PDB-2vl1: Crystal structure of beta-alanine synthase from Saccharomyces klu...

ID or keywords:

Entry

Database: PDB / ID: 2vl1

Title

Crystal structure of beta-alanine synthase from Saccharomyces kluyveri in complex with a gly-gly peptide

Components

BETA-ALANINE SYNTHASE

Beta-ureidopropionase

Keywords

HYDROLASE / DI-ZINC CENTER /

AMIDOHYDROLASE / ALPHA AND BETA PROTEIN / COMPLEX WITH GLYCINE-GLYCINE

Function / homology

Function and homology information

beta-ureidopropionase activity /

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

metal ion binding
Similarity search - Function

Biological species

SACCHAROMYCES KLUYVERI (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.15 Å

Authors

Andersen, B. / Lundgren, S. / Dobritzsch, D. / Piskur, J.

Citation

Journal: J.Mol.Biol. / Year: 2008
Title: A Recruited Protease is Involved in Catabolism of Pyrimidines.
Authors: Andersen, B. / Lundgren, S. / Dobritzsch, D. / Piskur, J.

History

Deposition	Jan 7, 2008	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 13, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Feb 19, 2014	Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Revision 1.3	Mar 29, 2017	Group: Structure summary
Revision 1.4	Jun 20, 2018	Group: Advisory / Data collection / Derived calculations Category: pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms ...pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._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
Revision 1.5	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_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_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_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

Remark 700

SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2vl1.cif.gz	357.4 KB	Display	PDBx/mmCIF format
PDB format	pdb2vl1.ent.gz	289.5 KB	Display	PDB format
PDBx/mmJSON format	2vl1.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vl/2vl1 ftp://data.pdbj.org/pub/pdb/validation_reports/vl/2vl1	HTTPS FTP

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Related structure data

Related structure data	2v8gS 1r3n 1r43 2v8d 2v8h 2v8v S: Starting model for refinement
Similar structure data	2v8g-1 2v8h-1 2v8g-2 2v8h-2 3lcm-d 1r6u-d 3ohh-d 4f8y-d 3c8v-2 3a04-1 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	#110 - Feb 2009 Auxin and TIR1 Ubiquitin Ligase similarity (5) #235 - Jul 2019 AMPA Receptor similarity (1) #142 - Oct 2011 PDB Pioneers similarity (1)

Deposited unit

A: BETA-ALANINE SYNTHASE

B: BETA-ALANINE SYNTHASE

C: BETA-ALANINE SYNTHASE

D: BETA-ALANINE SYNTHASE

hetero molecules

210 kDa, 4 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
105 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
105 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	49.835, 218.370, 81.499
Angle α, β, γ (deg.)	90.00, 91.85, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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

Dom-ID	Component-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	LEU	LEU	TRP	TRP	3	A	A	28 - 52	27 - 51
2	1	LEU	LEU	TRP	TRP	3	B	B	28 - 52	27 - 51
3	1	LEU	LEU	TRP	TRP	3	C	C	28 - 52	27 - 51
4	1	LEU	LEU	TRP	TRP	3	D	D	28 - 52	27 - 51
1	2	HIS	HIS	VAL	VAL	3	A	A	57 - 189	56 - 188
2	2	HIS	HIS	VAL	VAL	3	B	B	57 - 189	56 - 188
3	2	HIS	HIS	VAL	VAL	3	C	C	57 - 189	56 - 188
4	2	HIS	HIS	VAL	VAL	3	D	D	57 - 189	56 - 188
1	3	SER	SER	PHE	PHE	3	A	A	196 - 457	195 - 456
2	3	SER	SER	PHE	PHE	3	B	B	196 - 457	195 - 456
3	3	SER	SER	PHE	PHE	3	C	C	196 - 457	195 - 456
4	3	SER	SER	PHE	PHE	3	D	D	196 - 457	195 - 456
1	4	ZN	ZN	ZN	ZN	4	A	G	500
2	4	ZN	ZN	ZN	ZN	4	B	M	500
3	4	ZN	ZN	ZN	ZN	4	C	T	500
4	4	ZN	ZN	ZN	ZN	4	D	Y	500

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.674, 0.01, 0.739), (-0.012, -1, 0.002), (0.739, -0.008, 0.674)	9.94007, 0.2318, -4.49573
2	given	(-0.744, -0.031, -0.667), (-0.039, 0.999, -0.004), (0.667, 0.023, -0.745)	25.09054, -37.53083, 39.68869
3	given	(0.993, 0.036, -0.111), (0.037, -0.999, 0.012), (-0.111, -0.016, -0.994)	22.59219, 37.53157, 41.10304

