PDB-5wl8: Crystal structure of chalcone isomerase engineered from ancestral...

ID or keywords:

Entry

Database: PDB / ID: 5wl8

Title

Crystal structure of chalcone isomerase engineered from ancestral inference (epR4)

Components

Engineered Chalcone Isomerase epR4

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

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.58 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	5wl8.cif.gz	473.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5wl8.ent.gz	395.7 KB	Display	PDB format
PDBx/mmJSON format	5wl8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5wl8_validation.pdf.gz	462.3 KB	Display	wwPDB validaton report
Full document	5wl8_full_validation.pdf.gz	466.8 KB	Display
Data in XML	5wl8_validation.xml.gz	41.6 KB	Display
Data in CIF	5wl8_validation.cif.gz	62.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wl/5wl8 ftp://data.pdbj.org/pub/pdb/validation_reports/wl/5wl8	HTTPS FTP

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Related structure data

Related structure data	5wkrC 5wksC 5wl3C 5wl4C 5wl5C 5wl6C 5wl7C 4doiS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5wl4-2 5wl4-3 5wl4-1 5wl4-4 6vii-2 6ms8-1 5kci-d 5wl6-1 6ms8-7 5wl6-2 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 epR4

B: Engineered Chalcone Isomerase epR4

C: Engineered Chalcone Isomerase epR4

D: Engineered Chalcone Isomerase epR4

hetero molecules

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

1

A: Engineered Chalcone Isomerase epR4

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 epR4

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 epR4

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 epR4

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)	65.940, 112.670, 71.760
Angle α, β, γ (deg.)	90.00, 117.37, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Engineered Chalcone Isomerase epR4 Mass: 23963.102 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (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.: 1035 / 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: 2.47 Å³/Da / Density % sol: 50.2 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 29% PEG 4K, 2.5M ammonium formate, 50mM 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: Jun 25, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.58→58.57 Å / Num. obs: 126702 / % possible obs: 99.8 % / Redundancy: 5.3 % / Net I/σ(I): 8.33

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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: 1.58→58.57 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.07

	R_factor	Num. reflection	% reflection
R_free	0.1933	1995	1.58 %
R_work	0.1696	-	-
obs	0.17	126615	99.66 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.58→58.57 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6244	0	12	1035	7291

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	6364
X-RAY DIFFRACTION	f_angle_d	0.929	8624
X-RAY DIFFRACTION	f_dihedral_angle_d	12.777	2336
X-RAY DIFFRACTION	f_chiral_restr	0.036	1016
X-RAY DIFFRACTION	f_plane_restr	0.005	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 (%)
1.58-1.6195	0.285	143	0.2482	8900	X-RAY DIFFRACTION	100
1.6195-1.6633	0.2482	144	0.222	8892	X-RAY DIFFRACTION	100
1.6633-1.7123	0.2402	146	0.2149	8906	X-RAY DIFFRACTION	100
1.7123-1.7675	0.2387	141	0.2047	8859	X-RAY DIFFRACTION	100
1.7675-1.8307	0.2328	136	0.203	8947	X-RAY DIFFRACTION	100
1.8307-1.904	0.2459	144	0.1961	8886	X-RAY DIFFRACTION	100
1.904-1.9907	0.2371	144	0.1832	8955	X-RAY DIFFRACTION	100
1.9907-2.0956	0.2092	140	0.1704	8871	X-RAY DIFFRACTION	100
2.0956-2.2269	0.1737	142	0.1678	8926	X-RAY DIFFRACTION	100
2.2269-2.3989	0.1575	142	0.1599	8925	X-RAY DIFFRACTION	100
2.3989-2.6403	0.1946	145	0.1686	8902	X-RAY DIFFRACTION	100
2.6403-3.0223	0.1771	141	0.1721	8937	X-RAY DIFFRACTION	100
3.0223-3.8077	0.2062	144	0.1589	8959	X-RAY DIFFRACTION	100
3.8077-58.6141	0.1591	143	0.1484	8755	X-RAY DIFFRACTION	97

