PDB-2bwn: 5-Aminolevulinate Synthase from Rhodobacter capsulatus

ID or keywords:

Entry

Database: PDB / ID: 2bwn

Title

5-Aminolevulinate Synthase from Rhodobacter capsulatus

Components

5-AMINOLEVULINATE SYNTHASE

Aminolevulinic acid synthase

Keywords

TRANSFERASE / TETRAPYRROLE BIOSYNTHESIS /

HEME BIOSYNTHESIS / PYRIDOXAL PHOSPHATE DEPENDENT /

ACYLTRANSFERASE

Function / homology

Function and homology information

5-aminolevulinate synthase /

5-aminolevulinate synthase activity / hemoglobin biosynthetic process / protoporphyrinogen IX biosynthetic process /

pyridoxal phosphate binding
Similarity search - Function

Biological species

RHODOBACTER CAPSULATUS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Astner, I. / Schulze, J.O. / van den Heuvel, J.J. / Jahn, D. / Schubert, W.-D. / Heinz, D.W.

Citation

Journal: Embo J. / Year: 2005
Title: Crystal Structure of 5-Aminolevulinate Synthase, the First Enzyme of Heme Biosynthesis, and its Link to Xlsa in Humans.
Authors: Astner, I. / Schulze, J.O. / Van Den Heuvel, J.J. / Jahn, D. / Schubert, W.-D. / Heinz, D.W.

History

Deposition	Jul 15, 2005	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 27, 2005	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Dec 23, 2015	Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary
Revision 1.3	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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 650

HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

Remark 700

SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2bwn.cif.gz	331.4 KB	Display	PDBx/mmCIF format
PDB format	pdb2bwn.ent.gz	271.9 KB	Display	PDB format
PDBx/mmJSON format	2bwn.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/bw/2bwn ftp://data.pdbj.org/pub/pdb/validation_reports/bw/2bwn	HTTPS FTP

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Related structure data

Related structure data	2bwoC 2bwpC 1bs0S 1fc4S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4w1v-d 1pem-d 4w1w-d 3tft-d 1s06-d 2bwp-1 2bwp-2 4wyd-d 1qj5-d 5qqt-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	#4 - Apr 2000 Collagen similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1)

Deposited unit

A: 5-AMINOLEVULINATE SYNTHASE

B: 5-AMINOLEVULINATE SYNTHASE

D: 5-AMINOLEVULINATE SYNTHASE

E: 5-AMINOLEVULINATE SYNTHASE

hetero molecules

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

1

A: 5-AMINOLEVULINATE SYNTHASE

B: 5-AMINOLEVULINATE SYNTHASE

hetero molecules

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

2

D: 5-AMINOLEVULINATE SYNTHASE

E: 5-AMINOLEVULINATE SYNTHASE

hetero molecules

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

Unit cell

Length a, b, c (Å)	67.875, 92.872, 250.131
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 domain:

ID	Ens-ID	Details
1	1	A
2	1	D
3	1	E
1	2	D
2	2	A
3	2	E
1	3	E
2	3	A
3	3	D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	2	A	1 - 397
2	1	1	2	D	1 - 397
3	1	1	2	E	1 - 397
1	1	2	2	D	1 - 397
2	1	2	2	A	1 - 397
3	1	2	2	E	1 - 397
1	1	3	2	E	1 - 397
2	1	3	2	A	1 - 397
3	1	3	2	D	1 - 397

NCS ensembles :

ID
1
2
3

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Protein , 1 types, 4 molecules ABDE

#1: Protein	5-AMINOLEVULINATE SYNTHASE / Aminolevulinic acid synthase / 5-AMINOLEVULINIC ACID SYNTHASE / DELTA- AMINOLEVULINATE SYNTHASE / DELTA-ALA SYNTHETASE Mass: 43673.910 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Source: (natural) RHODOBACTER CAPSULATUS (bacteria) / References: UniProt: P18079, 5-aminolevulinate synthase

#1: Protein

5-AMINOLEVULINATE SYNTHASE /

Aminolevulinic acid synthase / 5-AMINOLEVULINIC ACID SYNTHASE / DELTA- AMINOLEVULINATE SYNTHASE / DELTA-ALA SYNTHETASE

Mass: 43673.910 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Source: (natural)

RHODOBACTER CAPSULATUS (bacteria) / References: UniProt: P18079,

5-aminolevulinate synthase

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Non-polymers , 7 types, 575 molecules

#2: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P
#3: Chemical	ChemComp-SIN / SUCCINIC ACID / Succinic acid Mass: 118.088 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₄H₆O₄
#4: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#6: Chemical	ChemComp-ACY / ACETIC ACID / Acetic acid Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₄O₂
#7: Chemical	ChemComp-FMT / FORMIC ACID / Formic acid Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH₂O₂
#8: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 562 / Source method: isolated from a natural source / Formula: H₂O

