PDB-6uvz: Amidohydrolase 2 from Bifidobacterium longum subsp. infantis

ID or keywords:

Entry

Database: PDB / ID: 6uvz

Title

Amidohydrolase 2 from Bifidobacterium longum subsp. infantis

Components

Amidohydrolase 2

Keywords

HYDROLASE / MCSG / structural genomics / PSI-Biology / Midwest Center for Structural Genomics

Function / homology

: / Amidohydrolase / Amidohydrolase-related / Metal-dependent hydrolase / hydrolase activity / CITRIC ACID / Amidohydrolase 2

Function and homology information

Biological species

Bifidobacterium longum subsp. infantis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.898 Å

Authors

Chang, C. / Xu, X. / Cui, H. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To Be Published
Title: Amidohydrolase 2 from Bifidobacterium longum subsp. infantis
Authors: Chang, C. / Xu, X. / Cui, H. / Savchenko, A. / Joachimiak, A.

History

Deposition	Nov 4, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 26, 2020	Provider: repository / Type: Initial release
Revision 1.1	Nov 6, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6uvz.cif.gz	497.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6uvz.ent.gz	413 KB	Display	PDB format
PDBx/mmJSON format	6uvz.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/uv/6uvz ftp://data.pdbj.org/pub/pdb/validation_reports/uv/6uvz	HTTPS FTP

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Related structure data

Similar structure data	1ydn-3 5ab3-1 4i6k-d 2p1f-d 2iw3-d 1ydn-1 4gj1-d 1ydn-4 5ac7-1 4mup-3 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) 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	TargetDB: MCSG-APC40143

Similar structure data

Other databases

TargetDB: MCSG-APC40143

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (2) #158 - Feb 2013 Proton-Gated Urea Channel similarity (2)

Deposited unit

A: Amidohydrolase 2

B: Amidohydrolase 2

C: Amidohydrolase 2

D: Amidohydrolase 2

E: Amidohydrolase 2

hetero molecules

147 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Amidohydrolase 2

hetero molecules

defined by author
29.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Amidohydrolase 2

hetero molecules

defined by author
29.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Amidohydrolase 2

defined by author
29 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Amidohydrolase 2

hetero molecules

defined by author
29.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

E: Amidohydrolase 2

hetero molecules

defined by author
29.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	166.528, 166.528, 151.693
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2

#1: Protein	Amidohydrolase 2 Mass: 28975.668 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bifidobacterium longum subsp. infantis (strain ATCC 15697 / DSM 20088 / JCM 1222 / NCTC 11817 / S12) (bacteria) Strain: ATCC 15697 / DSM 20088 / JCM 1222 / NCTC 11817 / S12 Gene: Blon_2306 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7GNK8
#2: Chemical	ChemComp-2PE / NONAETHYLENE GLYCOL Mass: 414.488 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₈H₃₈O₁₀ / Comment: precipitant*YM
#3: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₈O₇
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 3.67 Å³/Da / Density % sol: 66.44 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M Tris ph 8.5, 0.7 M tri-Sodium Citrate

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97912 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2010

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97912 Å / Relative weight: 1

Reflection

Resolution: 2.898→50 Å / Num. obs: 47403 / % possible obs: 98.9 % / Redundancy: 7.2 % / R_merge(I) obs: 0.154 / Χ²: 2.224 / Net I/σ(I): 7.4

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	Χ²	Diffraction-ID	% possible all
2.9-2.95	7.1	0.999	2349	2.282	1	99.6
2.95-3	7.2	0.9	2356	1.969	1	99.6
3-3.06	7.2	0.731	2329	1.826	1	99.6
3.06-3.12	7.2	0.618	2346	1.741	1	99.6
3.12-3.19	7.2	0.49	2357	1.522	1	99.6
3.19-3.27	7.2	0.384	2378	1.633	1	99.6
3.27-3.35	7.3	0.351	2325	1.578	1	99.6
3.35-3.44	7.3	0.315	2346	1.938	1	99.2
3.44-3.54	7.3	0.247	2352	1.778	1	99.2
3.54-3.65	7.3	0.215	2357	1.85	1	99.5
3.65-3.78	7.3	0.186	2374	2.052	1	99.2
3.78-3.94	7.3	0.156	2352	1.993	1	99.3
3.94-4.11	7.3	0.131	2361	1.888	1	99
4.11-4.33	7.3	0.113	2364	1.92	1	99
4.33-4.6	7.2	0.102	2377	2.147	1	98.9
4.6-4.96	7.2	0.092	2376	2.367	1	98.9
4.96-5.46	7.2	0.093	2381	2.39	1	98.4
5.46-6.24	7	0.097	2402	2.539	1	98.2
6.24-7.86	7	0.084	2414	3.396	1	97.5
7.86-50	6.7	0.068	2507	5.787	1	95.4

