PDB-5ubu: 2.75 Angstrom Resolution Crystal Structure of Acetamidase from Ye...

ID or keywords:

Entry

Database: PDB / ID: 5ubu

Title

2.75 Angstrom Resolution Crystal Structure of Acetamidase from Yersinia enterocolitica.

Components

Putative acetamidase/formamidase

Keywords

HYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Acetamidase

Function / homology

Acetamidase/Formamidase / Acetamidase/Formamidase family / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / Putative acetamidase/formamidase

Function and homology information

Biological species

Yersinia enterocolitica subsp. palearctica serotype O:3 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.75 Å

Authors

Minasov, G. / Shuvalova, L. / Flores, K. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: 2.75 Angstrom Resolution Crystal Structure of Acetamidase from Yersinia enterocolitica.
Authors: Minasov, G. / Shuvalova, L. / Flores, K. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Dec 21, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 4, 2017	Provider: repository / Type: Initial release
Revision 1.1	Oct 16, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _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_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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5ubu.cif.gz	530.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5ubu.ent.gz	441.9 KB	Display	PDB format
PDBx/mmJSON format	5ubu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5ubu_validation.pdf.gz	445.6 KB	Display	wwPDB validaton report
Full document	5ubu_full_validation.pdf.gz	450.8 KB	Display
Data in XML	5ubu_validation.xml.gz	56.5 KB	Display
Data in CIF	5ubu_validation.cif.gz	75.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ub/5ubu ftp://data.pdbj.org/pub/pdb/validation_reports/ub/5ubu	HTTPS FTP

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Related structure data

Similar structure data	1cez-d 2ex8-2 2pi4-d 5kaj-4 3slb-d 2pg8-d 3kzl-d 2ex2-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: CSGID-IDP93920

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Putative acetamidase/formamidase

B: Putative acetamidase/formamidase

C: Putative acetamidase/formamidase

D: Putative acetamidase/formamidase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	137.884, 137.884, 204.281
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	B
2	4	C
1	5	B
2	5	D
1	6	C
2	6	D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ALA	ALA	ALA	ALA	A	A	0 - 328	3 - 331
2	1	ALA	ALA	ALA	ALA	B	B	0 - 328	3 - 331
1	2	ALA	ALA	GLN	GLN	A	A	0 - 329	3 - 332
2	2	ALA	ALA	GLN	GLN	C	C	0 - 329	3 - 332
1	3	MSE	MSE	ALA	ALA	A	A	1 - 328	4 - 331
2	3	MSE	MSE	ALA	ALA	D	D	1 - 328	4 - 331
1	4	ALA	ALA	ALA	ALA	B	B	0 - 328	3 - 331
2	4	ALA	ALA	ALA	ALA	C	C	0 - 328	3 - 331
1	5	MSE	MSE	ALA	ALA	B	B	1 - 328	4 - 331
2	5	MSE	MSE	ALA	ALA	D	D	1 - 328	4 - 331
1	6	MSE	MSE	ALA	ALA	C	C	1 - 328	4 - 331
2	6	MSE	MSE	ALA	ALA	D	D	1 - 328	4 - 331

NCS ensembles :

ID
1
2
3
4
5
6

#1: Protein	Putative acetamidase/formamidase Mass: 37376.402 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia enterocolitica subsp. palearctica serotype O:3 (bacteria) Strain: DSM 13030 / CIP 106945 / Y11 / Gene: Y11_22331 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3NNJ4
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 389 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 3.27 Å³/Da / Density meas: 62.4 Mg/m³ / Density % sol: 62.12 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Protein: 8.2 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3); Screen: Classics II (B11), 2.1M DL-Malic acid (pH 7.0); Cryo: Screen : 50% Sucrose (1:1).

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 2, 2014 / Details: C(111)
Radiation	Monochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 2.75→30 Å / Num. obs: 51774 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.9 % / B_iso Wilson estimate: 53.7 Å² / R_merge(I) obs: 0.135 / R_sym value: 0.135 / Net I/σ(I): 17.8
Reflection shell	Resolution: 2.75→2.8 Å / Redundancy: 8 % / R_merge(I) obs: 0.736 / Mean I/σ(I) obs: 3.1 / Num. unique all: 2554 / CC_1/2: 0.849 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.75→29.81 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.93 / SU B: 20.527 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.67 / ESU R Free: 0.288 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21996	2618	5.1 %	RANDOM
R_work	0.1848	-	-	-
obs	0.18656	49001	99.61 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 46.485 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.19 Å²	0 Å²	0 Å²
2-	-	-2.19 Å²	0 Å²
3-	-	-	4.37 Å²

Refinement step

Cycle: 1 / Resolution: 2.75→29.81 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10227	0	8	389	10624