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Details

Sequence details	DIFFERENT STRAINS OF RHODOBACTER CAPSULATUS

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.27 Å³/Da / Density % sol: 45.4 %
Crystal grow	pH: 7.5 Details: 100 MM HEPES, PH 7.5, 200 MM NA ACETATE, 8% (V/V) ISOPROPANOL, 20% PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05
Detector	Type: MARRESEARCH / Detector: CCD / Date: Nov 6, 2003 / Details: MIRRORS
Radiation	Monochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.05 Å / Relative weight: 1
Reflection	Resolution: 2.1→50 Å / Num. obs: 370565 / % possible obs: 83.8 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / R_merge(I) obs: 0.08 / Net I/σ(I): 13.7
Reflection shell	Resolution: 2.1→2.18 Å / Redundancy: 4.7 % / R_merge(I) obs: 0.34 / Mean I/σ(I) obs: 3.8 / % possible all: 82.7

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
DENZO		data reduction
SCALEPACK		data scaling
EPMR		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1BS0 AND 1FC4

1bs0

1fc4

Resolution: 2.1→129.1 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.931 / SU B: 10.235 / SU ML: 0.138 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.295 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.217	3874	5 %	RANDOM
R_work	0.161	-	-	-
obs	0.164	74301	83.7 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 18.95 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.75 Å²	0 Å²	0 Å²
2-	-	0.49 Å²	0 Å²
3-	-	-	1.27 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→129.1 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12132	0	102	562	12796

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.021	0.021	13219
X-RAY DIFFRACTION	r_bond_other_d	0.005	0.02	12084
X-RAY DIFFRACTION	r_angle_refined_deg	1.693	1.963	18008
X-RAY DIFFRACTION	r_angle_other_deg	1.17	3	28064
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.465	5	1727
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.661	23.201	578
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.095	15	2175
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.682	15	98
X-RAY DIFFRACTION	r_chiral_restr	0.124	0.2	1938
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	15256
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	2749
X-RAY DIFFRACTION	r_nbd_refined	0.194	0.2	2800
X-RAY DIFFRACTION	r_nbd_other	0.172	0.2	12610
X-RAY DIFFRACTION	r_nbtor_refined	0.167	0.2	6463
X-RAY DIFFRACTION	r_nbtor_other	0.083	0.2	7366
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.151	0.2	697
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.048	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.163	0.2	19
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.219	0.2	96
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.132	0.2	14
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	2.826	2	10726
X-RAY DIFFRACTION	r_mcbond_other	0.566	2	3398
X-RAY DIFFRACTION	r_mcangle_it	3.21	3	13362
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	3.044	2	5640
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	4.132	3	4646
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

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	2062	tight positional	0.02	0.05
1	2	D	2062	tight positional	0.02	0.05
1	3	E	2062	tight positional	0.02	0.05
2	1	D	2062	tight positional	0.02	0.05
2	2	A	2062	tight positional	0.02	0.05
2	3	E	2062	tight positional	0.02	0.05
3	1	E	2062	tight positional	0.02	0.05
3	2	A	2062	tight positional	0.02	0.05
3	3	D	2062	tight positional	0.02	0.05
1	1	A	3105	medium positional	0.41	0.5
1	2	D	3105	medium positional	0.4	0.5
1	3	E	3105	medium positional	0.37	0.5
2	1	D	3105	medium positional	0.4	0.5
2	2	A	3105	medium positional	0.41	0.5
2	3	E	3105	medium positional	0.37	0.5
3	1	E	3105	medium positional	0.37	0.5
3	2	A	3105	medium positional	0.41	0.5
3	3	D	3105	medium positional	0.4	0.5
1	1	A	2062	tight thermal	0.05	0.5
1	2	D	2062	tight thermal	0.04	0.5
1	3	E	2062	tight thermal	0.04	0.5
2	1	D	2062	tight thermal	0.04	0.5
2	2	A	2062	tight thermal	0.05	0.5
2	3	E	2062	tight thermal	0.04	0.5
3	1	E	2062	tight thermal	0.04	0.5
3	2	A	2062	tight thermal	0.05	0.5
3	3	D	2062	tight thermal	0.04	0.5
1	1	A	3105	medium thermal	0.34	2
1	2	D	3105	medium thermal	0.32	2
1	3	E	3105	medium thermal	0.33	2
2	1	D	3105	medium thermal	0.32	2
2	2	A	3105	medium thermal	0.34	2
2	3	E	3105	medium thermal	0.33	2
3	1	E	3105	medium thermal	0.33	2
3	2	A	3105	medium thermal	0.34	2
3	3	D	3105	medium thermal	0.32	2

LS refinement shell

Resolution: 2.1→2.15 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.269	272	-
R_work	0.189	5346	-
obs	-	-	81.99 %

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	0.4645	-0.2911	-0.0102	0.878	-0.4077	1.5801	-0.0099	-0.0022	-0.0541	-0.0083	0.0667	-0.0528	0.1936	0.2389	-0.0568	0.0176	0.0497	-0.0028	-0.0145	0.0188	-0.0389	41.86	3.575	16.895
2	0.5372	0.4147	-0.1213	0.6815	0.031	0.6223	0.0017	0.0722	0.0464	0.0282	0.0577	0.0963	-0.0275	-0.0953	-0.0594	0.0299	0.0227	0.0168	0.005	0.07	-0.0094	15.106	11.025	9.835
3	0.7019	-0.2524	-0.0321	0.913	0.0919	0.894	0.0556	0.0843	-0.1043	-0.2238	0.0474	-0.0219	0.1783	0.1276	-0.103	0.0716	0.014	0.0183	0.0113	0.0164	-0.0615	37.083	2.356	-1.014
4	2.0452	1.9138	1.3129	2.6801	1.323	1.5483	0.0642	-0.2096	0.0941	0.1688	-0.1122	0.2288	-0.1158	-0.2551	0.0479	0.0584	0.0711	0.0845	-0.0145	0.0389	0.0242	8.798	28.272	23.273
5	0.6079	0.1042	-0.0795	1.5455	-0.608	0.7492	-0.0185	-0.108	-0.0614	0.341	0.0845	0.039	-0.1108	0.0485	-0.066	0.1457	0.0455	0.031	-0.0052	0.043	-0.0372	29.206	10.991	33.915
6	2.6506	1.219	-0.0796	2.2474	-1.0341	2.093	0.3921	0.0265	0.5335	0.7432	0.1366	0.4174	-0.3755	-0.1227	-0.5287	0.3622	0.1308	0.1907	-0.1565	0.0298	-0.0704	15.817	32.865	40.962
7	2.371	0.7904	-1.9364	1.0156	-0.5269	2.4261	0.0714	-0.2156	-0.133	0.3032	-0.0176	-0.2138	0.1947	0.4041	-0.0538	0.097	0.0449	-0.0452	0.1409	0.0354	-0.0063	10.534	-31.174	51.289
8	0.6185	0.1831	-0.0092	0.911	-0.1814	1.9771	0.0382	-0.0021	0.1577	0.1452	-0.0684	0.1268	-0.4025	0.0605	0.0302	0.1446	0.0112	0.0344	0.0127	0.0186	0.0324	-9.734	-12.058	44.783
9	2.5469	-0.0795	-0.6948	0.7075	0.1317	2.5819	0.1314	-0.4761	0.0751	0.4679	-0.0458	-0.0585	-0.1538	0.4874	-0.0856	0.2154	-0.0553	-0.0172	0.1523	0.0111	-0.0617	3.543	-20.59	65.155
10	0.8348	-0.6118	0.0403	1.2857	0.0908	1.4792	0.0141	0.2001	0.0343	-0.0389	-0.0691	0.0464	-0.1326	-0.2691	0.055	0.0237	0.0727	-0.0003	0.0435	0.0473	0.0069	-22.611	-20.576	28.461
11	0.6261	0.057	-0.1727	0.9244	0.0112	1.0419	0.0551	0.0381	0.0124	-0.0542	-0.0797	-0.0812	0.0799	0.2309	0.0246	0.0682	0.0576	0.036	0.0727	0.0475	-0.0096	4.087	-30.792	29.752
12	1.1564	-0.5269	-0.125	1.1475	0.1488	1.2592	0.0768	0.1734	0.0123	-0.1657	-0.0952	0.0963	0.0752	-0.0789	0.0184	0.1033	0.0517	-0.029	0.0333	-0.0248	-0.0062	-17.883	-33.838	16.066

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 52
2	X-RAY DIFFRACTION	2	A	53 - 296
3	X-RAY DIFFRACTION	3	A	297 - 394
4	X-RAY DIFFRACTION	4	B	1 - 52
5	X-RAY DIFFRACTION	5	B	53 - 296
6	X-RAY DIFFRACTION	6	B	297 - 394
7	X-RAY DIFFRACTION	7	D	1 - 52
8	X-RAY DIFFRACTION	8	D	53 - 296
9	X-RAY DIFFRACTION	9	D	297 - 394
10	X-RAY DIFFRACTION	10	E	1 - 52
11	X-RAY DIFFRACTION	11	E	53 - 296
12	X-RAY DIFFRACTION	12	E	297 - 394

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Non-polymers , 7 types, 575 molecules

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Sample preparation

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-Non-polymers , 7 types, 575 molecules

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-Experimental details

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-Data collection

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-Feb 9, 2022. New format data for meta-information of EMDB entries

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Protein , 1 types, 4 molecules ABDE

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Non-polymers , 7 types, 575 molecules

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