PDB-9dz7: Structure of ALAS bound to glycine from S. cerevisiae

ID or keywords:

Entry

Database: PDB / ID: 9dz7

Title

Structure of ALAS bound to glycine from S. cerevisiae

Components

5-aminolevulinate synthase, mitochondrial

Keywords

TRANSFERASE / heme biosynthesis / 5-aminolevulinic acid / pyridoxal 5-phosphate

Function / homology

Function and homology information

positive regulation of organelle assembly / Heme biosynthesis / 5-aminolevulinate synthase / 5-aminolevulinate synthase activity / protoporphyrinogen IX biosynthetic process / heme biosynthetic process / pyridoxal phosphate binding / mitochondrial matrix / mitochondrion
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.487 Å

Authors

Tran, J.U. / Brown, B.L.

Funding support

United States, 2items

Citation

Journal: To Be Published
Title: Structure of ALAS bound to glycine from S. cerevisiae
Authors: Tran, J.U. / Brown, B.L.

History

Deposition	Oct 15, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 22, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9dz7.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb9dz7.ent.gz	913.4 KB	Display	PDB format
PDBx/mmJSON format	9dz7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9dz7_validation.pdf.gz	2.1 MB	Display	wwPDB validaton report
Full document	9dz7_full_validation.pdf.gz	2.1 MB	Display
Data in XML	9dz7_validation.xml.gz	120.3 KB	Display
Data in CIF	9dz7_validation.cif.gz	155.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dz/9dz7 ftp://data.pdbj.org/pub/pdb/validation_reports/dz/9dz7	HTTPS FTP

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Related structure data

Similar structure data	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	#196 - Apr 2016 Lead Poisoning similarity (1)

Deposited unit

F: 5-aminolevulinate synthase, mitochondrial

A: 5-aminolevulinate synthase, mitochondrial

C: 5-aminolevulinate synthase, mitochondrial

E: 5-aminolevulinate synthase, mitochondrial

D: 5-aminolevulinate synthase, mitochondrial

B: 5-aminolevulinate synthase, mitochondrial

hetero molecules

328 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

F: 5-aminolevulinate synthase, mitochondrial

E: 5-aminolevulinate synthase, mitochondrial

hetero molecules

defined by author&software
Evidence: gel filtration
110 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: 5-aminolevulinate synthase, mitochondrial

B: 5-aminolevulinate synthase, mitochondrial

hetero molecules

defined by author&software
Evidence: gel filtration
109 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: 5-aminolevulinate synthase, mitochondrial

D: 5-aminolevulinate synthase, mitochondrial

hetero molecules

defined by author&software
Evidence: gel filtration
109 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	59.672, 112.518, 117.388
Angle α, β, γ (deg.)	115.76, 98.31, 91.49
Int Tables number	1
Space group name H-M	P1

#1: Protein	5-aminolevulinate synthase, mitochondrial / 5-aminolevulinic acid synthase / Delta-ALA synthase / Delta-aminolevulinate synthase Mass: 53970.113 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: HEM1, CYD1, YDR232W, YD9934.16 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P09950, 5-aminolevulinate synthase
#2: Chemical	ChemComp-PLG / N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] / N-PYRIDOXYL-GLYCINE-5-MONOPHOSPHATE Mass: 306.209 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₂O₇P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	... ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 630 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.16 Å³/Da / Density % sol: 43.12 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.15 M magnesium chloride, 0.1 M HEPES, pH 7.5, 25% v/v PEG3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920105 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 8, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.920105 Å / Relative weight: 1
Reflection	Resolution: 2.487→48.912 Å / Num. obs: 93703 / % possible obs: 98.4 % / Redundancy: 3.6 % / B_iso Wilson estimate: 43.52 Å² / CC_1/2: 0.988 / R_rim(I) all: 0.177 / Net I/σ(I): 6.27
Reflection shell	Resolution: 2.49→2.63 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.43 / Num. unique obs: 14980 / CC_1/2: 0.577 / R_rim(I) all: 0.892 / % possible all: 97.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.487→48.91 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.939 / SU B: 21.19 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2074	5044	5.4 %	RANDOM
R_work	0.16761	-	-	-
obs	0.1698	88660	98.59 %	-

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: 48.209 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.48 Å²	-0.51 Å²	-0.65 Å²
2-	-	-0.23 Å²	-0.39 Å²
3-	-	-	0.87 Å²

Refinement step

Cycle: 1 / Resolution: 2.487→48.91 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	21950	0	161	630	22741

