PDB-1r3n: Crystal structure of beta-alanine synthase from Saccharomyces kluyveri

ID or keywords:

Entry

Database: PDB / ID: 1r3n

Title

Crystal structure of beta-alanine synthase from Saccharomyces kluyveri

Components

beta-alanine synthase

Beta-ureidopropionase

Keywords

HYDROLASE / alpha and beta protein / di-zinc center

Function / homology

Function and homology information

beta-ureidopropionase / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines /

beta-ureidopropionase activity /

metal ion binding
Similarity search - Function

Biological species

Lachancea kluyveri (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Lundgren, S. / Gojkovic, Z. / Piskur, J. / Dobritzsch, D.

Citation

Journal: J.Biol.Chem. / Year: 2003
Title: Yeast beta-Alanine Synthase Shares a Structural Scaffold and Origin with Dizinc-dependent Exopeptidases
Authors: Lundgren, S. / Gojkovic, Z. / Piskur, J. / Dobritzsch, D.

History

Deposition	Oct 2, 2003	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 11, 2003	Provider: repository / Type: Initial release
Revision 1.1	Apr 29, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Feb 14, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Apr 3, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	1r3n.cif.gz	649 KB	Display	PDBx/mmCIF format
PDB format	pdb1r3n.ent.gz	534.2 KB	Display	PDB format
PDBx/mmJSON format	1r3n.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r3/1r3n ftp://data.pdbj.org/pub/pdb/validation_reports/r3/1r3n	HTTPS FTP

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Related structure data

Related structure data	1r43C C: citing same article (ref.)
Similar structure data	1r43-d 2v8d-d 1z2l-d 6c0d-1 1o65-d 5zon-d 3tii-d 4w7k-d 1xcc-d 5tp4-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) 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

Related structure data

1r43C

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#110 - Feb 2009 Auxin and TIR1 Ubiquitin Ligase similarity (5)

Deposited unit

A: beta-alanine synthase

B: beta-alanine synthase

C: beta-alanine synthase

D: beta-alanine synthase

E: beta-alanine synthase

F: beta-alanine synthase

G: beta-alanine synthase

H: beta-alanine synthase

hetero molecules

408 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: beta-alanine synthase

B: beta-alanine synthase

hetero molecules

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

2

C: beta-alanine synthase

D: beta-alanine synthase

hetero molecules

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

3

E: beta-alanine synthase

F: beta-alanine synthase

hetero molecules

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

4

G: beta-alanine synthase

H: beta-alanine synthase

hetero molecules

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

Unit cell

Length a, b, c (Å)	117.230, 77.120, 225.520
Angle α, β, γ (deg.)	90.00, 95.05, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	ALA	ALA	PRO	PRO	2	A	A	248 - 363	247 - 362
2	1	1	ALA	ALA	PRO	PRO	2	B	B	248 - 363	247 - 362
3	1	1	ALA	ALA	PRO	PRO	2	C	C	248 - 363	247 - 362
4	1	1	ALA	ALA	PRO	PRO	2	D	D	248 - 363	247 - 362
5	1	1	ALA	ALA	PRO	PRO	2	E	E	248 - 363	247 - 362
6	1	1	ALA	ALA	PRO	PRO	2	F	F	248 - 363	247 - 362
7	1	1	ALA	ALA	PRO	PRO	2	G	G	248 - 363	247 - 362
8	1	1	ALA	ALA	PRO	PRO	2	H	H	248 - 363	247 - 362
1	1	2	ALA	ALA	LEU	LEU	3	A	A	31 - 186	30 - 185
2	1	2	ALA	ALA	LEU	LEU	3	B	B	31 - 186	30 - 185
3	1	2	ALA	ALA	LEU	LEU	3	C	C	31 - 186	30 - 185
4	1	2	ALA	ALA	LEU	LEU	3	D	D	31 - 186	30 - 185
5	1	2	ALA	ALA	LEU	LEU	3	F	F	31 - 186	30 - 185
6	1	2	ALA	ALA	LEU	LEU	3	H	H	31 - 186	30 - 185
7	1	2	ALA	ALA	LEU	LEU	3	E	E	31 - 186	30 - 185
8	1	2	ALA	ALA	LEU	LEU	3	G	G	31 - 186	30 - 185
9	2	2	VAL	VAL	VAL	VAL	3	A	A	197 - 246	196 - 245
10	2	2	VAL	VAL	VAL	VAL	3	B	B	197 - 246	196 - 245
11	2	2	VAL	VAL	VAL	VAL	3	C	C	197 - 246	196 - 245
12	2	2	VAL	VAL	VAL	VAL	3	D	D	197 - 246	196 - 245
13	2	2	VAL	VAL	VAL	VAL	3	F	F	197 - 246	196 - 245
14	2	2	VAL	VAL	VAL	VAL	3	H	H	197 - 246	196 - 245
15	2	2	VAL	VAL	VAL	VAL	3	E	E	197 - 246	196 - 245
16	2	2	VAL	VAL	VAL	VAL	3	G	G	197 - 246	196 - 245
17	3	2	VAL	VAL	TYR	TYR	3	A	A	365 - 423	364 - 422
18	3	2	VAL	VAL	TYR	TYR	3	B	B	365 - 423	364 - 422
19	3	2	VAL	VAL	TYR	TYR	3	C	C	365 - 423	364 - 422
20	3	2	VAL	VAL	TYR	TYR	3	D	D	365 - 423	364 - 422
21	3	2	VAL	VAL	TYR	TYR	3	F	F	365 - 423	364 - 422
22	3	2	VAL	VAL	TYR	TYR	3	H	H	365 - 423	364 - 422
23	3	2	VAL	VAL	TYR	TYR	3	E	E	365 - 423	364 - 422
24	3	2	VAL	VAL	TYR	TYR	3	G	G	365 - 423	364 - 422
25	4	2	GLU	GLU	ILE	ILE	3	A	A	431 - 452	430 - 451
26	4	2	GLU	GLU	ILE	ILE	3	B	B	431 - 452	430 - 451
27	4	2	GLU	GLU	ILE	ILE	3	C	C	431 - 452	430 - 451
28	4	2	GLU	GLU	ILE	ILE	3	D	D	431 - 452	430 - 451
29	4	2	GLU	GLU	ILE	ILE	3	F	F	431 - 452	430 - 451
30	4	2	GLU	GLU	ILE	ILE	3	H	H	431 - 452	430 - 451
31	4	2	GLU	GLU	ILE	ILE	3	E	E	431 - 452	430 - 451
32	4	2	GLU	GLU	ILE	ILE	3	G	G	431 - 452	430 - 451
33	5	2	ZN	ZN	ZN	ZN	1	A	I - J	500 - 501
34	5	2	ZN	ZN	ZN	ZN	1	B	L - M	500 - 501
35	5	2	ZN	ZN	ZN	ZN	1	C	O - P	500 - 501
36	5	2	ZN	ZN	ZN	ZN	1	D	R - S	500 - 501
37	5	2	ZN	ZN	ZN	ZN	1	F	Y - Z	500 - 501
38	5	2	ZN	ZN	ZN	ZN	1	H	EA - FA	500 - 501
39	5	2	ZN	ZN	ZN	ZN	1	E	U - V	500 - 501
40	5	2	ZN	ZN	ZN	ZN	1	G	AA - BA	500 - 501

NCS ensembles :

ID
1
2

Details

The biological assembly is a dimer. The asymmetric unit contains four such dimers.

#1: Protein	beta-alanine synthase / Beta-ureidopropionase Mass: 50728.598 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lachancea kluyveri (fungus) / Gene: PYD3 / Plasmid: P491 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus / References: UniProt: Q96W94, beta-ureidopropionase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-BIB / BETA-AMINO ISOBUTYRATE Mass: 102.112 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₄H₈NO₂
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 509 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal

Density Matthews: 2.5 Å³/Da / Density % sol: 50.82 %

Crystal grow

Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: trisodium citrate, dioxane, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal grow

*PLUS

Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop

Components of the solutions

*PLUS

ID	Conc.	Common name	Crystal-ID	Sol-ID	Details	Chemical formula
1	4.0-4.5 mg/ml	protein	1	drop
2	50 mM	Tris	1	drop	pH7.5
3	1 mM	dithiothreitol	1	drop
4	100 mM		1	drop		NaCl
5	0.88 M	trisodium citrate	1	reservoir
6	0.1 M	sodium citrate	1	reservoir	pH6.0
7	5 %(v/v)	dioxane	1	reservoir

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 10, 2001 / Details: diamond monochromator and bent multilayer
Radiation	Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.933 Å / Relative weight: 1
Reflection	Resolution: 2.7→25 Å / Num. obs: 106190 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / B_iso Wilson estimate: 54.6 Å² / R_merge(I) obs: 0.083 / Net I/σ(I): 14.8
Reflection shell	Resolution: 2.7→2.85 Å / Redundancy: 2.6 % / R_merge(I) obs: 0.261 / Mean I/σ(I) obs: 3.7 / Num. unique all: 13170 / % possible all: 82.2
Reflection shell	PLUS % possible obs*: 82.2 %

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Processing

Software

Name	Version	Classification
REFMAC	5.1.24	refinement
MOSFLM		data reduction
CCP4	(SCALA)	data scaling
EPMR		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: model of seleno-methionine substituted beta-alanine synthase from the same source

Resolution: 2.7→25 Å / Cor.coef. F_o:F_c: 0.944 / Cor.coef. F_o:F_c free: 0.904 / SU B: 15.258 / SU ML: 0.301 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.387 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26577	5296	5 %	RANDOM
R_work	0.20837	-	-	-
obs	0.21118	100879	95.84 %	-
all	-	100879	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 16.339 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.21 Å²	0 Å²	2.2 Å²
2-	-	-2.46 Å²	0 Å²
3-	-	-	1.63 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	26906	0	72	519	27497

