNTHASE / ALKYLGLYCERONE-PHOSPHATE SYNTHASE Mass: 72938.695 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CAVIA PORCELLUS (domestic guinea pig) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: P97275, 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-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 790 / 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: 2.24 Å³/Da / Density % sol: 50 % / Description: NONE
Crystal grow	pH: 7.5 / Details: pH 7.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1
Detector	Type: ADSC QUANTUM 315r / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.9→20 Å / Num. obs: 184434 / % possible obs: 91.8 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / R_merge(I) obs: 0.15 / Net I/σ(I): 7.4
Reflection shell	Resolution: 1.9→2 Å / Redundancy: 1.8 % / R_merge(I) obs: 0.36 / Mean I/σ(I) obs: 2.3 / % possible all: 78.4

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Processing

Software

Name	Version	Classification
REFMAC	5.7.0027	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2UUU

2uuu

Resolution: 1.9→19.98 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.912 / SU B: 5.604 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23978	2004	1.1 %	RANDOM
R_work	0.19128	-	-	-
obs	0.19179	182430	92.28 %	-

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: 32.016 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.02 Å²	0.42 Å²	0.1 Å²
2-	-	0.06 Å²	-0.86 Å²
3-	-	-	-0.01 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→19.98 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17450	0	232	790	18472

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.023	0.02	18145
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.233	1.968	24584
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.675	5	2213
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.397	23.991	847
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.803	15	3111
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.887	15	117
X-RAY DIFFRACTION	r_chiral_restr	0.162	0.2	2646
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.021	13763
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
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

Refine LS restraints NCS

Ens-ID: 1 / Number: 2909 / Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.5

Dom-ID	Auth asym-ID	Rms dev position (Å)
1	A	2.49
2	B	2.36
3	C	2.5
4	D	2.67

LS refinement shell

Resolution: 1.898→1.947 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.263	123	-
R_work	0.239	11341	-
obs	-	-	78.28 %

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	0.5501	-0.2299	0.0272	0.34	0.089	0.859	0.0229	0.1648	0.1316	-0.1017	0.0518	-0.0899	-0.1696	0.0695	-0.0747	0.0802	-0.046	0.0345	0.1094	0.0201	0.0432	43.118	60.622	28.396
2	0.4377	-0.0675	-0.3999	0.7582	0.3374	1.0606	-0.1096	-0.2663	0.0026	0.2177	0.1612	-0.1015	0.2839	0.2717	-0.0517	0.1618	0.0979	-0.0428	0.1816	-0.0177	0.0166	46.122	42.455	78.19
3	0.5761	-0.3093	-0.239	0.9505	0.6626	1.1764	0.0142	0.0167	-0.1093	-0.0325	0.0695	-0.0194	0.1214	0.0703	-0.0838	0.063	-0.0288	-0.0046	0.0396	-0.0241	0.0402	33.786	79.962	-17.623
4	0.2035	0.0856	0.1194	1.6789	1.4536	1.8913	0.0249	-0.0747	0.0684	0.0572	0.1882	-0.1104	-0.1112	0.1284	-0.2131	0.057	-0.0178	0.0473	0.1005	-0.0566	0.0696	28.997	120.499	18.514
5	0.7995	-0.3593	-0.0488	0.5182	0.1497	0.7806	0.0052	0.0415	0.0706	-0.0378	0.0362	-0.0424	-0.1591	-0.0884	-0.0413	0.0478	-0.0026	0.007	0.0484	0.0082	0.0082	29.34	60.433	42.674
6	0.6583	0.0209	-0.2965	0.7482	0.4191	1.1974	-0.0965	-0.1083	-0.008	0.1905	0.0638	0.0605	0.303	-0.0198	0.0327	0.1126	0.0152	0.0102	0.0382	0.0073	0.0066	32.37	39.856	64.307
7	0.7003	-0.2588	-0.2001	0.8433	0.5788	1.1	0.0454	0.054	-0.0249	-0.1158	-0.0453	0.0638	-0.0494	-0.1435	-0.0001	0.0474	-0.0205	-0.0047	0.0395	-0.0014	0.0089	19.369	93.787	-14.19
8	0.1719	0.0114	-0.2823	1.5879	1.0644	2.1899	0.0338	0.017	0.024	0.2165	-0.0594	0.1844	0.0651	-0.3609	0.0256	0.0422	-0.012	0.037	0.1268	-0.0018	0.0341	16.255	106.075	11.761

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	11 - 30
2	X-RAY DIFFRACTION	1	A	75 - 313
3	X-RAY DIFFRACTION	1	A	543 - 588
4	X-RAY DIFFRACTION	2	B	11 - 30
5	X-RAY DIFFRACTION	2	B	75 - 313
6	X-RAY DIFFRACTION	2	B	543 - 588
7	X-RAY DIFFRACTION	3	C	11 - 30
8	X-RAY DIFFRACTION	3	C	75 - 313
9	X-RAY DIFFRACTION	3	C	543 - 588
10	X-RAY DIFFRACTION	4	D	11 - 30
11	X-RAY DIFFRACTION	4	D	75 - 313
12	X-RAY DIFFRACTION	4	D	543 - 588
13	X-RAY DIFFRACTION	5	A	31 - 74
14	X-RAY DIFFRACTION	5	A	314 - 542
15	X-RAY DIFFRACTION	6	B	31 - 74
16	X-RAY DIFFRACTION	6	B	314 - 542
17	X-RAY DIFFRACTION	7	C	31 - 74
18	X-RAY DIFFRACTION	7	C	314 - 542
19	X-RAY DIFFRACTION	8	D	31 - 74
20	X-RAY DIFFRACTION	8	D	314 - 542

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