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.019	10527
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	9767
X-RAY DIFFRACTION	r_angle_refined_deg	1.673	1.985	14264
X-RAY DIFFRACTION	r_angle_other_deg	0.905	3	22749
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	2.354	5	1320
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.26	24.396	439
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.066	15	1595
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	9.524	15	56
X-RAY DIFFRACTION	r_chiral_restr	0.095	0.2	1578
X-RAY DIFFRACTION	r_gen_planes_refined	0.023	0.021	11592
X-RAY DIFFRACTION	r_gen_planes_other	0.019	0.02	1992
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	0.769	1.732	5286
X-RAY DIFFRACTION	r_mcbond_other	0.769	1.731	5285
X-RAY DIFFRACTION	r_mcangle_it	1.348	2.593	6604
X-RAY DIFFRACTION	r_mcangle_other	1.348	2.593	6605
X-RAY DIFFRACTION	r_scbond_it	1.327	1.839	5241
X-RAY DIFFRACTION	r_scbond_other	1.327	1.838	5238
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.849	2.695	7659
X-RAY DIFFRACTION	r_long_range_B_refined	4.642	20.924	11218
X-RAY DIFFRACTION	r_long_range_B_other	4.576	20.815	11172
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 / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	21104	0.05
1	2	B	21104	0.05
2	1	A	21146	0.06
2	2	C	21146	0.06
3	1	A	21070	0.05
3	2	D	21070	0.05
4	1	B	21110	0.06
4	2	C	21110	0.06
5	1	B	21042	0.06
5	2	D	21042	0.06
6	1	C	21034	0.06
6	2	D	21034	0.06

LS refinement shell

Resolution: 2.751→2.821 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.34	185	-
R_work	0.313	3470	-
obs	-	-	97.52 %

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	2.499	-0.1248	0.3622	1.1575	0.045	0.8348	0.0289	-0.3141	0.2061	-0.0668	-0.1458	-0.016	-0.2039	0.0434	0.1169	0.1328	0.0394	0.0291	0.3475	-0.0257	0.0734	-17.5557	56.4637	17.7097
2	2.3815	0.8579	1.0859	1.0536	-0.1341	1.0209	0.0026	-0.3538	0.1499	-0.0243	-0.1408	0.1525	-0.0831	-0.0589	0.1382	0.2738	0.0518	0.0051	0.4037	-0.0545	0.2329	-29.7424	53.2633	13.0408
3	12.1115	3.6602	0.2827	5.9038	1.3826	0.978	0.1805	-0.8235	0.2578	0.4254	-0.373	0.3621	0.0506	-0.0985	0.1925	0.1292	0.0114	0.0529	0.4151	-0.0684	0.0633	-38.2789	54.1735	27.867
4	1.4002	0.8643	0.7524	1.4514	0.0315	1.1595	0.0421	-0.4143	-0.0221	-0.0011	-0.1661	-0.1202	-0.0661	-0.0551	0.124	0.148	0.0649	0.0115	0.3202	0.0313	0.1025	-19.3112	49.0432	15.2345
5	1.6585	0.5773	-0.0416	2.5299	-0.4743	1.3885	0.1436	-0.5113	-0.4708	-0.1361	-0.2019	-0.2787	0.1138	0.0198	0.0583	0.1254	0.0569	0.0416	0.3528	0.172	0.2669	-21.5315	32.1273	16.1279
6	3.5854	0.0715	-1.8178	2.9765	0.6342	3.8525	0.1426	-0.5066	-0.2347	0.5091	-0.1338	0.5366	0.1895	-0.2736	-0.0088	0.1105	-0.0441	0.0425	0.5888	0.2494	0.3763	-55.5268	19.1712	27.9535
7	1.261	0.4987	-0.1946	1.0733	-0.3237	0.7914	0.0649	-0.3613	-0.3159	-0.1791	-0.0385	-0.159	0.2712	-0.097	-0.0264	0.1934	0.0096	0.0333	0.2679	0.2395	0.4037	-40.5336	12.8273	14.2918
8	11.2285	2.4369	0.991	5.6986	-1.7834	1.3877	0.1003	-0.568	-0.2307	0.2794	-0.2195	-0.1009	-0.0418	0.1057	0.1192	0.1092	-0.0101	-0.0365	0.3687	0.2626	0.2056	-26.8577	15.3061	29.0213
9	0.8412	0.5037	-0.7097	1.0851	-0.2257	1.3292	0.0958	-0.2578	-0.1103	-0.0533	-0.0511	0.0574	0.1304	-0.1024	-0.0447	0.2388	-0.0063	-0.0061	0.4387	0.2263	0.4823	-45.9519	20.0111	16.6363
10	2.2014	1.049	0.3718	2.6575	-0.3564	1.6524	0.0893	-0.6432	0.0358	0.0835	-0.0682	0.3095	-0.1848	-0.0639	-0.021	0.1132	0.0578	0.0278	0.4041	0.0527	0.2152	-45.512	37.0301	16.1153
11	0.6166	0.6584	-0.8563	3.7301	-0.4397	2.892	-0.2358	0.2619	0.0741	-0.7072	0.0029	-0.1017	0.0571	0.0676	0.2329	0.7339	-0.06	0.1155	0.3896	0.0489	0.2834	-17.4622	55.7533	-27.6158
12	1.7714	0.1966	-0.7501	1.5777	-0.1016	1.4393	-0.2319	-0.0002	-0.1516	-0.2878	0.008	-0.5	0.0969	0.2517	0.224	0.4264	0.0431	0.1742	0.1938	0.0101	0.2071	-10.9482	47.7095	-15.1139
13	2.0191	1.142	-0.6908	1.3472	-1.4366	1.9288	-0.312	0.1166	-0.7571	-0.4348	0.0661	-0.4215	0.2716	0.0098	0.2459	0.6778	0.0562	0.3724	0.2055	-0.0342	0.5974	-13.256	28.8131	-17.6758
14	1.9121	0.529	-0.3921	1.0452	-0.2689	1.0293	-0.2588	0.0162	-0.1232	-0.3903	0.0851	-0.265	0.141	0.0741	0.1736	0.339	0.0443	0.1456	0.0632	0.0051	0.0903	-19.48	47.6863	-16.3228
15	3.029	1.2658	0.4227	1.778	-0.3048	2.0735	-0.3579	0.1117	-0.0362	-0.5425	0.2592	0.1087	0.1031	-0.1241	0.0986	0.4179	-0.0031	0.0099	0.1028	-0.0138	0.0812	-36.1638	44.6856	-16.3174
16	3.7738	1.3134	-0.9158	1.7432	0.5594	2.6333	-0.4882	0.389	-0.8745	-0.8714	0.2953	-0.065	0.2234	-0.2463	0.1929	0.7729	-0.1636	0.0539	0.1627	-0.0625	0.5274	-51.9329	10.4804	-21.5627
17	2.4404	0.9413	-0.0995	4.3026	0.791	0.4796	-0.4921	-0.0572	-0.2464	-0.3365	0.3938	0.0501	0.1942	-0.1427	0.0982	0.545	-0.0485	-0.0124	0.2769	0.0006	0.2749	-55.6573	22.9258	-13.114
18	2.0601	1.5047	-0.1889	2.8881	-0.2339	0.482	-0.3611	0.1375	-0.0354	-0.8376	0.2818	0.1626	0.1556	-0.1985	0.0793	0.4881	-0.0284	-0.0979	0.1656	-0.0193	0.2085	-52.5221	34.071	-15.6965
19	3.022	0.5629	-0.2524	2.429	-0.0131	0.7318	-0.4783	0.1798	-0.767	-0.7087	0.2764	-0.2093	0.112	-0.1408	0.2019	0.4966	-0.0579	0.0821	0.1169	-0.0999	0.2712	-47.7688	21.6878	-16.9034
20	3.8052	1.4273	-0.1038	1.7927	0.1384	0.547	-0.3398	0.0066	-1.0289	-0.5318	0.1582	-0.3947	0.2111	0.0706	0.1816	0.5761	0.0033	0.2617	0.0438	-0.0118	0.4146	-31.4049	20.5684	-15.7388

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 88
2	X-RAY DIFFRACTION	2	A	89 - 146
3	X-RAY DIFFRACTION	3	A	147 - 166
4	X-RAY DIFFRACTION	4	A	167 - 247
5	X-RAY DIFFRACTION	5	A	248 - 329
6	X-RAY DIFFRACTION	6	B	-1 - 33
7	X-RAY DIFFRACTION	7	B	34 - 144
8	X-RAY DIFFRACTION	8	B	145 - 164
9	X-RAY DIFFRACTION	9	B	165 - 244
10	X-RAY DIFFRACTION	10	B	245 - 329
11	X-RAY DIFFRACTION	11	C	0 - 33
12	X-RAY DIFFRACTION	12	C	34 - 105
13	X-RAY DIFFRACTION	13	C	106 - 167
14	X-RAY DIFFRACTION	14	C	168 - 248
15	X-RAY DIFFRACTION	15	C	249 - 329
16	X-RAY DIFFRACTION	16	D	1 - 55
17	X-RAY DIFFRACTION	17	D	56 - 105
18	X-RAY DIFFRACTION	18	D	106 - 183
19	X-RAY DIFFRACTION	19	D	184 - 241
20	X-RAY DIFFRACTION	20	D	242 - 329

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