#1: Protein	BETA-ALANINE SYNTHASE / Beta-ureidopropionase Mass: 52006.809 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-455 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES KLUYVERI (fungus) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96W94, beta-ureidopropionase
#2: Chemical	ChemComp-GLY / GLYCINE / Glycine Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C₂H₅NO₂
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1028 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	THE N-TERMINAL METHIONINE IS ABSENT, MOST LIKELY DUE TO POSTTRANSLATIONAL MODIFICATION. THE LAST 20 ...THE N-TERMINAL METHIONINE IS ABSENT, MOST LIKELY DUE TO POSTTRANSLATIONAL MODIFICATION. THE LAST 20 AMINO ACIDS CORRESPOND TO THE C-TERMINAL HIS-TAG.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.1 Å³/Da / Density % sol: 41 % / Description: NONE
Crystal grow	pH: 8.75 / Details: PEG 6000, TRIS PH 8.5, BICINE PH 9.0, LICL

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.939
Detector	Type: ADSC CCD / Detector: CCD / Date: Jul 15, 2006
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.939 Å / Relative weight: 1
Reflection	Resolution: 2.15→50 Å / Num. obs: 89524 / % possible obs: 95.2 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / R_merge(I) obs: 0.13 / Net I/σ(I): 8.7
Reflection shell	Resolution: 2.15→2.27 Å / Redundancy: 2.8 % / R_merge(I) obs: 0.45 / Mean I/σ(I) obs: 2.2 / % possible all: 97.1

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
MOSFLM		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V8G

2v8g

Resolution: 2.15→50 Å / Cor.coef. F_o:F_c: 0.927 / Cor.coef. F_o:F_c free: 0.883 / SU B: 12.395 / SU ML: 0.174 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.332 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.263	4495	5 %	RANDOM
R_work	0.202	-	-	-
obs	0.205	84976	95.1 %	-

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: 18.65 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.83 Å²	0 Å²	0.26 Å²
2-	-	-2.47 Å²	0 Å²
3-	-	-	0.66 Å²

Refinement step

Cycle: LAST / Resolution: 2.15→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13393	0	77	1028	14498

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	13869
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.197	1.941	18807
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.03	5	1762
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.781	24.49	657
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.642	15	2251
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.785	15	71
X-RAY DIFFRACTION	r_chiral_restr	0.088	0.2	2015
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	10747
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.184	0.2	6511
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.298	0.2	9311
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.153	0.2	1053
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined	0.22	0.2	4
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.177	0.2	104
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.107	0.2	22
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	0.316	1.5	8912
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.531	2	13883
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.153	3	5681
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.804	4.5	4910
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 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	1664	tight positional	0.04	0.05
2	B	1664	tight positional	0.03	0.05
3	C	1664	tight positional	0.03	0.05
4	D	1664	tight positional	0.04	0.05
1	A	1	medium positional	0.11	0.5
2	B	1	medium positional	0.09	0.5
3	C	1	medium positional	0.04	0.5
4	D	1	medium positional	0.08	0.5
1	A	1529	loose positional	0.41	5
2	B	1529	loose positional	0.38	5
3	C	1529	loose positional	0.41	5
4	D	1529	loose positional	0.39	5
1	A	1664	tight thermal	0.09	0.5
2	B	1664	tight thermal	0.07	0.5
3	C	1664	tight thermal	0.08	0.5
4	D	1664	tight thermal	0.07	0.5
1	A	1	medium thermal	2.13	2
2	B	1	medium thermal	0.83	2
3	C	1	medium thermal	2.21	2
4	D	1	medium thermal	0.9	2
1	A	1529	loose thermal	1.1	10
2	B	1529	loose thermal	1.02	10
3	C	1529	loose thermal	0.97	10
4	D	1529	loose thermal	1.06	10

LS refinement shell

Resolution: 2.15→2.21 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.315	321	-
R_work	0.241	6402	-
obs	-	-	97.29 %

