PDB-4mup: Crystal structure of Agrobacterium tumefaciens ATU3138 (EFI targe...

ID or keywords:

Entry

Database: PDB / ID: 4mup

Title

Crystal structure of Agrobacterium tumefaciens ATU3138 (EFI target 505157), apo structure

Components

AMIDOHYDROLASE

Keywords

HYDROLASE / AMIDOHYDROLASE FAMILY MEMBER / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics

Function / homology

Function and homology information

D-galactarolactone isomerase / isomerase activity / hydrolase activity
Similarity search - Function

Biological species

Agrobacterium fabrum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Vetting, M.W. / Bouvier, J.T. / Groninger-Poe, F. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)

Citation

Journal: To be Published
Title: Crystal structure of Agrobacterium tumefaciens ATU3138 (EFI target 505157), apo structure
Authors: Vetting, M.W. / Bouvier, J.T. / Groninger-Poe, F. / Imker, H.J. / Gerlt, J.A. / Almo, S.C.

History

Deposition	Sep 23, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 29, 2014	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	4mup_validation.pdf.gz	437.2 KB	Display	wwPDB validaton report
Full document	4mup_full_validation.pdf.gz	438.7 KB	Display
Data in XML	4mup_validation.xml.gz	40.3 KB	Display
Data in CIF	4mup_validation.cif.gz	63 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mu/4mup ftp://data.pdbj.org/pub/pdb/validation_reports/mu/4mup	HTTPS FTP

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Related structure data

Related structure data	2ffiS 4di8S 4diaS 4do7S 4i6kS S: Starting model for refinement
Similar structure data	1sfq-2 1mh0-1 2gvv-d 7k2j-2 1de7-2 1ba8-d 4o5s-2 3jz2-d 1sgi-2 6qdx-4 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	TargetTrack: EFI-505157

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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

B: AMIDOHYDROLASE

C: AMIDOHYDROLASE

103 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: AMIDOHYDROLASE

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

2

B: AMIDOHYDROLASE

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

3

C: AMIDOHYDROLASE

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

Unit cell

Length a, b, c (Å)	53.202, 77.557, 99.714
Angle α, β, γ (deg.)	90.000, 95.490, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	AMIDOHYDROLASE Mass: 34195.812 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium fabrum (bacteria) / Strain: C58 / ATCC 33970 / Gene: Atu3138 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A9CEQ7
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1073 / 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 Å³/Da / Density % sol: 38.38 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Protein (10 mg/ml in 20 mM Tris, pH 7.9, 150 mM NaCl, 5 mM MgCl2). Reservoir (0.1 M HEPES, pH 7.5, 20% (w/v) PEG 4000, 10% (w/v) Isopropanol) (MCSG4 G11)). Cryoprotection (Reservoir+20% ...Details: Protein (10 mg/ml in 20 mM Tris, pH 7.9, 150 mM NaCl, 5 mM MgCl2). Reservoir (0.1 M HEPES, pH 7.5, 20% (w/v) PEG 4000, 10% (w/v) Isopropanol) (MCSG4 G11)). Cryoprotection (Reservoir+20% isopropanol), vapor diffusion, sitting drop, temperature 298K, VAPOR DIFFUSION, SITTING DROP

Crystal

Density Matthews: 2 Å³/Da / Density % sol: 38.38 %

Crystal grow

Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein (10 mg/ml in 20 mM Tris, pH 7.9, 150 mM NaCl, 5 mM MgCl2). Reservoir (0.1 M HEPES, pH 7.5, 20% (w/v) PEG 4000, 10% (w/v) Isopropanol) (MCSG4 G11)). Cryoprotection (Reservoir+20% ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 31-ID / Wavelength: 0.9793 Å

Detector

Type: RAYONIX MX225HE / Detector: CCD / Date: Jun 2, 2013 / Details: MIRRORS

Radiation

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

Radiation wavelength

Wavelength: 0.9793 Å / Relative weight: 1

Reflection

Resolution: 1.6→99.257 Å / Num. all: 103208 / Num. obs: 103208 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / B_iso Wilson estimate: 14.25 Å² / R_merge(I) obs: 0.095 / R_sym value: 0.095 / Net I/σ(I): 8.5

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
1.6-1.69	3.5	0.541	1.4	54371	15449	0.541	100
1.69-1.79	3.7	0.397	2	53656	14568	0.397	99.8
1.79-1.91	3.7	0.281	2.7	50904	13729	0.281	99.4
1.91-2.07	3.7	0.182	4.2	46087	12566	0.182	97.9
2.07-2.26	3.6	0.128	5.7	41198	11379	0.128	96.4
2.26-2.53	3.7	0.1	7	37973	10392	0.1	96.8
2.53-2.92	3.6	0.079	9.2	32311	8934	0.079	94.8
2.92-3.58	3.5	0.059	11.4	26141	7383	0.059	92.1
3.58-5.06	3.5	0.045	14.3	19746	5616	0.045	90.2
5.06-99.257	3.5	0.037	16.9	11086	3192	0.037	91.8

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Processing

Software

Name	Version	Classification
SCALA	3.3.20	data scaling
PHENIX	1.8.1_1168	refinement
PDB_EXTRACT	3.11	data extraction
MOSFLM		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entries 2ffi,4do7, 4i6k, 4dia, 4di8

Resolution: 1.6→31.598 Å / Occupancy max: 1 / Occupancy min: 0.48 / FOM work R set: 0.8981 / SU ML: 0.15 / σ(F): 0 / σ(I): 0 / Phase error: 17.48 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1809	5138	4.98 %	RANDOM
R_work	0.1469	-	-	-
all	0.1486	103114	-	-
obs	0.1486	103114	96.99 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 77.46 Å² / B_iso mean: 20.1631 Å² / B_iso min: 5.14 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→31.598 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6517	0	0	1073	7590

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	6708
X-RAY DIFFRACTION	f_angle_d	1.276	9141
X-RAY DIFFRACTION	f_chiral_restr	0.075	976
X-RAY DIFFRACTION	f_plane_restr	0.008	1209
X-RAY DIFFRACTION	f_dihedral_angle_d	12.611	2434

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.6-1.6182	0.2335	186	0.2175	3378	3564	100
1.6182-1.6372	0.2574	173	0.2123	3298	3471	100
1.6372-1.6572	0.2372	171	0.2022	3374	3545	100
1.6572-1.6782	0.2222	188	0.1903	3337	3525	100
1.6782-1.7002	0.2325	163	0.1938	3331	3494	100
1.7002-1.7235	0.2123	181	0.1905	3381	3562	100
1.7235-1.7482	0.2342	175	0.1877	3303	3478	100
1.7482-1.7742	0.2242	190	0.1736	3385	3575	100
1.7742-1.802	0.2007	157	0.1676	3354	3511	100
1.802-1.8315	0.218	188	0.1699	3330	3518	100
1.8315-1.8631	0.2226	179	0.1683	3282	3461	100
1.8631-1.897	0.2143	182	0.1715	3340	3522	99
1.897-1.9334	0.2531	163	0.2085	3248	3411	96
1.9334-1.9729	0.2006	179	0.1682	3285	3464	98
1.9729-2.0158	0.2032	179	0.1581	3314	3493	99
2.0158-2.0627	0.1851	164	0.1532	3321	3485	98
2.0627-2.1142	0.1872	169	0.1639	3229	3398	96
2.1142-2.1714	0.1852	163	0.1407	3315	3478	99
2.1714-2.2353	0.1779	176	0.1408	3299	3475	98
2.2353-2.3074	0.2087	164	0.1565	3158	3322	93
2.3074-2.3898	0.171	195	0.1338	3223	3418	97
2.3898-2.4855	0.1603	157	0.1316	3260	3417	96
2.4855-2.5986	0.186	160	0.129	3239	3399	96
2.5986-2.7355	0.1668	174	0.136	3162	3336	94
2.7355-2.9068	0.1578	167	0.1328	3211	3378	95
2.9068-3.131	0.1734	173	0.1311	3165	3338	93
3.131-3.4458	0.1495	151	0.1309	3086	3237	92
3.4458-3.9436	0.1513	152	0.1179	3063	3215	90
3.9436-4.9654	0.1393	168	0.1125	3101	3269	91
4.9654-31.6037	0.1539	151	0.1491	3204	3355	92

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	2.156	0.0528	0.2923	1.6162	-0.4735	0.9357	0.0403	0.0339	0.4298	-0.0148	-0.014	-0.0252	-0.4361	0.027	-0.0007	0.232	0.0304	0.0307	0.0854	-0.0043	0.1582	-10.0052	52.394	82.9991
2	0.9969	-0.8656	0.3232	1.159	0.3857	1.2582	0.0264	0.0074	0.2218	0.0736	0.155	-0.5811	-0.1384	0.5825	0.0918	0.1193	-0.0304	-0.0313	0.2579	-0.0743	0.2495	5.4195	40.0813	92.6973
3	0.7982	-0.2774	-0.0819	0.7624	-0.0722	1.0049	0.0185	-0.0664	0.1608	0.1051	0.0277	-0.1311	-0.2091	0.1378	-0.065	0.1332	-0.0127	-0.0055	0.1022	-0.0425	0.1117	-5.2076	43.8559	93.2583
4	1.0193	-1.0766	-0.2218	2.1566	0.7141	0.9175	-0.2153	-0.2737	-0.2156	0.286	0.1008	0.1928	0.3147	0.1868	0.1023	0.1832	0.0549	0.018	0.1169	0.0104	0.1189	-9.9493	26.4396	101.1372
5	0.826	-0.538	-0.4844	0.437	0.4993	1.0217	-0.0605	0.0333	-0.1237	0.0421	-0.0071	0.0288	0.2422	0.0749	0.0474	0.1285	0.0181	0.009	0.0988	-0.0185	0.0951	-7.9068	25.4721	89.0795
6	0.3465	0.0365	-0.3963	0.4671	0.3638	1.4764	-0.0202	0.0248	-0.1157	-0.036	-0.058	0.0238	0.1332	-0.0221	0.0361	0.122	0.0119	-0.0137	0.0892	-0.0305	0.1039	-11.0319	24.9342	80.1705
7	0.9184	0.2282	-0.2037	0.6729	-0.0314	1.0316	-0.0308	0.1815	-0.0497	-0.1726	-0.0717	0.0792	0.2114	-0.0804	0.0897	0.1504	0.0099	-0.0054	0.1292	-0.0333	0.1158	-13.7187	28.7894	73.9627
8	0.5446	0.0339	-0.3955	0.4415	-0.1733	0.9319	0.1059	0.1564	0.0146	-0.0745	-0.1038	-0.0075	-0.0828	-0.0629	0.023	0.1075	0.0322	-0.0016	0.1249	0.004	0.0693	-9.945	38.9603	71.197
9	0.7581	0.2163	0.2531	1.4129	-0.0815	1.4257	0.1364	0.1576	0.1456	-0.0851	-0.0633	-0.12	-0.24	0.1225	-0.0575	0.1476	0.02	0.0449	0.1121	0.002	0.1274	-5.664	45.9827	77.9166
10	0.5625	0.026	0.5422	0.7019	-0.6619	2.0622	0.1342	0.0836	0.0564	-0.0297	-0.05	0.1335	-0.2664	-0.3036	-0.0959	0.1105	0.0711	0.011	0.1519	-0.0014	0.1084	-21.3787	43.9196	83.2587
11	1.4783	0.2048	0.4762	0.4804	0.056	0.6612	0.0079	-0.0712	-0.3438	0.1528	-0.0118	-0.2941	0.3009	0.4699	-0.1537	0.1371	0.0635	-0.0473	0.3233	0.0532	0.1951	18.9826	32.5617	53.7597
12	0.6258	0.6152	0.1364	0.9726	-0.0736	0.6339	-0.2108	0.0884	-0.3657	-0.2926	0.0558	-0.2241	0.2913	0.0411	0.0069	0.1868	-0.0081	0.0545	0.0717	-0.0043	0.2045	2.4887	25.1063	44.4595
13	0.9575	0.0818	0.0109	0.4948	0.222	0.8332	-0.1653	-0.1396	-0.2518	0.1032	-0.0119	0.0092	0.4067	0.1258	0.0078	0.1403	0.0391	0.0264	0.097	0.0621	0.1408	4.5396	29.7389	53.1861
14	1.0663	-0.0637	0.3553	0.2933	0.0527	3.8349	-0.1357	0.0017	-0.2125	0.1034	0.0145	0.2288	-0.0795	-0.6565	0.0424	0.0996	0.0093	0.0341	0.182	0.0128	0.1991	-13.4489	37.8337	52.4904
15	0.6186	0.1248	-0.2386	0.5911	0.0815	1.7218	-0.1127	0.0643	-0.0895	-0.0454	0.0136	0.1271	-0.0186	-0.2646	0.0716	0.0885	0.0111	-0.0077	0.0819	-0.0014	0.1049	-6.2575	42.0842	43.6907
16	0.3729	0.1422	-0.4059	0.5798	-0.398	1.0816	0.0608	0.1245	0.0081	-0.1204	-0.0198	0.0109	-0.2113	-0.1692	-0.0512	0.1611	0.0417	-0.0056	0.096	0.0147	0.0855	-0.9243	49.3578	40.4052
17	0.7956	-0.2204	-0.2523	0.3703	0.209	0.6812	0.0482	0.0374	0.0616	-0.1017	-0.0028	-0.0601	-0.2425	0.1326	-0.021	0.1321	-0.0359	0.0155	0.0745	-0.003	0.0917	11.2757	49.089	40.6516
18	1.4283	-0.0608	-0.1043	1.1787	-0.3707	0.8657	-0.0984	-0.0521	-0.2106	-0.1158	0.0921	-0.116	0.0663	0.366	0.0004	0.0946	0.0126	0.0208	0.1683	0.0016	0.1246	16.4141	36.3471	45.5641
19	1.3434	0.1089	-0.1308	1.0387	-0.2761	0.1221	-0.0419	-0.398	0.0197	0.2042	0.1132	-0.0711	-0.1353	0.3662	-0.0315	0.1042	-0.0207	-0.0259	0.2212	-0.0285	0.066	11.985	46.6636	58.0202
20	1.4126	-0.0455	0.0634	2.4577	0.074	1.4363	0.0253	-0.2207	-0.0628	0.1378	0.0165	-0.2328	0.2096	0.5452	0.0087	0.0771	0.0497	-0.0255	0.2889	0.0114	0.1042	21.183	1.3207	85.2878
21	1.3175	-0.7644	-0.6603	0.7912	0.3203	0.416	-0.0145	-0.2179	0.1199	0.1081	0.0638	-0.109	-0.3198	0.2545	-0.0068	0.3197	-0.1742	0.0592	0.4239	-0.1325	0.2897	20.6216	21.4254	89.4288
22	0.4526	0.0857	-0.4377	0.3962	-0.0691	1.0436	0.1094	-0.4171	0.1387	0.0738	0.0013	-0.2225	-0.1113	0.8924	0.2819	0.0068	-0.0223	-0.0314	0.3622	-0.0301	0.1343	23.3985	9.2779	82.5153
23	2.215	-1.576	-0.7217	1.9784	0.4373	1.5798	0.3839	0.1909	0.4083	-0.2703	-0.2409	-0.1647	-0.4536	0.3077	0.0472	0.1772	-0.0051	0.0524	0.1314	0.0419	0.1752	15.9536	19.0636	66.921
24	0.9634	-0.3591	-0.7953	0.8127	0.3381	1.4477	0.0937	0.018	0.1056	-0.089	-0.0908	0.0685	-0.2807	0.0241	0.0376	0.1207	-0.0075	0.0082	0.0808	-0.0062	0.1123	7.2189	15.807	74.8705
25	1.7375	-0.0365	-0.9147	0.3093	-0.0322	1.7283	0.0513	0.0374	-0.0651	-0.0527	-0.0222	0.0868	-0.0754	-0.1141	-0.0246	0.0901	0.0103	-0.001	0.0573	-0.0011	0.0976	-0.0044	9.7241	77.2436
26	0.5118	-0.026	-0.231	0.4498	-0.2045	1.2881	0.0125	-0.016	-0.0495	-0.0493	0.0082	0.0304	0.1008	-0.046	-0.02	0.0881	-0.0097	-0.0084	0.0786	0.0032	0.093	1.2197	2.3423	84.2817
27	0.8188	0.1628	-0.4107	0.4225	-0.4878	1.0384	-0.0639	-0.1809	-0.1083	-0.0483	-0.0586	-0.0863	0.3359	0.3032	0.0459	0.1272	0.0464	0.0045	0.1351	0.0131	0.1119	11.7165	-3.5332	84.864

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 6:25 )	A
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 26:49 )	A
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 50:95 )	A
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESID 96:111 )	A
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESID 112:141 )	A
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESID 142:163 )	A
7	X-RAY DIFFRACTION	7	CHAIN A AND (RESID 164:197 )	A
8	X-RAY DIFFRACTION	8	CHAIN A AND (RESID 198:230 )	A
9	X-RAY DIFFRACTION	9	CHAIN A AND (RESID 231:265 )	A
10	X-RAY DIFFRACTION	10	CHAIN A AND (RESID 266:289 )	A
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESID 4:23 )	B
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESID 24:49 )	B
13	X-RAY DIFFRACTION	13	CHAIN B AND (RESID 50:95 )	B
14	X-RAY DIFFRACTION	14	CHAIN B AND (RESID 96:111 )	B
15	X-RAY DIFFRACTION	15	CHAIN B AND (RESID 112:141 )	B
16	X-RAY DIFFRACTION	16	CHAIN B AND (RESID 142:164 )	B
17	X-RAY DIFFRACTION	17	CHAIN B AND (RESID 165:230 )	B
18	X-RAY DIFFRACTION	18	CHAIN B AND (RESID 231:265 )	B
19	X-RAY DIFFRACTION	19	CHAIN B AND (RESID 266:289 )	B
20	X-RAY DIFFRACTION	20	CHAIN C AND (RESID 12:31 )	C
21	X-RAY DIFFRACTION	21	CHAIN C AND (RESID 32:49 )	C
22	X-RAY DIFFRACTION	22	CHAIN C AND (RESID 50:95 )	C
23	X-RAY DIFFRACTION	23	CHAIN C AND (RESID 96:111 )	C
24	X-RAY DIFFRACTION	24	CHAIN C AND (RESID 112:141 )	C
25	X-RAY DIFFRACTION	25	CHAIN C AND (RESID 142:163 )	C
26	X-RAY DIFFRACTION	26	CHAIN C AND (RESID 164:217 )	C
27	X-RAY DIFFRACTION	27	CHAIN C AND (RESID 218:289 )	C

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