PDB-5wl4: Crystal structure of chalcone isomerase engineered from ancestral...

ID or keywords:

Entry

Database: PDB / ID: 5wl4

Title

Crystal structure of chalcone isomerase engineered from ancestral inference (ancR3)

Components

Engineered Chalcone Isomerase ancR3

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 / FORMIC ACID

Function and homology information

Biological species

unidentified (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 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	5wl4.cif.gz	332.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5wl4.ent.gz	274.1 KB	Display	PDB format
PDBx/mmJSON format	5wl4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5wl4_validation.pdf.gz	461.5 KB	Display	wwPDB validaton report
Full document	5wl4_full_validation.pdf.gz	472.5 KB	Display
Data in XML	5wl4_validation.xml.gz	34.6 KB	Display
Data in CIF	5wl4_validation.cif.gz	48.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wl/5wl4 ftp://data.pdbj.org/pub/pdb/validation_reports/wl/5wl4	HTTPS FTP

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Related structure data

Related structure data	5wkrC 5wksC 5wl3C 5wl5C 5wl6C 5wl7C 5wl8C 4doiS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5wl8-1 5wl8-2 5wl6-2 5wl8-4 5hha-1 3m2x-d 6ms8-2 5wl8-3 4oa5-2 1a2k-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) 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 ancR3

B: Engineered Chalcone Isomerase ancR3

C: Engineered Chalcone Isomerase ancR3

D: Engineered Chalcone Isomerase ancR3

hetero molecules

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

1

A: Engineered Chalcone Isomerase ancR3

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 ancR3

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 ancR3

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 ancR3

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)	69.220, 117.690, 71.850
Angle α, β, γ (deg.)	90.00, 118.63, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Engineered Chalcone Isomerase ancR3 Mass: 23951.156 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-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH₂O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.68 Å³/Da / Density % sol: 54.13 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 25% PEG 4K, 2.5mM ammonium formate, 100mM succinic acid

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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: Oct 15, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2→53.99 Å / Num. obs: 68082 / % possible obs: 100 % / Redundancy: 7.2 % / Net I/σ(I): 11.7

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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→53.987 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.37

	R_factor	Num. reflection	% reflection
R_free	0.2165	1976	2.91 %
R_work	0.1924	-	-
obs	0.1931	67983	99.87 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2→53.987 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6244	0	12	336	6592

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	6368
X-RAY DIFFRACTION	f_angle_d	0.987	8624
X-RAY DIFFRACTION	f_dihedral_angle_d	13.924	2332
X-RAY DIFFRACTION	f_chiral_restr	0.043	1008
X-RAY DIFFRACTION	f_plane_restr	0.004	1108