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	0.0155	0.0041	0.0103	0.0065	-0.0035	0.0092	0.0398	0.0098	0.0026	0.0075	-0.032	-0.0235	0.0557	0.0895	0.0077	0.349	0.0405	0.0829	0.201	0.0037	0.1752	92.8965	-28.0641	23.9271
2	0.0442	-0.0321	0.0018	0.0255	-0.0022	0.0011	0.0487	0.0588	-0.0393	0.1126	-0.0426	0.1018	0.0856	-0.0137	0.0164	0.208	-0.0185	0.0793	0.1364	0.0046	0.1658	91.2528	-29.3375	12.4829
3	0.0277	-0.0009	0.0316	0.0173	0.0009	0.0259	0.0461	0.0207	0.045	0.0272	-0.0047	0.0983	0.0559	-0.0853	0.0115	0.1583	-0.0394	0.0622	0.1543	-0.0141	0.1662	88.0945	-29.9742	14.1045
4	0.0106	-0.0063	0.0003	0.0136	0.0058	0.0054	0.0019	0.0357	0.0683	-0.024	0.0079	0.0944	0.0549	-0.1216	-0.0004	0.1735	-0.0842	0.0544	0.2551	-0.0033	0.2359	74.8434	-36.2345	12.7763
5	0.0062	0.0059	0.0092	0.0248	0.0172	0.0172	0.0157	-0.0255	-0.0089	0.0559	0.0014	0.0281	0.014	-0.0594	-0.0007	0.143	-0.0132	0.0576	0.1366	-0.0042	0.1559	91.0538	-22.4802	15.8153
6	0.0304	0.0464	-0.0184	0.0761	-0.0405	0.0311	-0.0355	0.0058	0.1312	0.0456	0.1078	0.1296	-0.0987	-0.0753	0.0456	0.106	0.0086	0.0277	0.1617	0.0327	0.1965	84.6222	-10.7522	6.8771
7	0.0027	-0.0007	-0.0015	0.0047	-0.004	0.0001	0.018	-0.0352	0.0255	0.1728	0.0184	0.1212	-0.0082	-0.0369	0.0125	0.1374	-0.0059	0.0724	0.1226	-0.0028	0.1783	90.2725	-17.223	18.6443
8	0.0026	0.0003	0.0013	0.0058	0.0093	0.0099	0.1084	0.0023	0.0092	0.1059	0.0171	-0.0283	-0.0351	0.0059	-0	0.204	-0.0103	0.0482	0.1822	-0.0317	0.2657	91.444	-13.6164	22.9711
9	0.0124	-0.0019	0.0099	0.0176	0.0018	0.0102	0.036	0.04	0.0257	-0.0558	0.0782	0.075	0.0014	-0.0693	0.0143	0.1311	-0.0224	0.0394	0.1917	0.0392	0.193	81.4924	-22.005	9.1801
10	0.005	0.0038	-0.0038	0.0027	-0.0014	0.0049	0.0611	-0.067	-0.0551	0.0009	0.0505	0.0017	0.0344	-0.0626	0.002	0.2116	-0.0676	0.0149	0.1657	0.0221	0.1734	83.1432	-37.7089	15.5751
11	0.0255	-0.0186	0.0051	0.0273	-0.0284	0.0389	-0.0146	0.0166	0.033	-0.0002	-0.0021	-0.0201	-0.0367	0.0133	0.0355	0.3653	-0.0063	-0.1461	0.1393	0.0645	0.1108	90.8251	10.7038	-22.1236
12	0.1137	0.0557	-0.0204	0.0339	-0.0079	0.0037	0.0616	-0.0464	0.0323	-0.0966	-0.095	0.0892	-0.0874	-0.0191	0.0156	0.2235	0.0717	-0.1562	0.1125	0.0334	0.1564	89.1113	9.8416	-10.9506
13	0.06	0.0212	-0.0455	0.0513	-0.023	0.0255	0.0691	-0.0509	0.0046	-0.0389	-0.0498	0.1428	-0.087	-0.0811	0.0297	0.1314	0.1164	-0.1157	0.2035	-0.0203	0.1662	85.8777	10.125	-12.8465
14	0.0049	-0.0015	-0.0008	0.0009	-0	0.0012	0.0519	0.0049	0.0229	0.0451	0.0108	0.0039	-0.0093	-0.0129	0	0.1689	0.1128	-0.0301	0.3314	0.0096	0.3586	70.8891	16.4231	-10.6833
15	0.017	-0.0076	-0.0187	0.016	0.0029	0.0186	-0.0042	0.0187	-0.0126	0.0018	0.0156	0.1163	-0.0086	-0.087	-0.0093	0.1094	0.022	-0.0504	0.1579	0.0116	0.1775	83.8064	4.7449	-13.779
16	0.0038	0.0044	-0.0081	0.0078	-0.0156	0.0191	-0.0158	-0.0529	-0.0941	-0.0341	0.0448	0.0651	0.1456	-0.1146	0.0007	0.1346	-0.0434	-0.0468	0.149	0.0428	0.1712	86.2314	-10.8011	-8.3466
17	0.0684	0.0232	-0.013	0.1026	-0.009	0.0471	0.0639	0.0578	-0.0956	-0.1304	0.0214	0.0361	0.049	-0.1164	0.0666	0.1342	0.0065	-0.0606	0.17	0.012	0.1787	89.1431	-1.9257	-16.9166
18	0.0121	-0.0088	-0.0043	0.0142	0.0241	0.0431	0.0464	0.0021	0.085	0.0038	0.0623	0.0348	-0.0304	-0.0478	0.0201	0.175	0.1072	-0.0716	0.1431	0.0103	0.2692	79.299	16.3375	-13.1134
19	0.006	-0.0056	-0.002	0.0082	-0.0031	0.004	0.0037	0.0382	0.0127	-0.0411	-0.0614	-0.037	0.0304	0.0135	-0	0.2314	0.0586	-0.13	0.3888	-0.0765	0.4245	122.2254	2.2162	6.5978
20	0.0452	-0.0115	-0.0407	0.0706	0.0513	0.0562	-0.029	-0.041	-0.0341	0.2624	0.0134	-0.0415	0.0519	-0.0099	-0.0152	0.211	-0.0007	-0.148	0.1361	0.0381	0.1745	112.363	-0.0919	10.6509
21	0.0002	0.0011	-0.0009	0.0007	-0.0003	0.0016	-0.0227	-0.0115	-0.0282	0.0449	0.0118	0.0308	0.0266	-0.0131	-0.0432	0.5367	-0.0937	-0.3178	0.1637	0.1428	0.1486	112.962	-8.7616	26.3958
22	0.017	-0.012	-0.0003	0.0184	-0.0017	0.0096	0.0861	-0.033	-0.0428	0.1298	-0.0016	-0.1155	0.019	0.0004	0.0165	0.2143	-0.0245	-0.1091	0.1624	0.0377	0.1756	113.0047	4.9573	14.9508
23	0.1249	-0.0858	-0.0032	0.1114	-0.0111	0.0914	0.0424	-0.0826	0.0449	0.1566	-0.0219	-0.1845	-0.116	-0.0309	0.0206	0.1913	-0.0232	-0.051	0.1702	0.0195	0.1526	110.3687	15.1842	12.7375
24	0.0219	0.0076	-0.0065	0.006	-0	0.0075	-0.0011	0.0082	-0.0322	0.0557	0.0885	-0.0369	0.1099	0.0011	0.0499	0.3461	-0.0156	-0.3493	0.1141	0.0804	0.1067	114.9599	-7.1607	17.622
25	0.0025	0.0002	-0.0013	0.0022	0.0018	0.0015	-0.018	-0.0006	-0.0044	0.0171	0.0189	-0.0044	-0.0263	-0.013	0	0.3077	-0.1285	0.0837	0.2928	-0.1019	0.3908	116.8329	-12.1287	-3.4571
26	0.01	0.0179	0.0145	0.0346	0.046	0.0606	0.0678	0.0207	0.0568	-0.2389	-0.0623	-0.1812	-0.0128	0.0304	-0.0244	0.1602	0.0007	0.2674	0.1448	0.0166	0.2218	115.4495	-17.9679	-10.801
27	0.0629	0.0234	0.0428	0.0125	0.0166	0.0284	0.0466	-0.0012	0.0515	-0.0648	0.0949	0.0571	-0.1187	-0.0692	0.037	0.3339	0.0503	0.1375	0.2022	0.0686	0.2117	110.6574	-13.8914	-26.4214
28	0.0207	-0.0216	-0.0004	0.0324	0.0116	0.0094	0.0535	0.0253	0.0064	0.0212	0.0303	-0.066	0.0629	0.0524	0.0173	0.1719	0.0255	0.0733	0.185	-0.0045	0.1878	115.5545	-23.6368	-7.8473
29	0.0667	0.0405	-0.0388	0.0763	0.0067	0.0416	0.0182	0.1026	-0.0304	-0.0813	0.0032	-0.1373	0.2022	0.1381	0.0142	0.2153	0.0601	0.0461	0.2088	-0.014	0.1695	113.7686	-32.6344	-11.0695
30	0.0176	-0.0005	0.0057	0.0005	-0.0024	0.0014	-0.0232	-0.0162	0.0155	-0.0337	0.0664	-0.0211	-0.0799	0.0018	0.0132	0.3803	0.0315	0.2949	0.1147	0.0636	0.1691	112.872	-10.3281	-18.3971

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 84 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 85 through 100 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 101 through 139 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 140 through 163 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 164 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 24 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 25 through 38 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 39 through 60 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 61 through 75 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 76 through 100 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 101 through 137 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 138 through 196 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 197 through 212 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 6 through 24 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 25 through 60 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 61 through 75 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 76 through 100 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 101 through 196 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 197 through 212 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 6 through 15 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 16 through 60 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 61 through 84 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 85 through 100 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 101 through 196 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 197 through 212 )

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-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

-
Basic information

-
Structure visualization

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Downloads & links

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Download

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Validation report

-
Related structure data

-
Links

-
Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi