PDB-4i6v: The crystal structure of an amidohydrolase 2 from Planctomyces li...

ID or keywords:

Entry

Database: PDB / ID: 4i6v

Title

The crystal structure of an amidohydrolase 2 from Planctomyces limnophilus DSM 3776

Components

Amidohydrolase 2

Keywords

HYDROLASE / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG

Function / homology

Function and homology information

glucuronate catabolic process / glucuronate isomerase activity / hydrolase activity / metal ion binding
Similarity search - Function

Biological species

Planctomyces limnophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.137 Å

Authors

Fan, Y. / Tan, K. / Wu, R. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: The crystal structure of an amidohydrolase 2 from Planctomyces limnophilus DSM 3776
Authors: Fan, Y. / Tan, K. / Wu, R. / Bearden, J. / Joachimiak, A.

History

Deposition	Nov 30, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 6, 2013	Provider: repository / Type: Initial release
Revision 1.1	Nov 20, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_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_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_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.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4i6v.cif.gz	524.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4i6v.ent.gz	433.9 KB	Display	PDB format
PDBx/mmJSON format	4i6v.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/i6/4i6v ftp://data.pdbj.org/pub/pdb/validation_reports/i6/4i6v	HTTPS FTP

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Related structure data

Similar structure data	1j5s-d 3iac-d 2q6e-d 2q08-3 2qee-4 6qpx-1 2qee-1 3w2w-d 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: MCSG-APC100597

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #158 - Feb 2013 Proton-Gated Urea Channel similarity (1)

Deposited unit

A: Amidohydrolase 2

B: Amidohydrolase 2

C: Amidohydrolase 2

hetero molecules

151 kDa, 3 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)	81.224, 111.245, 147.148
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Details

The chains A, B and C form a trimer.

#1: Protein	Amidohydrolase 2 Mass: 49908.598 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Planctomyces limnophilus (bacteria) / Strain: DSM 3776 / Gene: Planctomyces limnophilus, Plim_2160 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: D5SMT1
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 394 / 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: 2.22 Å³/Da / Density % sol: 44.6 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 HEPES:NaOH, 25% (w/v) PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 7, 2010 / Details: mirror
Radiation	Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97915 Å / Relative weight: 1
Reflection	Resolution: 2.137→46 Å / Num. all: 73652 / Num. obs: 73652 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / R_merge(I) obs: 0.112 / Net I/σ(I): 25.4
Reflection shell	Resolution: 2.15→2.19 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.665 / Mean I/σ(I) obs: 2.6 / Num. unique all: 3289 / % possible all: 90.2

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
SHELXD		phasing
MLPHARE		phasing
DM		model building
ARP		model building
WARP		model building
HKL-3000		phasing
PHENIX	(phenix.refine: 1.7.1_743)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
DM		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.137→45.893 Å / SU ML: 0.58 / σ(F): 1.34 / Phase error: 23.26 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2181	3711	5.05 %	random
R_work	0.1679	-	-	-
all	0.1705	73465	-	-
obs	0.1705	73465	98.58 %	-

Solvent computation

Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 28.568 Å² / k_sol: 0.333 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.5757 Å²	0 Å²	-0 Å²
2-	-	5.0944 Å²	0 Å²
3-	-	-	-1.5187 Å²

Refinement step

Cycle: LAST / Resolution: 2.137→45.893 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10347	0	71	394	10812

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	10723
X-RAY DIFFRACTION	f_angle_d	1.072	14559
X-RAY DIFFRACTION	f_dihedral_angle_d	14.119	3874
X-RAY DIFFRACTION	f_chiral_restr	0.073	1549
X-RAY DIFFRACTION	f_plane_restr	0.005	1887

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.1367-2.1637	0.3036	121	0.2079	2185	X-RAY DIFFRACTION	86
2.1637-2.1922	0.2687	112	0.2062	2415	X-RAY DIFFRACTION	92
2.1922-2.2222	0.2841	126	0.2024	2435	X-RAY DIFFRACTION	94
2.2222-2.254	0.3087	122	0.2057	2501	X-RAY DIFFRACTION	96
2.254-2.2876	0.2426	135	0.204	2520	X-RAY DIFFRACTION	98
2.2876-2.3233	0.2903	135	0.2043	2588	X-RAY DIFFRACTION	99
2.3233-2.3614	0.3199	152	0.2125	2556	X-RAY DIFFRACTION	100
2.3614-2.4022	0.2532	149	0.199	2611	X-RAY DIFFRACTION	100
2.4022-2.4458	0.2927	124	0.196	2568	X-RAY DIFFRACTION	100
2.4458-2.4929	0.2521	126	0.1949	2626	X-RAY DIFFRACTION	100
2.4929-2.5438	0.2782	135	0.1914	2617	X-RAY DIFFRACTION	100
2.5438-2.5991	0.2526	133	0.1881	2611	X-RAY DIFFRACTION	100
2.5991-2.6595	0.276	132	0.1881	2572	X-RAY DIFFRACTION	100
2.6595-2.726	0.2668	130	0.1893	2638	X-RAY DIFFRACTION	100
2.726-2.7997	0.271	131	0.1853	2595	X-RAY DIFFRACTION	100
2.7997-2.8821	0.2272	146	0.1866	2600	X-RAY DIFFRACTION	100
2.8821-2.9751	0.2436	127	0.1943	2605	X-RAY DIFFRACTION	100
2.9751-3.0814	0.2783	145	0.1966	2611	X-RAY DIFFRACTION	100
3.0814-3.2047	0.2371	129	0.1862	2640	X-RAY DIFFRACTION	100
3.2047-3.3506	0.2293	159	0.1817	2612	X-RAY DIFFRACTION	100
3.3506-3.5271	0.2229	158	0.1745	2601	X-RAY DIFFRACTION	100
3.5271-3.748	0.2066	119	0.1583	2639	X-RAY DIFFRACTION	100
3.748-4.0373	0.176	147	0.1365	2650	X-RAY DIFFRACTION	100
4.0373-4.4433	0.1713	138	0.1228	2661	X-RAY DIFFRACTION	100
4.4433-5.0855	0.1615	145	0.1192	2680	X-RAY DIFFRACTION	100
5.0855-6.4044	0.1759	162	0.1698	2664	X-RAY DIFFRACTION	100
6.4044-45.9035	0.1767	173	0.1543	2753	X-RAY DIFFRACTION	98

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	1.5391	0.0563	-0.337	0.0798	-0.0116	0.4873	0.0238	-0.1775	-0.0554	0.0632	0.0216	-0.034	0.1211	-0.0268	-0.0415	0.2959	-0.0192	-0.0237	0.3015	0.0671	0.3024	50.3802	99.8423	30.9961
2	2.2636	-0.3512	-0.6946	1.577	-0.5122	1.6771	-0.0855	-0.2748	-0.2204	0.1791	0.0083	-0.0546	0.1028	0.0876	0.0815	0.2485	-0.027	-0.0224	0.3098	0.0527	0.2156	46.8606	97.352	40.7743
3	1.219	-1.0042	0.3953	3.1355	-0.0783	0.9784	-0.0163	-0.0532	0.0316	0.1944	0.0767	-0.0862	-0.05	-0.0425	-0.0829	0.2179	-0.0112	0.0101	0.2943	0.0009	0.2437	64.3142	123.9245	32.6217
4	1.2713	-0.8522	0.2744	2.0504	0.0861	1.0517	0.0381	-0.1529	0.0648	-0.0051	0.0235	-0.0249	-0.1307	-0.0253	-0.0201	0.2052	-0.01	0.0113	0.2972	0.022	0.2528	54.8679	132.8987	26.07
5	1.6775	0.5615	-0.3613	0.4291	-0.0334	1.4164	-0.0346	-0.1131	-0.0429	0.0156	-0.0094	-0.0001	-0.0284	-0.0214	0.0399	0.2135	0.0168	-0.0149	0.2336	0.0063	0.234	49.9686	120.3972	20.1411
6	2.6713	-1.117	-0.6295	1.7211	-1.3465	2.5714	0.1003	0.0035	-0.0983	0.148	0.1911	0.1418	-0.358	-0.1462	-0.2544	0.2348	-0.0384	0.0208	0.2176	0.0231	0.2623	48.9381	104.8413	17.1926
7	1.7988	-0.0219	0.7562	1.4912	0.9692	3.9203	0.0106	-0.0257	-0.2022	0.0347	-0.007	0.0421	0.2184	-0.0313	-0.0212	0.1988	0.021	-0.0054	0.1743	0.0265	0.2697	53.22	97.5472	15.23
8	2.2163	-1.0458	-0.383	3.5474	0.4906	2.6232	-0.3501	0.3596	-0.4988	0.1105	0.2211	0.5465	0.6992	-0.1381	0.243	0.4003	-0.0907	0.0276	0.3585	0.0047	0.3626	18.2492	86.9747	20.2609
9	0.6584	-0.0933	-0.0821	0.4808	0.2977	1.6159	-0.0372	0.1393	-0.0325	-0.0604	0.0161	0.1511	0.0254	-0.145	0.0248	0.23	-0.0031	-0.0153	0.3023	0.0275	0.2976	3.5659	107.1908	13.259
10	2.4969	1.1501	-0.2389	4.499	-1.149	2.9067	0.0745	-0.1645	0.4107	0.0701	-0.0391	0.4867	-0.3357	-0.5354	-0.0268	0.271	0.0886	0.0078	0.3317	-0.0422	0.3053	4.1467	128.631	36.1915
11	1.5401	-0.1378	0.5966	0.3858	0.695	2.5281	-0.012	-0.0477	0.2476	-0.0327	0.0236	-0.0065	-0.3795	0.1065	-0.0243	0.2839	-0.0345	0.028	0.2884	0.0153	0.2621	16.8602	127.4753	26.3249
12	0.4577	0.0676	0.1002	1.179	0.3512	0.5646	-0.0429	-0.037	-0.0133	-0.0534	0.0362	-0.0668	0.0216	-0.0462	0.0184	0.2368	-0.0109	0.0227	0.2804	0.0209	0.2308	23.8787	105.1856	25.572
13	0.8796	-0.2415	0.4252	0.1953	-0.2988	0.442	-0.049	-0.0831	0.0491	-0.0143	-0.0833	0.0481	0.1459	0.0791	0.1598	0.3496	0.0186	0.0401	0.2876	-0.0199	0.2513	42.5027	106.2845	-11.1335
14	1.2858	-0.4995	-0.2662	0.808	0.0419	2.5203	0.1326	0.0765	0.1884	-0.3334	0.1262	-0.2799	-0.0905	0.5706	0.0157	0.2695	-0.0261	0.0486	0.4131	-0.0225	0.2938	62.7813	112.4031	-7.0303
15	1.7116	-0.8838	0.4592	1.3208	0.0158	0.9312	0.1063	0.231	-0.1899	-0.212	0.0023	-0.1497	0.213	0.1163	-0.0794	0.2786	0.0063	0.0263	0.3201	-0.0274	0.3013	49.4909	102.476	-15.2028
16	0.4568	-0.2734	0.3045	2.383	0.9845	1.1799	-0.0015	0.1391	0.0236	-0.2617	0.1709	-0.3516	-0.0029	0.2828	-0.0422	0.2718	0.0074	0.0531	0.3687	0.0221	0.2644	36.8093	126.2119	-16.9753
17	1.1683	0.0144	0.3444	1.5254	0.0302	0.8002	-0.0694	0.0162	0.2289	-0.0253	0.0182	-0.1278	-0.0964	0.1498	0.0654	0.2401	0.0198	-0.0045	0.2872	0.0209	0.2688	33.3156	137.7758	-11.6693
18	1.7815	-0.9246	0.3694	1.1332	-0.5617	0.673	-0.0726	0.0221	0.0783	0.1083	0.0065	-0.0514	-0.0701	0.0433	-0.0014	0.2139	0.0076	0.0185	0.2403	0.0174	0.1983	35.8416	128.4895	-2.7845
19	1.1946	-0.6127	0.0419	2.2122	0.1631	1.1008	-0.046	0.0117	-0.0874	0.1411	0.0573	0.0115	0.1278	0.0341	-0.0048	0.2146	-0.0144	-0	0.2283	-0.0072	0.182	28.2961	115.2265	0.1954
20	2.9064	0.5151	-0.4891	1.2801	-0.5048	2.2968	-0.0454	0.3025	-0.1129	-0.0417	0.0278	0.0299	0.0846	-0.1246	0.0251	0.2365	0.0111	-0.0015	0.2051	-0.0395	0.1935	27.8579	101.3131	-6.5603

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 6:54)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 55:145)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 146:208)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 209:245)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 246:348)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 349:377)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 378:431)
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 1:23)
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 24:173)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 174:208)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 209:298)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 299:431)
13	X-RAY DIFFRACTION	13	chain 'C' and (resseq 6:53)
14	X-RAY DIFFRACTION	14	chain 'C' and (resseq 54:82)
15	X-RAY DIFFRACTION	15	chain 'C' and (resseq 83:145)
16	X-RAY DIFFRACTION	16	chain 'C' and (resseq 146:173)
17	X-RAY DIFFRACTION	17	chain 'C' and (resseq 174:245)
18	X-RAY DIFFRACTION	18	chain 'C' and (resseq 246:298)
19	X-RAY DIFFRACTION	19	chain 'C' and (resseq 299:377)
20	X-RAY DIFFRACTION	20	chain 'C' and (resseq 378:431)

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