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	28.1237	-7.961	5.2143	51.6629	7.6504	7.811	-0.4379	-0.4391	1.1754	-1.1255	-0.0366	-0.3899	-0.4404	-0.3076	0.4744	-0.0002	0.0014	-0.0017	-0.0002	-0.0008	0.0017	45.1313	47.6263	42.2551
2	0.8927	-0.0458	0.0213	0.5759	0.0255	0.5964	-0.0329	-0.0293	-0.0136	0.0581	0.025	-0.0199	-0.0147	0.0575	0.0079	-0.0686	-0.0051	0.002	-0.0452	0	-0.093	32.6704	27.8271	51.8824
3	0.2287	0.169	0.1372	1.2332	0.1071	0.2033	-0.0179	0.048	0.0088	-0.0321	0.0132	0.0557	-0.0267	-0.0089	0.0048	-0.0686	0.0056	0.0176	-0.043	-0.0041	-0.1034	22.0583	21.1772	35.8547
4	9.0209	-6.6345	-1.4771	33.7252	5.8505	6.1781	-0.235	-0.6061	-0.5524	-0.0898	0.6309	0.4923	0.393	0.0005	-0.396	0.0007	0.0014	0.0001	0.001	-0.0006	0.0004	9.289	-44.1043	58.691
5	0.6972	-0.1435	-0.1109	0.8257	0.0248	0.406	-0.008	-0.1369	0.0572	0.1101	0.0195	-0.1093	0.0226	0.0466	-0.0115	0.0038	0.0025	-0.0271	0.0063	-0.0056	0.0024	25.9362	-27.5403	54.9793
6	0.0243	0.0826	-0.0264	1.4908	-0.3023	0.2509	-0.0038	0.0229	-0.0371	-0.1078	0.0091	-0.0024	0.0657	-0.0167	-0.0053	-0.0366	0.0018	-0.0014	-0.0342	-0.0084	-0.0435	21.6602	-21.3309	36.2815
7	58.9615	5.4571	9.7801	31.7981	-11.7433	12.1896	-0.0869	-0.0312	0.6695	0.8401	0.7595	0.3355	0.0008	1.0439	-0.6726	0.0006	-0.0005	-0.0014	0.0005	0.0007	0.0016	-16.3135	82.9772	-16.2348
8	0.6745	0.1266	0.122	1.246	-0.1038	0.6888	-0.0054	0.0963	-0.0583	-0.1407	-0.0091	-0.0939	0.0234	0.0229	0.0144	0.0097	-0.0074	-0.0081	-0.0044	0.0032	-0.0103	-0.5557	65.0814	-14.5899
9	0.0369	-0.0878	-0.0443	1.4573	-0.3256	0.2019	-0.0084	-0.0168	0.0322	0.1721	-0.0065	-0.0446	-0.0598	-0.0006	0.0149	0.0042	-0.0105	-0.0334	-0.0392	-0.0061	-0.0219	-2.154	58.9994	4.3656
10	93.6644	22.7767	20.1854	33.6865	37.3238	52.7304	0.0543	-1.5758	0.2139	-0.0743	-0.5557	-0.5408	0.5145	1.5072	0.5014	0.002	0.002	-0.0001	0.0071	0.0046	0.0033	21.2071	-11.7268	-2.5751
11	0.7445	0.0602	0.1326	1.0096	0.0796	0.493	-0.0118	0.0817	-0.0067	-0.0237	-0.0155	-0.053	0.0359	0.0655	0.0273	-0.0553	0.0054	0.0129	-0.0249	0.0152	-0.0797	8.5877	9.696	-11.8899
12	0.2019	-0.2883	-0.0848	1.3229	0.0199	0.281	-0.044	-0.0407	-0.0085	0.1111	0.0242	0.0159	0.0304	-0.0038	0.0198	-0.0386	-0.0112	-0.0008	-0.0518	0.0023	-0.0869	-0.5514	16.4174	5.106

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	18 - 30
2	X-RAY DIFFRACTION	2	A	31 - 215
3	X-RAY DIFFRACTION	3	A	216 - 455
4	X-RAY DIFFRACTION	4	B	18 - 33
5	X-RAY DIFFRACTION	5	B	34 - 212
6	X-RAY DIFFRACTION	6	B	213 - 455
7	X-RAY DIFFRACTION	7	C	18 - 30
8	X-RAY DIFFRACTION	8	C	31 - 209
9	X-RAY DIFFRACTION	9	C	210 - 455
10	X-RAY DIFFRACTION	10	D	18 - 28
11	X-RAY DIFFRACTION	11	D	29 - 215
12	X-RAY DIFFRACTION	12	D	216 - 455

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Movie

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Structure viewers

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Validation report

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Assembly

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Data collection

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About Yorodumi

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

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Aug 12, 2020. Covid-19 info

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

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Yorodumi