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 (%)
2.0001-2.0501	0.3179	141	0.2742	4668	X-RAY DIFFRACTION	100
2.0501-2.1055	0.2636	148	0.2592	4704	X-RAY DIFFRACTION	100
2.1055-2.1675	0.3017	151	0.2465	4684	X-RAY DIFFRACTION	100
2.1675-2.2374	0.2734	126	0.2258	4718	X-RAY DIFFRACTION	100
2.2374-2.3174	0.2295	135	0.2224	4718	X-RAY DIFFRACTION	100
2.3174-2.4102	0.255	146	0.2228	4680	X-RAY DIFFRACTION	100
2.4102-2.5199	0.2946	140	0.2323	4684	X-RAY DIFFRACTION	100
2.5199-2.6527	0.2626	138	0.2299	4751	X-RAY DIFFRACTION	100
2.6527-2.8189	0.2426	143	0.2285	4700	X-RAY DIFFRACTION	100
2.8189-3.0365	0.2596	144	0.2275	4708	X-RAY DIFFRACTION	100
3.0365-3.3421	0.2486	129	0.2214	4720	X-RAY DIFFRACTION	100
3.3421-3.8256	0.2215	140	0.1822	4771	X-RAY DIFFRACTION	100
3.8256-4.8193	0.1472	143	0.1453	4734	X-RAY DIFFRACTION	100
4.8193-54.0067	0.1779	152	0.1488	4767	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	3.4956	1.4244	-0.8438	5.5065	0.2536	5.6786	0.1786	0.074	-0.3272	0.3289	-0.2029	-0.0372	0.2474	0.2619	0.0956	0.4435	0.0162	0.0455	0.3351	0.011	0.3449	23.8128	-33.518	22.3682
2	3.1803	-0.1698	-1.9021	2.9528	-0.2486	5.2104	0.0142	0.2162	-0.1194	0.282	0.0035	0.1546	0.4638	-0.1863	-0.0484	0.3247	-0.0409	0.0355	0.2693	-0.041	0.401	22.6866	-33.6261	10.7611
3	3.2137	-0.095	-1.3697	2.5969	-0.0508	4.1647	0.0376	0.1283	-0.0053	0.1666	0.002	0.3174	0.3502	-0.4138	-0.0639	0.3488	-0.1135	0.0372	0.3427	-0.03	0.4079	19.1353	-33.8067	12.473
4	3.5593	0.1635	-1.6878	3.0558	0.6732	3.9058	-0.1659	0.9906	-0.3628	-0.2819	0.2935	0.1593	0.4275	-1.3006	0.094	0.6811	-0.4466	0.1112	1.146	-0.088	0.6202	4.6101	-41.0526	10.0229
5	2.8362	0.3981	-1.14	2.6906	0.2166	4.2099	0.0228	0.4463	0.0896	0.0733	0.1197	0.4717	0.1952	-0.5961	-0.1319	0.2963	-0.0426	0.0747	0.3518	0.044	0.4389	16.8882	-28.7991	12.7347
6	8.5218	-2.4708	2.6154	1.8518	-0.3929	3.4529	-0.0371	0.5147	0.9395	-0.2255	0.2375	0.416	-0.3775	-0.1584	-0.4178	0.441	-0.0471	0.0757	0.4476	0.1082	0.5035	19.9463	-18.5172	3.502
7	5.719	-1.8718	2.4457	2.1843	-0.7144	4.1267	0.1839	0.3047	1.2385	0.3011	-0.0531	0.3655	-0.854	-0.2663	-0.3085	0.4874	0.0193	0.2159	0.4791	0.0996	0.6168	16.6437	-11.2881	8.3137
8	4.7405	-0.0579	0.2623	3.7021	-0.2082	3.5795	0.1425	-0.3576	0.2265	0.5787	0.1534	0.1616	-0.3691	-0.0073	-0.2958	0.3938	-0.0532	0.1087	0.2953	-0.0352	0.35	24.3338	-20.4109	19.0255
9	3.2019	-0.9165	-1.2351	5.9999	0.8917	2.9165	-0.0798	0.4834	-0.2392	-0.2183	0.3692	0.8983	-0.0123	-0.7322	-0.2502	0.3342	-0.0523	0.0805	0.4615	0.0846	0.4753	14.4091	-25.0629	7.9264
10	8.8843	4.3939	-7.5188	4.371	-4.2834	6.9796	-0.3285	0.3717	-1.0632	-0.2707	0.2421	-0.264	0.9192	-0.9143	0.1104	0.4336	-0.2289	0.0221	0.5084	-0.0041	0.4841	12.9452	-40.6075	13.0593
11	1.8516	-0.224	0.9054	2.6101	-0.1475	3.2698	-0.1071	0.1953	0.1604	-0.4191	0.182	-0.0189	-0.5306	0.0988	-0.0603	0.3823	0.0039	-0.0516	0.3183	0.0544	0.3322	27.0284	7.5925	-19.0269
12	2.2157	0.8342	0.0958	1.3945	0.4439	2.3674	-0.1038	0.1715	0.2886	-0.1619	0.0334	0.4021	-0.3406	-0.395	0.0033	0.3895	0.1202	-0.0774	0.3229	0.0239	0.378	22.9761	9.1293	-13.9077
13	2.8266	-1.0405	0.67	2.1123	0.6477	2.302	-0.1746	-0.3954	0.1257	0.137	0.1952	0.3468	-0.5102	-1.0121	-0.0675	0.4273	0.212	-0.0479	0.6946	0.0971	0.4146	16.2307	10.2331	-13.2929
14	4.7232	1.0328	-0.6905	1.7274	-0.0632	3.4104	0.1437	-0.4701	-0.6572	0.1009	0.2054	0.4447	0.5198	-0.6786	-0.3077	0.4859	-0.0311	-0.0963	0.5606	0.2163	0.5686	18.7712	-9.358	-6.1714
15	4.7596	-0.4538	0.716	3.3776	-0.4908	2.6044	-0.0322	0.264	-0.3232	-0.5271	0.3344	0.3119	0.4111	-0.2004	-0.2974	0.4177	-0.0034	-0.1393	0.3508	0.0418	0.3413	25.3921	-5.2459	-19.6005
16	5.8084	4.6672	1.2773	6.3038	0.69	1.9675	0.1995	-0.5224	-0.0277	0.3324	0.0424	0.667	-0.1388	-0.6214	-0.1484	0.3365	0.0915	-0.0446	0.5632	0.1401	0.4192	16.821	1.7413	-8.6606
17	6.1478	-1.913	5.3464	4.6715	-5.0034	7.414	-0.1762	-0.3028	0.907	0.3883	-0.0994	-0.1264	-1.3739	-0.7814	0.2902	0.5591	0.3609	-0.0414	0.6113	0.0217	0.4683	18.1706	16.9412	-15.2514
18	4.3603	-1.3316	0.0039	3.7921	-2.1625	2.0659	0.483	0.4662	-1.0835	-0.0519	-0.3995	-1.005	0.5713	0.6592	-0.1805	0.5745	0.1731	-0.0752	0.7815	0.0103	0.854	57.6721	-5.6901	6.9847
19	1.5275	0.0482	1.8018	1.75	-0.515	4.5977	0.4129	-0.2156	-0.3661	0.2375	-0.1298	-0.2487	0.3834	-0.015	-0.2426	0.4441	0.016	-0.1621	0.3599	0.0385	0.415	47.7478	-4.103	15.5319
20	4.2609	-0.8173	-1.6662	3.2228	0.5402	5.7912	-0.0106	-0.0252	0.4041	0.0212	-0.0848	-0.0657	-0.8379	0.3719	0.0754	0.4713	-0.0843	-0.0671	0.3087	0.0362	0.3378	45.6034	14.3227	10.0185
21	2.2274	0.1969	0.6967	3.7022	-0.6665	3.7438	0.2146	0.1022	-0.1985	0.3015	-0.1367	-0.5478	0.0618	0.3793	-0.0511	0.3368	-0.0215	-0.1271	0.39	0.0014	0.3471	52.4789	2.5622	13.0799
22	1.5274	1.8691	-1.5435	2.5705	-2.0176	1.7018	0.7363	-0.325	0.8339	0.4735	-0.3458	-1.5865	-0.1852	1.0087	-0.4327	0.477	-0.1546	0.0807	1.2552	-0.1651	0.9904	56.1516	-23.6267	-7.2175
23	0.5384	0.8807	-0.3977	3.0046	-0.0208	3.4927	0.4574	-0.5703	0.5381	-0.2387	-0.1131	-0.4315	-0.4463	0.4131	-0.3557	0.3428	-0.0537	0.1566	0.5163	-0.0542	0.4501	44.8063	-22.9545	-9.0924
24	0.1865	-0.0064	0.2218	1.6823	-0.0863	3.8889	0.0845	-0.4314	0.2708	-0.3477	0.1463	-0.2884	-0.0256	0.4016	-0.2559	0.4701	-0.1319	0.1686	0.4965	-0.0849	0.479	46.6645	-22.4476	-12.562
25	2.0712	1.4987	-2.5162	2.5567	-0.3715	4.6622	0.2922	-0.0075	0.2904	-0.3903	0.0725	-0.1387	-0.5655	-0.171	-0.334	0.4194	0.0561	0.1759	0.389	0.0027	0.4187	46.4241	-22.3424	-19.6549
26	2.6266	0.5169	1.3531	2.1771	1.994	2.2075	-0.1558	0.0234	0.0097	-0.377	0.065	-0.1497	0.1496	-0.1907	0.1363	0.4787	0.0297	0.0776	0.4288	0.0487	0.3794	36.9435	-37.4234	-13.3667
27	4.8065	0.8129	0.3252	3.0687	0.7721	6.3857	-0.4122	-0.1951	-0.649	-0.193	0.0952	-0.3024	1.044	0.5298	0.1562	0.5463	0.1149	0.2108	0.3975	0.0949	0.4635	42.5412	-42.5768	-11.737
28	3.6979	0.3995	-2.6023	3.3929	0.2026	4.7545	-0.0662	-0.9488	-0.4942	-0.3435	-0.274	-0.9103	0.7001	1.7596	0.2426	0.4195	0.1736	0.1534	0.6769	0.1255	0.5418	52.6213	-35.2703	-12.6647
29	3.6448	0.8892	0.2047	3.6995	1.8044	2.7373	-0.5738	-1.1551	-0.0603	0.2025	0.4178	-0.9129	0.1444	1.6803	0.1058	0.6561	0.3005	0.0736	1.2034	0.0917	0.7239	55.6701	-38.0979	-7.8703
30	3.1999	-2.0767	-2.6465	2.8458	3.2932	4.2107	0.2683	0.2067	0.1217	-1.1966	-0.2183	0.0033	0.0042	-0.0791	-0.0948	0.4971	0.0679	0.1142	0.4117	0.0602	0.3321	41.9685	-30.8326	-18.265
31	8.5395	3.9839	-3.2886	5.3563	-2.838	7.0879	0.6877	-0.4059	0.8771	0.03	0.1807	-0.3838	-1.9198	0.7674	-0.7528	0.6747	-0.0375	0.3051	0.4368	-0.0824	0.5438	47.9515	-15.333	-18.2251

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 6 through 24 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 25 through 38 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 39 through 60 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 61 through 75 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 76 through 100 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 101 through 118 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 119 through 137 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 138 through 178 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 179 through 196 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 197 through 212 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 6 through 38 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 39 through 60 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 61 through 100 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 101 through 138 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 139 through 178 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 179 through 196 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 197 through 212 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 6 through 24 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 25 through 100 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 101 through 146 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 147 through 212 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 6 through 24 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 25 through 38 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 39 through 60 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 61 through 100 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 101 through 118 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 119 through 146 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 147 through 163 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 164 through 178 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 179 through 196 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 197 through 212 )

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