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
PHENIX	1.16_3549	refinement
PDB_EXTRACT	3.25	data extraction
HKL-3000		data reduction
HKL-3000		phasing

Refinement

Method to determine structure:

MAD / Resolution: 2.898→44.794 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.6

	R_factor	Num. reflection	% reflection
R_free	0.2172	2368	5.06 %
R_work	0.1806	-	-
obs	0.1825	46756	97.64 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 153 Å² / B_iso mean: 53.9248 Å² / B_iso min: 5.42 Å²

Refinement step

Cycle: final / Resolution: 2.898→44.794 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9803	0	110	61	9974
B_iso mean	-	-	68.96	31.93	-
Num. residues	-	-	-	-	1248

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
2.898-2.9571	0.4371	141	0.324	2497	95
2.9571-3.0213	0.3202	120	0.2829	2576	97
3.0213-3.0916	0.275	142	0.2343	2560	97
3.0916-3.1689	0.2606	113	0.2294	2588	98
3.1689-3.2546	0.2975	151	0.2118	2572	98
3.2546-3.3503	0.2425	157	0.2091	2546	98
3.3503-3.4584	0.2567	137	0.2059	2615	98
3.4584-3.5819	0.2749	143	0.181	2578	98
3.5819-3.7253	0.1998	140	0.1657	2582	97
3.7253-3.8947	0.1939	140	0.1546	2602	98
3.8947-4.1	0.187	145	0.1555	2587	98
4.1-4.3566	0.1675	146	0.1443	2627	99
4.3566-4.6927	0.1797	128	0.1391	2660	99
4.6927-5.1643	0.1771	146	0.1424	2660	99
5.1643-5.9101	0.2048	160	0.1633	2648	98
5.9101-7.4406	0.2172	115	0.1895	2712	98
7.4406-44.794	0.1899	144	0.192	2778	96

