PDB-8eim: Structure of ALAS with C-terminal truncation from S. cerevisiae

ID or keywords:

Entry

Database: PDB / ID: 8eim

Title

Structure of ALAS with C-terminal truncation 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 / hemoglobin biosynthetic process / 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: 2.1 Å

Authors

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

Funding support

United States, 1items

Citation

Journal: Protein Sci. / Year: 2023
Title: The yeast ALA synthase C-terminus positively controls enzyme structure and function.
Authors: Tran, J.U. / Brown, B.L.

History

Deposition	Sep 15, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 15, 2023	Provider: repository / Type: Initial release
Revision 1.1	Apr 12, 2023	Group: Database references / Refinement description Category: citation / citation_author ...citation / citation_author / refine_ls_restr_ncs / struct_ncs_dom / struct_ncs_dom_lim Item: _citation.journal_volume / _citation_author.identifier_ORCID ..._citation.journal_volume / _citation_author.identifier_ORCID / _refine_ls_restr_ncs.pdbx_auth_asym_id / _struct_ncs_dom.details / _struct_ncs_dom_lim.beg_auth_asym_id / _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_asym_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
Revision 1.2	Oct 25, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8eim.cif.gz	461.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8eim.ent.gz	293 KB	Display	PDB format
PDBx/mmJSON format	8eim.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8eim_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	8eim_full_validation.pdf.gz	1.1 MB	Display
Data in XML	8eim_validation.xml.gz	33.8 KB	Display
Data in CIF	8eim_validation.cif.gz	47.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ei/8eim ftp://data.pdbj.org/pub/pdb/validation_reports/ei/8eim	HTTPS FTP

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Related structure data

Related structure data	5txrS S: Starting model for refinement
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

A: 5-aminolevulinate synthase, mitochondrial

B: 5-aminolevulinate synthase, mitochondrial

hetero molecules

106 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	79.280, 99.550, 120.260
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 1 / Auth seq-ID: 69 - 534 / Label seq-ID: 12 - 477

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

#1: Protein	5-aminolevulinate synthase, mitochondrial / 5-aminolevulinic acid synthase / Delta-ALA synthase / Delta-aminolevulinate synthase Mass: 52460.332 Da / Num. of mol.: 2 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-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate Mass: 247.142 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C₈H₁₀NO₆P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.26 Å³/Da / Density % sol: 45.58 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.9 / Details: 0.2M magensium acetate, 20% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: RAYONIX MX-300 / Detector: CCD / Date: Dec 1, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 2.1→47.91 Å / Num. obs: 56191 / % possible obs: 99.7 % / Redundancy: 6.5 % / CC_1/2: 0.998 / R_rim(I) all: 0.119 / Net I/σ(I): 11.8
Reflection shell	Resolution: 2.1→2.22 Å / Mean I/σ(I) obs: 1.27 / Num. unique obs: 8843 / CC_1/2: 0.594 / R_rim(I) all: 1.714 / % possible all: 98.5

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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
Starting model: 5TXR

5txr

Resolution: 2.1→47.909 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.952 / SU B: 14.9 / SU ML: 0.178 / Cross valid method: FREE R-VALUE / ESU R: 0.211 / ESU R Free: 0.174
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2244	2809	5.001 %
R_work	0.1878	53365	-
all	0.19	-	-
obs	-	56174	99.849 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 58.625 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.352 Å²	-0 Å²	0 Å²
2-	-	0.381 Å²	-0 Å²
3-	-	-	-1.733 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→47.909 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6767	0	63	189	7019

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	6966
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	6397
X-RAY DIFFRACTION	r_angle_refined_deg	1.316	1.646	9434
X-RAY DIFFRACTION	r_angle_other_deg	0.443	1.574	14917
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.299	5	866
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	11.452	5	31
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.522	10	1176
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.327	10	304
X-RAY DIFFRACTION	r_chiral_restr	0.062	0.2	1067
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	7825
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1314
X-RAY DIFFRACTION	r_nbd_refined	0.21	0.2	1537
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.186	0.2	6072
X-RAY DIFFRACTION	r_nbtor_refined	0.174	0.2	3455
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.076	0.2	3733
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.166	0.2	224
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.057	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.23	0.2	23
X-RAY DIFFRACTION	r_nbd_other	0.213	0.2	69
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.237	0.2	7
X-RAY DIFFRACTION	r_mcbond_it	1.449	2.264	3487
X-RAY DIFFRACTION	r_mcbond_other	1.44	2.261	3485
X-RAY DIFFRACTION	r_mcangle_it	2.168	3.383	4344
X-RAY DIFFRACTION	r_mcangle_other	2.168	3.383	4345
X-RAY DIFFRACTION	r_scbond_it	2.122	2.545	3479
X-RAY DIFFRACTION	r_scbond_other	2.122	2.547	3480
X-RAY DIFFRACTION	r_scangle_it	3.13	3.715	5090
X-RAY DIFFRACTION	r_scangle_other	3.13	3.716	5091
X-RAY DIFFRACTION	r_lrange_it	5.535	31.629	7844
X-RAY DIFFRACTION	r_lrange_other	5.526	31.457	7814
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.086	0.05	13419

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.08648	0.05008
1	2	B	X-RAY DIFFRACTION	Local ncs	0.08648	0.05008

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	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.1-2.154	0.339	203	0.337	3850	0.337	4106	0.93	0.931	98.7092	0.316
2.154-2.213	0.328	200	0.308	3799	0.309	3999	0.936	0.941	100	0.282
2.213-2.277	0.324	193	0.281	3684	0.283	3878	0.932	0.952	99.9742	0.248
2.277-2.347	0.263	189	0.246	3578	0.246	3767	0.962	0.964	100	0.21
2.347-2.424	0.264	183	0.236	3492	0.237	3675	0.956	0.968	100	0.197
2.424-2.509	0.274	178	0.233	3377	0.235	3556	0.955	0.968	99.9719	0.19
2.509-2.603	0.253	171	0.215	3241	0.217	3413	0.96	0.975	99.9707	0.172
2.603-2.709	0.243	166	0.202	3164	0.204	3330	0.968	0.977	100	0.161
2.709-2.829	0.268	159	0.193	3024	0.197	3183	0.957	0.979	100	0.154
2.829-2.967	0.253	153	0.18	2894	0.183	3048	0.965	0.981	99.9672	0.147
2.967-3.127	0.214	145	0.184	2749	0.185	2894	0.971	0.981	100	0.154
3.127-3.316	0.163	137	0.157	2613	0.157	2752	0.983	0.986	99.9273	0.135
3.316-3.543	0.216	129	0.164	2447	0.166	2576	0.974	0.985	100	0.148
3.543-3.825	0.195	121	0.17	2307	0.171	2433	0.977	0.983	99.7945	0.159
3.825-4.188	0.176	112	0.152	2125	0.153	2238	0.982	0.986	99.9553	0.148
4.188-4.678	0.182	102	0.149	1938	0.15	2040	0.98	0.986	100	0.152
4.678-5.393	0.226	90	0.176	1718	0.179	1810	0.972	0.982	99.8895	0.185
5.393-6.584	0.292	78	0.209	1475	0.213	1554	0.962	0.977	99.9357	0.215
6.584-9.225	0.184	62	0.163	1183	0.164	1246	0.981	0.984	99.9197	0.182
9.225-47.909	0.204	38	0.171	706	0.173	749	0.973	0.98	99.3324	0.208

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	1.0308	-0.9089	0.4037	12.5511	1.8606	5.5192	0.1119	0.5564	0.2997	-1.7499	-0.1297	-0.2458	-0.4779	0.389	0.0177	0.3893	-0.0148	-0.0921	0.3388	0.1012	0.4775	-3.132	-23.392	-46.524
2	5.0034	1.8584	-2.9206	5.5364	-3.3122	6.1441	-0.0427	0.2239	-0.6095	-0.0332	-0.095	-0.5932	0.0314	-0.18	0.1377	0.1658	0.0075	-0.0819	0.0524	-0.0737	0.6945	26.709	-33.583	-32.783
3	2.6581	-0.1653	-0.116	4.3001	0.1653	0.4796	0.08	-0.0652	0.2358	0.3139	-0.0239	-0.5165	0.0131	0.0441	-0.0561	0.0884	-0.0057	-0.1041	0.0058	-0.0085	0.5465	29.689	-9.127	-27.37
4	1.9578	0.0953	1.6925	1.6469	-0.8173	6.0866	-0.146	0.3669	-0.0028	-0.6515	0.3051	-0.4726	0.049	-0.3588	-0.1591	0.3422	-0.0458	0.1905	0.27	-0.0068	0.6619	32.95	-17.702	-54.067
5	3.2371	-1.2524	2.546	8.5765	-5.7152	13.8572	-0.0636	0.3439	-0.006	0.0102	0.0596	-0.7496	-0.1224	0.0772	0.004	0.0591	0.0357	0.0036	0.2345	-0.0853	0.7159	47.668	-17.432	-36.472
6	11.0048	4.3596	-9.1794	7.6229	-11.5985	19.6682	-0.1323	-0.4801	-0.3785	0.5445	-0.0744	0.076	-0.0782	-0.3478	0.2066	0.6263	-0.0983	-0.0069	0.4646	-0.1263	0.4634	24.117	-1.314	-11.131
7	5.6953	0.9382	-2.0926	4.2986	0.4867	5.7707	0.2982	-0.3753	-0.5043	0.4905	-0.2047	-0.6002	-0.077	0.3963	-0.0936	0.236	-0.0057	-0.1702	0.0625	0.0202	0.562	16.809	-37.612	-23.327
8	2.1594	0.0434	0.0763	5.3025	0.5384	0.896	0.0814	-0.0366	0.4082	-0.0312	-0.0728	0.5505	-0.046	0.0655	-0.0086	0.0482	-0.0209	0.0072	0.0144	-0.0271	0.4807	-3.55	-22.051	-29.071
9	3.846	1.7151	-1.6439	4.7054	1.0838	3.145	0.8505	-1.0694	0.1128	1.8773	-0.6575	0.1682	-0.0442	0.348	-0.193	0.873	-0.3075	0.0105	0.3088	0.0002	0.4489	4.691	-31.943	-7.449
10	1.426	1.8524	2.7797	9.576	-0.8912	8.2726	0.4821	-0.028	-0.005	0.7504	-0.2876	0.4853	0.9076	0.1135	-0.1945	0.1808	-0.0036	0.0822	0.0196	0.0701	0.7118	-7.184	-44.255	-23.363

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	68 - 102
2	X-RAY DIFFRACTION	2	ALL	A	103 - 156
3	X-RAY DIFFRACTION	3	ALL	A	157 - 381
4	X-RAY DIFFRACTION	4	ALL	A	382 - 508
5	X-RAY DIFFRACTION	5	ALL	A	509 - 534

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