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	22541
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	20859
X-RAY DIFFRACTION	r_angle_refined_deg	1.286	1.647	30468
X-RAY DIFFRACTION	r_angle_other_deg	0.447	1.572	48654
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.208	5	2799
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	17.672	5	113
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.699	10	3838
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.062	0.2	3421
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	25310
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4236
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	1.807	2.609	11253
X-RAY DIFFRACTION	r_mcbond_other	1.807	2.609	11254
X-RAY DIFFRACTION	r_mcangle_it	2.82	3.903	14033
X-RAY DIFFRACTION	r_mcangle_other	2.82	3.903	14034
X-RAY DIFFRACTION	r_scbond_it	2.349	2.876	11288
X-RAY DIFFRACTION	r_scbond_other	2.349	2.877	11289
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.607	4.195	16436
X-RAY DIFFRACTION	r_long_range_B_refined	5.522	34.311	25114
X-RAY DIFFRACTION	r_long_range_B_other	5.523	34.314	25115
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.487→2.552 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.29	322	-
R_work	0.281	6461	-
obs	-	-	97.54 %

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	1.1247	-2.6339	0.491	7.5971	-1.7513	0.5746	0.0294	-0.0033	-0.0557	-0.0794	-0.1024	-0.3547	0.0946	0.1933	0.073	0.2655	0.0004	-0.054	0.3381	-0.0507	0.3483	15.211	16.376	22.28
2	0.7827	0.4056	0.5645	1.1948	0.4755	1.5481	-0.0551	-0.0715	0.0441	0.0598	-0.0319	0.0549	0.1192	-0.103	0.0871	0.0728	-0.0255	0.0131	0.1044	-0.0031	0.1163	-11.169	11.896	10.922
3	3.766	-0.3193	-0.726	3.3031	0.7262	2.1163	0.0484	0.186	-0.2624	-0.1441	-0.0029	-0.2488	0.2529	0.1039	-0.0454	0.0873	-0.022	-0.0007	0.0917	0.0309	0.1985	13.202	24.784	2.085
4	1.8644	0.5164	-0.3553	6.223	-2.4921	3.094	0.2103	-0.2866	0.1841	0.5042	0.0219	0.6167	-0.2103	-0.1293	-0.2322	0.1634	-0.0114	-0.0711	0.2599	-0.0654	0.2412	-19.191	23.711	7.931
5	0.624	-0.1198	0.3349	0.4404	0.8059	2.8954	-0.0127	-0.1987	0.0083	0.1398	-0.2093	0.232	0.3234	-0.6033	0.222	0.179	-0.0294	0.0367	0.3258	-0.0843	0.2685	-16.198	12.502	31.666
6	0.9	-0.5195	0.2324	2.506	0.2519	1.3555	0.018	-0.0893	-0.1298	0.1616	-0.0459	-0.0935	0.2825	0.0733	0.0279	0.1925	-0.0418	-0.0082	0.1628	0.0214	0.176	6.496	1.313	36.499
7	3.3039	-0.8254	1.0455	1.9436	0.2802	1.395	0.016	-0.2405	-0.7234	0.3388	-0.0637	0.4654	0.434	-0.5855	0.0477	0.3476	-0.1353	0.1557	0.4713	-0.0852	0.3236	-16.179	3.382	46.812
8	2.7812	-1.1425	-0.5426	1.7586	0.0796	2.1554	-0.1121	-0.0069	-0.3469	0.2473	0.0499	0.1073	0.0647	-0.2751	0.0623	0.421	-0.0675	0.0221	0.3139	-0.078	0.1762	-7.002	9.216	49.058
9	0.7516	-0.1608	-0.1474	1.4759	0.3054	1.4482	-0.0278	0.0387	0.0607	-0.0686	-0.017	-0.0687	-0.1508	-0.0007	0.0448	0.1034	-0.0116	-0.0383	0.0749	0.0407	0.1513	17.147	-35.539	7.406
10	3.5483	0.6038	0.4232	3.1523	-0.4897	1.4767	0.0352	0.2262	0.2182	-0.0985	-0.0377	-0.2739	-0.2104	0.3455	0.0025	0.1224	-0.0202	-0.0047	0.1891	0.0392	0.1439	37.175	-33.849	23.581
11	1.6147	-0.7268	-1.6659	1.4379	-1.0996	4.9443	0.0161	0.2074	-0.1084	-0.0742	0.0646	0.1268	0.1951	-0.5722	-0.0806	0.2485	0.0379	-0.0161	0.186	0.012	0.286	8.345	-34.615	19.214
12	4.5383	4.1841	0.8391	10.0362	-2.0832	2.6056	-0.1276	0.3606	0.0726	-0.9469	-0.1306	0.7434	0.1048	-0.1594	0.2582	0.4177	0.1501	-0.1374	0.4238	-0.1179	0.4825	0.675	-30.916	-10.393
13	1.0621	0.2048	-0.8566	1.6683	-0.2982	1.5953	-0.0227	0.1802	-0.0939	-0.1412	0.0152	-0.0007	-0.0048	-0.0948	0.0076	0.0801	-0.0102	-0.0272	0.0615	0.0274	0.1833	23.487	-55.408	-11.825
14	12.8499	2.0766	-2.017	4.3084	0.4661	5.3743	0.0432	0.7036	1.3387	-0.3074	0.1449	0.3561	-0.6283	-0.2353	-0.1881	0.2253	0.0524	-0.0416	0.3598	0.0492	0.4797	-2.591	-54.529	-14.257
15	2.5585	0.5524	-1.3611	2.5033	0.5437	1.1305	0.0282	0.5224	0.1103	-0.2209	-0.0933	0.1791	0.0778	-0.3735	0.0651	0.3001	-0.03	0.0354	0.2018	-0.0011	0.2188	14.021	-64.417	-15.519
16	0.7859	-1.0732	-0.8094	3.6376	0.4798	1.0303	0.1224	-0.3015	0.2149	0.1011	-0.0171	-0.7264	-0.2049	0.496	-0.1053	0.2341	-0.0911	0.0047	0.4869	0.0631	0.2971	8.661	-8.814	-50.121
17	1.0049	0.3675	0.1082	1.17	-0.3061	2.5934	0.0334	-0.044	0.0942	0.1727	0.0106	0.0687	-0.2196	-0.0256	-0.044	0.0502	-0.0007	-0.0019	0.0554	0.0226	0.088	-11.074	-12.613	-33.209
18	4.1754	-0.2811	0.2659	0.6382	-0.2217	1.0826	0.0679	-0.0246	-0.0836	0.0683	-0.0663	-0.0974	0.0582	0.128	-0.0016	0.1363	-0.0072	-0.0088	0.0978	-0.0085	0.0987	7.34	-27.799	-44.74
19	2.603	-3.3105	0.1733	6.6223	-1.0191	0.312	0.4171	0.5134	-0.3451	-0.1953	-0.4201	0.7923	-0.1192	-0.1149	0.003	0.484	0.0757	-0.0494	0.7882	-0.1665	0.7036	-25.519	-8.663	-45.362
20	4.8801	-1.8848	2.4524	0.7721	-1.1347	5.3662	0.0373	-0.0146	0.2245	0.079	0.1166	0.0288	-0.8475	-0.481	-0.1539	0.5475	0.0536	0.1403	0.5865	0.0249	0.54	-22.814	1.259	-25.681
21	1.2305	0.4605	0.462	1.5158	0.0502	2.4671	0.0163	-0.0976	0.2252	0.1933	-0.0523	-0.0365	-0.3688	0.2235	0.036	0.2052	-0.1118	0.0047	0.187	0.0447	0.1966	0.916	14.181	-45.56
22	4.688	0.3687	-0.1147	1.0084	0.0259	1.823	0.1024	-0.7464	0.1106	0.2573	-0.0714	0.1453	-0.34	-0.0437	-0.0311	0.4479	0.0063	0.0114	0.3008	0.0367	0.2826	-13.321	21.172	-48.877