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	0.1502	-0.0039	-0.0075	0.2828	0.1832	0.1188	0.1949	0.026	0.2405	0.0829	0.1416	-0.1124	-0.2689	0.0171	0.5116	0.1925	0.3633	0.2262	0.0691	0.0397	0.3222	61.1971	-23.094	-3.7633
2	0.176	0.0558	0.0853	0.0223	0.0294	0.0497	0.1208	0.1266	-0.0542	-0.104	-0.0317	0.0044	-0.1064	-0.2089	0.0687	0.257	0.3382	-0.0271	0.2857	0.1259	0.1268	59.5992	-30.7231	-22.7567
3	0.2569	-0.2369	0.1292	0.2138	-0.1037	0.3409	0.2343	0.2003	0.0861	-0.0685	0.1028	-0.0295	-0.1087	-0.2347	0.3396	0.3821	0.3096	0.08	0.4219	0.078	0.3565	49.0419	-21.0323	-12.0541
4	0.2667	-0.0681	-0.0625	0.1981	-0.0418	0.2348	0.2157	-0.1037	0.2817	0.0536	0.2068	-0.0797	-0.3177	0.384	0.52	0.1983	0.0167	0.1539	0.5186	-0.1643	0.3442	68.3438	-25.7493	17.3704
5	0.0085	-0.043	0.0183	0.4113	-0.087	0.0253	0.0274	-0.3267	0.0304	0.016	0.0089	0.0704	0.0363	0.3055	0.0598	0.1355	0.0172	0.0098	0.5474	-0.1164	0.2001	61.8631	-30.6115	36.5344
6	0.3738	0.0599	0.1832	0.107	-0.0889	0.2224	0.0276	-0.2586	0.0257	0.0737	0.3032	-0.0407	0.0338	0.2479	0.3577	0.2035	0.0473	0.025	1.0664	-0.1623	0.3244	78.4575	-33.9258	29.2442
7	0.1372	-0.057	-0.0897	0.0392	0.0417	0.0754	0.0839	-0.0905	0.1845	-0.1475	0.1023	-0.0066	0.0588	-0.0867	0.0198	0.1862	-0.0279	-0.0277	0.1543	0.0528	0.2914	28.4116	-33.5446	27.4687
8	0.1504	0.0022	-0.0289	0.0467	-0.0136	0.0153	0.0976	0.331	0.0971	-0.2314	0.0029	-0.0229	0.3209	-0.0354	0.0076	0.3957	-0.0002	-0.0703	0.3527	0.0156	0.2283	34.2389	-37.3436	8.1502
9	0.0017	0.0001	-0.0081	-0.0007	-0.0017	0.0462	0.0221	0.1487	0.0256	-0.0976	0.2006	0.1857	0.3932	-0.1174	0.0005	0.4046	-0.0562	-0.1391	0.2584	0.0899	0.3631	21.7872	-44.3137	19.1821
10	0.0572	-0.0191	0.0202	0.0121	0.0088	0.2362	0.0476	0.0439	-0.1486	0.0403	-0.0159	0.1299	0.273	0.0906	0.0174	0.1326	0.0414	0.0034	0.0832	-0.003	0.1642	30.6338	1.5029	3.8251
11	0.164	0.1417	0.0454	0.1424	0.042	0.0219	-0.0285	0.1463	0.0988	-0.1216	-0.114	0.0214	0.103	0.0783	-0.0392	0.2381	0.083	0.0492	0.2284	0.0067	0.1303	29.8343	9.3918	-15.0407
12	0.0741	-0.0646	0.1479	0.1259	-0.1053	0.3136	0.0528	0.1678	0.0116	-0.179	-0.1996	-0.1436	0.0432	0.3299	-0.0252	0.2849	0.1258	0.0638	0.2817	0.0545	0.2663	42.9792	2.803	-4.7406
13	0.1764	0.0924	0.056	0.1349	0.0571	0.113	0.0703	0.0052	-0.0738	-0.0618	0.0755	-0.0305	0.1132	-0.0547	0.3907	0.0895	-0.0321	0.0188	0.0944	0.0552	0.1962	24.4136	1.7019	24.8922
14	0.0181	0.0167	-0.0107	0.0173	-0.0141	0.0056	0.0293	-0.0135	0.1029	0.0834	-0.0544	0.0165	-0.0865	0.0827	-0.0217	0.2844	-0.1399	0.0307	0.1392	-0.0066	0.1776	36.2782	9.6312	39.8983
15	0.1069	-0.0456	0.0378	0.0635	0.0269	0.0636	0.0254	-0.2213	-0.0007	0.0858	0.0229	0.0002	-0.057	0.0376	0.1173	0.3732	-0.1473	0.1747	0.3677	-0.0447	0.1564	20.7101	6.4026	47.2875
16	0.0864	0.014	-0.0967	0.0033	-0.0186	0.0996	0.0812	-0.1237	0.0291	0.0619	0.0229	0.1174	-0.0214	-0.0627	0.0964	0.2214	-0.0847	0.0537	0.1197	0.0156	0.2064	12.7529	5.5602	33.6336

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 83 )	A	0 - 83
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 84 through 213 )	A	84 - 213
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 214 through 255 )	A	214 - 255
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 2 through 83 )	B	2 - 83
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 84 through 195 )	B	84 - 195
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 196 through 255 )	B	196 - 255
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 2 through 83 )	C	2 - 83
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 84 through 213 )	C	84 - 213
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 214 through 255 )	C	214 - 255
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 2 through 83 )	D	2 - 83
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 84 through 213 )	D	84 - 213
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 214 through 255 )	D	214 - 255
13	X-RAY DIFFRACTION	13	chain 'E' and (resid 2 through 83 )	E	2 - 83
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 84 through 137 )	E	84 - 137
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 138 through 213 )	E	138 - 213
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 214 through 255 )	E	214 - 255

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