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.021	27622
X-RAY DIFFRACTION	r_angle_refined_deg	1.189	1.938	37391
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.301	5	3477
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	4048
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	21260
X-RAY DIFFRACTION	r_nbd_refined	0.205	0.2	12807
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.164	0.2
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.222	0.2	143
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.218	0.2	20
X-RAY DIFFRACTION	r_mcbond_it	0.185	1.5	17236
X-RAY DIFFRACTION	r_mcangle_it	0.447	2	27646
X-RAY DIFFRACTION	r_scbond_it	0.97	3	10386
X-RAY DIFFRACTION	r_scangle_it	1.621	4.5	9745

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	464	tight positional	0.04	0.05
1	2	B	464	tight positional	0.04	0.05
1	3	C	464	tight positional	0.04	0.05
1	4	D	464	tight positional	0.04	0.05
1	5	E	464	tight positional	0.03	0.05
1	6	F	464	tight positional	0.04	0.05
1	7	G	464	tight positional	0.03	0.05
1	8	H	464	tight positional	0.03	0.05
2	1	A	1150	tight positional	0.07	0.05
2	2	B	1150	tight positional	0.03	0.05
2	3	C	1150	tight positional	0.04	0.05
2	4	D	1150	tight positional	0.03	0.05
2	5	F	1150	tight positional	0.04	0.05
2	6	H	1150	tight positional	0.03	0.05
2	7	E	1150	tight positional	0.03	0.05
2	8	G	1150	tight positional	0.03	0.05
1	1	A	427	medium positional	0.47	0.5
1	2	B	427	medium positional	0.49	0.5
1	3	C	427	medium positional	0.47	0.5
1	4	D	427	medium positional	0.46	0.5
1	5	E	427	medium positional	0.47	0.5
1	6	F	427	medium positional	0.46	0.5
1	7	G	427	medium positional	0.48	0.5
1	8	H	427	medium positional	0.5	0.5
2	1	A	1081	loose positional	0.58	5
2	2	B	1081	loose positional	0.71	5
2	3	C	1081	loose positional	0.56	5
2	4	D	1081	loose positional	0.7	5
2	5	F	1081	loose positional	0.59	5
2	6	H	1081	loose positional	0.64	5
2	7	E	1081	loose positional	1.07	5
2	8	G	1081	loose positional	0.8	5
1	1	A	464	tight thermal	0.08	0.5
1	2	B	464	tight thermal	0.06	0.5
1	3	C	464	tight thermal	0.06	0.5
1	4	D	464	tight thermal	0.05	0.5
1	5	E	464	tight thermal	0.06	0.5
1	6	F	464	tight thermal	0.05	0.5
1	7	G	464	tight thermal	0.05	0.5
1	8	H	464	tight thermal	0.05	0.5
2	1	A	1150	tight thermal	0.07	0.5
2	2	B	1150	tight thermal	0.05	0.5
2	3	C	1150	tight thermal	0.06	0.5
2	4	D	1150	tight thermal	0.05	0.5
2	5	F	1150	tight thermal	0.07	0.5
2	6	H	1150	tight thermal	0.06	0.5
2	7	E	1150	tight thermal	0.06	0.5
2	8	G	1150	tight thermal	0.06	0.5
1	1	A	427	medium thermal	0.66	2
1	2	B	427	medium thermal	0.45	2
1	3	C	427	medium thermal	0.5	2
1	4	D	427	medium thermal	0.45	2
1	5	E	427	medium thermal	0.44	2
1	6	F	427	medium thermal	0.47	2
1	7	G	427	medium thermal	0.48	2
1	8	H	427	medium thermal	0.46	2
2	1	A	1081	loose thermal	1.51	10
2	2	B	1081	loose thermal	1.1	10
2	3	C	1081	loose thermal	1.54	10
2	4	D	1081	loose thermal	1.08	10
2	5	F	1081	loose thermal	1.36	10
2	6	H	1081	loose thermal	1.15	10
2	7	E	1081	loose thermal	1.45	10
2	8	G	1081	loose thermal	1.53	10

LS refinement shell

Resolution: 2.7→2.77 Å / Total num. of bins used: 20

	R_factor	Num. reflection
R_free	0.355	318
R_work	0.277	6251
obs	-	6632

Refinement

*PLUS

Highest resolution: 2.7 Å / Lowest resolution: 30 Å / R_factor R_free: 0.266 / R_factor R_work: 0.208

Solvent computation

*PLUS

Displacement parameters

*PLUS

Refine LS restraints

*PLUS

Refine-ID	Type	Dev ideal
X-RAY DIFFRACTION	r_bond_d	0.009
X-RAY DIFFRACTION	r_angle_d
X-RAY DIFFRACTION	r_angle_deg	1.2

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi