PDB-5wl3: Crystal structure of chalcone isomerase engineered from ancestral...

ID or keywords:

Entry

Database: PDB / ID: 5wl3

Title

Crystal structure of chalcone isomerase engineered from ancestral inference (ancR2)

Components

Engineered Chalcone Isomerase ancR2

Keywords

ISOMERASE / chalcone isomerase / naringenin / flavanone

Function / homology

10k-s Protein, Hypothetical Protein A; Chain A - #20 / Chalcone isomerase - #10 / 10k-s Protein, Hypothetical Protein A; Chain A / Chalcone isomerase / 3-Layer(bba) Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta

Function and homology information

Biological species

unidentified (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Burke, J.R. / Kaltenbach, M. / Tawfik, D.S. / Noel, J.P.

Citation

Journal: Nat. Chem. Biol. / Year: 2018
Title: Evolution of chalcone isomerase from a noncatalytic ancestor.
Authors: Kaltenbach, M. / Burke, J.R. / Dindo, M. / Pabis, A. / Munsberg, F.S. / Rabin, A. / Kamerlin, S.C.L. / Noel, J.P. / Tawfik, D.S.

History

Deposition	Jul 25, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 9, 2018	Provider: repository / Type: Initial release
Revision 1.1	May 30, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Oct 4, 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5wl3.cif.gz	463.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5wl3.ent.gz	395.4 KB	Display	PDB format
PDBx/mmJSON format	5wl3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5wl3_validation.pdf.gz	458.4 KB	Display	wwPDB validaton report
Full document	5wl3_full_validation.pdf.gz	464.3 KB	Display
Data in XML	5wl3_validation.xml.gz	29.3 KB	Display
Data in CIF	5wl3_validation.cif.gz	39.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wl/5wl3 ftp://data.pdbj.org/pub/pdb/validation_reports/wl/5wl3	HTTPS FTP

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Related structure data

Related structure data	5wkrC 5wksC 5wl4C 5wl5C 5wl6C 5wl7C 5wl8C 4doiS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3wv9-1 5l9b-1 2lnc-d 2g1m-d 6j5y-d 2uwb-2 4urj-2 4dok-1 6zbn-6 4xe2-d 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 - HomologyF&H Search

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Engineered Chalcone Isomerase ancR2

B: Engineered Chalcone Isomerase ancR2

C: Engineered Chalcone Isomerase ancR2

D: Engineered Chalcone Isomerase ancR2

hetero molecules

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

1

A: Engineered Chalcone Isomerase ancR2

hetero molecules

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

2

B: Engineered Chalcone Isomerase ancR2

hetero molecules

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

3

C: Engineered Chalcone Isomerase ancR2

hetero molecules

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

4

D: Engineered Chalcone Isomerase ancR2

hetero molecules

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

Unit cell

Length a, b, c (Å)	82.740, 219.430, 104.520
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	Engineered Chalcone Isomerase ancR2 Mass: 23963.100 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli K-12 (bacteria)
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.62 Å³/Da / Density % sol: 53.12 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 40% PEG 500-MME, 100mM TAPS, 0.3M MgCl

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.4→75.68 Å / Num. obs: 37657 / % possible obs: 100 % / Redundancy: 10.1 % / Net I/σ(I): 13.8

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
iMOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB:4DOI

4doi

Resolution: 2.4→75.677 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.88 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2553	2000	5.32 %
R_work	0.2086	-	-
obs	0.211	37626	99.93 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.4→75.677 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6364	0	4	21	6389

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	6481
X-RAY DIFFRACTION	f_angle_d	0.861	8786
X-RAY DIFFRACTION	f_dihedral_angle_d	12.868	2372
X-RAY DIFFRACTION	f_chiral_restr	0.032	1036
X-RAY DIFFRACTION	f_plane_restr	0.004	1127

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 (%)
2.4-2.46	0.3563	140	0.3	2505	X-RAY DIFFRACTION	100
2.46-2.5265	0.3595	141	0.284	2512	X-RAY DIFFRACTION	100
2.5265-2.6009	0.3123	142	0.2646	2509	X-RAY DIFFRACTION	100
2.6009-2.6849	0.3335	141	0.259	2526	X-RAY DIFFRACTION	100
2.6849-2.7808	0.3199	141	0.2609	2517	X-RAY DIFFRACTION	100
2.7808-2.8922	0.3098	142	0.257	2520	X-RAY DIFFRACTION	100
2.8922-3.0238	0.2938	142	0.2504	2522	X-RAY DIFFRACTION	100
3.0238-3.1832	0.2965	142	0.2519	2536	X-RAY DIFFRACTION	100
3.1832-3.3826	0.2778	142	0.2415	2538	X-RAY DIFFRACTION	100
3.3826-3.6438	0.2609	143	0.2165	2531	X-RAY DIFFRACTION	100
3.6438-4.0105	0.2185	143	0.1953	2551	X-RAY DIFFRACTION	100
4.0105-4.5908	0.2096	144	0.1719	2578	X-RAY DIFFRACTION	100
4.5908-5.7836	0.2359	146	0.1724	2588	X-RAY DIFFRACTION	100
5.7836-75.7143	0.2353	151	0.1858	2693	X-RAY DIFFRACTION	99

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	1.5753	-0.3819	-0.3518	1.8899	0.795	5.1756	-0.652	0.0935	-0.2012	0.0771	0.518	-0.3063	0.4352	-0.5651	0.0887	0.947	0.0246	0.0758	0.6228	-0.0526	0.6396	21.0514	453.7969	141.8986
2	0.9523	-1.3289	0.5179	2.7889	-1.9343	3.691	0.2848	-0.2234	-0.0908	0.505	-0.0722	0.2657	0.2839	-0.1963	-0.2444	0.8049	0.0005	0.1278	0.5471	0.0312	0.4366	14.9327	445.8849	132.716
3	4.6405	-0.3163	0.4881	4.2613	-0.0475	4.0224	0.0818	0.4842	0.2115	0.0775	0.1319	0.7721	-0.3881	-0.5333	-0.1968	0.5398	0.0628	0.1395	0.6604	0.0634	0.6421	8.7832	455.8029	121.5747
4	2.5539	-0.0325	0.0129	6.4667	-2.0355	3.9968	-0.1301	-0.16	0.0043	1.0957	0.2387	-0.1478	-0.1526	0.076	-0.1229	0.6946	-0.0165	0.0446	0.5126	-0.0021	0.399	22.9731	444.7946	133.4635
5	4.4351	-0.9559	2.561	3.0382	-1.6763	9.0389	0.0412	0.0444	-0.4793	0.4565	-0.1303	-0.2097	0.9888	0.2338	0.1717	0.7191	0.0033	0.0311	0.4706	0.0165	0.6101	23.5944	435.257	121.967
6	3.0771	0.7503	-0.9992	4.4492	0.7342	5.2445	-0.0849	-0.2226	-0.1548	0.5747	0.1057	-0.6181	-0.0875	0.7015	-0.0548	0.5768	0.0247	-0.0807	0.506	-0.0137	0.5188	31.2484	442.7069	127.8147
7	1.7195	-0.3919	0.7133	1.8432	-0.9594	1.867	0.0389	-0.1775	-0.128	0.5206	0.1032	0.4903	0.244	-0.411	-0.1149	0.5124	-0.0336	0.1712	0.4456	0.0114	0.4043	14.7906	448.1806	125.819
8	1.2631	2.0543	0.7617	4.8413	1.5142	0.6926	-0.6483	-0.2547	-0.5449	-1.5723	0.2929	0.1526	0.3361	-0.2803	0.1848	0.5898	-0.1275	0.2265	0.6065	0.0465	0.79	45.5463	481.6886	93.3431
9	4.4198	1.2067	-0.4113	3.1503	-0.8483	2.2122	0.1056	-0.0601	0.9965	0.0697	0.1508	-0.2585	-0.0744	0.0213	-0.1615	0.3648	0.0228	0.1	0.4714	0.0775	0.5395	37.92	470.9868	98.3678
10	4.715	-0.0014	0.6592	3.6063	-1.2137	3.0501	0.0986	0.1682	0.3975	-0.2082	0.0506	-0.2541	0.0438	0.4482	-0.4342	0.311	-0.0025	0.0772	0.5262	0.0644	0.5685	41.9198	466.2304	98.259
11	5.6571	0.263	0.0527	5.497	-0.1229	4.576	-0.0309	-0.9689	-0.5216	0.8263	0.0868	-0.597	0.3323	0.9127	-0.1172	0.5392	0.0683	-0.0376	0.727	0.0618	0.6425	49.505	460.8343	110.0817
12	2.7221	0.244	-0.6168	4.1692	0.7042	3.9624	0.0377	0.4383	0.2996	-0.1827	-0.1148	0.3999	0.0203	-0.3338	0.0169	0.3678	-0.0121	0.0429	0.5708	0.0713	0.5264	28.2855	460.747	96.2888
13	2.0317	0.6058	0.0412	1.8823	0.7015	2.4948	0.13	-0.0313	-0.0619	-0.0282	-0.0642	-0.2324	0.3401	0.1488	-0.0988	0.2941	0.0156	0.0717	0.388	0.0421	0.4713	42.7056	460.9493	101.8696
14	1.5267	-2.1758	0.397	3.6005	-1.6414	3.5768	0.0949	-0.1101	-0.8442	0.4555	-0.5705	0.9532	0.2432	0.2727	0.4885	0.4152	0.099	-0.0925	0.4377	-0.0082	0.8628	7.2578	505.946	116.8214
15	1.4492	-2.0409	0.7317	3.5472	0.3375	4.5707	-0.401	0.0099	0.5714	0.395	-0.0634	-0.5782	-0.4066	0.1534	0.4239	0.5195	0.0386	-0.0878	0.4524	0.0441	0.699	16.0412	494.908	117.6755
16	3.1638	-1.5453	2.0027	2.9331	1.0278	3.1024	-0.3548	0.0176	0.0137	-0.2596	-0.0684	-0.208	-0.0197	0.0974	0.4513	0.5818	0.0563	0.0228	0.4562	0.049	0.5444	12.468	490.4703	114.8102
17	6.5721	-0.3121	0.0199	4.7492	-1.4322	2.7529	-0.4578	1.0533	0.0107	-0.8245	-0.047	-0.1535	0.2281	0.1657	0.4682	0.6542	0.005	-0.0008	0.5232	0.0158	0.5237	15.1985	487.0854	108.9057
18	2.5648	-1.4159	-1.2145	6.2567	3.403	3.8856	-0.376	-0.3441	0.1867	0.9388	0.4934	0.1316	0.3838	0.0435	-0.0116	0.6694	0.0493	0.1407	0.5359	0.0264	0.5441	16.8518	475.6172	124.9475
19	2.5807	-1.1113	-1.4934	7.2423	2.3059	5.4205	-0.522	-0.2112	-0.4267	0.5505	0.2853	-0.5628	0.2712	0.5443	0.1292	0.6603	0.1084	0.0622	0.554	0.0426	0.5953	25.8104	474.788	126.1878
20	3.7722	0.8211	-1.6567	6.3602	-0.6975	3.9782	-0.1827	-0.4166	0.6887	0.4953	0.003	-0.9583	-0.3215	0.2882	0.1646	0.4252	0.0441	-0.1358	0.5116	-0.043	0.6619	23.995	490.5529	125.4076
21	3.6481	0.9119	0.4035	1.7972	-0.9327	2.7164	-0.3134	0.6386	0.0005	-0.417	0.1528	0.1404	0.1919	0.0786	0.1445	0.4535	-0.0275	-0.0185	0.4509	0.0294	0.4624	14.079	485.0103	111.7576
22	2.163	-1.0127	-0.951	4.5794	-2.9564	4.2108	0.2561	-0.2946	-0.0033	0.2049	0.184	0.3132	0.2353	0.6044	-0.4348	0.7031	-0.0753	0.0633	0.8526	-0.0981	0.5682	-5.9526	459.1402	106.0338
23	4.5006	0.3599	-3.0316	2.5716	-1.9009	3.4016	0.2469	-0.4056	1.1048	0.0478	0.0788	0.3494	-0.6666	0.2313	-0.1469	0.7493	-0.0926	0.0624	0.7411	-0.2172	0.768	-9.9019	467.5184	102.3478
24	3.9452	1.4433	0.4936	3.162	-0.2421	3.3972	-0.176	-0.7196	0.871	0.2434	0.3556	0.5393	-0.3848	0.1475	-0.1311	0.7578	-0.101	0.0841	0.7076	-0.1353	0.8469	-10.1363	470.2336	101.0103
25	4.6849	-0.1074	0.3895	7.1854	-3.1797	5.0596	0.6337	0.5872	0.3965	-2.3119	0.2321	-0.449	0.2514	0.5996	-0.9089	1.3024	-0.1615	-0.0102	0.6147	-0.0312	0.6533	-3.2203	467.2062	84.4136
26	3.8357	0.7464	0.4735	2.8309	-0.5807	6.0472	-0.1078	0.0585	0.2255	-0.3914	-0.0229	-0.5768	-0.3762	1.2715	0.1534	0.7413	-0.1292	0.097	0.9388	-0.1313	0.6937	5.3296	465.4902	92.5927
27	3.0157	-0.6199	-0.3669	3.7029	1.0116	2.9362	0.1551	0.1779	0.5546	-0.7607	-0.0357	0.5001	-1.1236	-0.1271	-0.1128	0.7109	-0.1256	-0.0179	0.5373	-0.0719	0.7445	-10.4254	470.2107	98.6651

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 26 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 27 through 60 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 61 through 84 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 85 through 100 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 101 through 118 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 119 through 178 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 179 through 211 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1 through 10 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 11 through 38 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 39 through 60 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 61 through 84 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 85 through 178 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 179 through 211 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 1 through 10 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 11 through 38 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 39 through 60 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 61 through 100 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 101 through 118 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 119 through 138 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 139 through 178 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 179 through 211 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 1 through 38 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 39 through 64 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 65 through 100 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 101 through 118 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 119 through 178 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 179 through 211 )

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