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	69 - 114
2	X-RAY DIFFRACTION	2	A	115 - 395
3	X-RAY DIFFRACTION	3	A	396 - 508
4	X-RAY DIFFRACTION	4	A	513 - 548
5	X-RAY DIFFRACTION	5	B	69 - 151
6	X-RAY DIFFRACTION	6	B	152 - 380
7	X-RAY DIFFRACTION	7	B	381 - 458
8	X-RAY DIFFRACTION	8	B	459 - 548
9	X-RAY DIFFRACTION	9	C	69 - 394
10	X-RAY DIFFRACTION	10	C	395 - 500
11	X-RAY DIFFRACTION	11	C	501 - 547
12	X-RAY DIFFRACTION	12	D	68 - 93
13	X-RAY DIFFRACTION	13	D	94 - 429
14	X-RAY DIFFRACTION	14	D	430 - 452
15	X-RAY DIFFRACTION	15	D	453 - 547
16	X-RAY DIFFRACTION	16	E	69 - 141
17	X-RAY DIFFRACTION	17	E	142 - 381
18	X-RAY DIFFRACTION	18	E	382 - 532
19	X-RAY DIFFRACTION	19	E	533 - 547
20	X-RAY DIFFRACTION	20	F	69 - 93
21	X-RAY DIFFRACTION	21	F	94 - 426
22	X-RAY DIFFRACTION	22	F	427 - 547

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