PDB-6uae: Ketosteroid isomerase (C. testosteroni) with truncated & designed...

ID or keywords:

Entry

Database: PDB / ID: 6uae

Title

Ketosteroid isomerase (C. testosteroni) with truncated & designed loop for precise positioning of a catalytic E38

Components

Ketosteroid isomerase with designed loop

Keywords

ISOMERASE

Function / homology

Function and homology information

steroid Delta-isomerase / steroid delta-isomerase activity / steroid metabolic process
Similarity search - Function

Biological species

Comamonas testosteroni (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.93 Å

Authors

Krivacic, C. / Kundert, K. / Thompson, M.C. / Fraser, J.S. / Kortemme, T.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	R01-GM110089	United States
National Science Foundation (NSF, United States)	DBI-1564692	United States

Citation

Journal: To Be Published
Title: Ketosteroid isomerase (C. testosteroni) with truncated & designed loop for precise positioning of a catalytic E38
Authors: Krivacic, C. / Kundert, K. / Thompson, M.C. / Fraser, J.S. / Kortemme, T.

History

Deposition	Sep 10, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 16, 2020	Provider: repository / Type: Initial release
Revision 1.1	Mar 13, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6uae.cif.gz	315.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6uae.ent.gz	268.4 KB	Display	PDB format
PDBx/mmJSON format	6uae.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6uae_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	6uae_full_validation.pdf.gz	1.7 MB	Display
Data in XML	6uae_validation.xml.gz	28.2 KB	Display
Data in CIF	6uae_validation.cif.gz	37.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ua/6uae ftp://data.pdbj.org/pub/pdb/validation_reports/ua/6uae	HTTPS FTP

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Related structure data

Related structure data	6uadC C: citing same article (ref.)
Similar structure data	1ogz-d 3qzo-2 3sub-1 2itf-1 8cho-d 5bpq-4 6l2a-d 3wsr-1 6c17-d 2qvt-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 - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

6uadC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#44 - Aug 2003 Calmodulin similarity (1)

Deposited unit

A: Ketosteroid isomerase with designed loop

B: Ketosteroid isomerase with designed loop

C: Ketosteroid isomerase with designed loop

D: Ketosteroid isomerase with designed loop

hetero molecules

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

1

A: Ketosteroid isomerase with designed loop

hetero molecules

defined by author&software
Evidence: gel filtration
14.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Ketosteroid isomerase with designed loop

hetero molecules

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

3

C: Ketosteroid isomerase with designed loop

hetero molecules

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

4

D: Ketosteroid isomerase with designed loop

hetero molecules

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

Unit cell

Length a, b, c (Å)	73.012, 209.997, 39.639
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x+1/2,y+1/2,-z #4: -x,-y,z

#1: Protein	Ketosteroid isomerase with designed loop Mass: 13848.505 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: partial computational redesign / Source: (gene. exp.) Comamonas testosteroni (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P00947*PLUS
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-DXC / (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID / DEOXYCHOLIC ACID Mass: 392.572 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂₄H₄₀O₄ / Comment: detergent*YM
#4: Chemical	ChemComp-EQU / EQUILENIN Mass: 266.334 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₈H₁₈O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 372 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.8 Å³/Da / Density % sol: 56.03 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 1.6M Ammonium Sulfate, 50 mM potassium phosphate pH 7.2

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 28, 2019
Radiation	Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.1158 Å / Relative weight: 1
Reflection	Resolution: 1.93→105 Å / Num. obs: 46239 / % possible obs: 98.1 % / Redundancy: 19.1 % / B_iso Wilson estimate: 26.59 Å² / CC_1/2: 0.995 / R_merge(I) obs: 0.253 / R_pim(I) all: 0.059 / Net I/σ(I): 9.3
Reflection shell	Resolution: 1.93→1.96 Å / Redundancy: 17.7 % / R_merge(I) obs: 3.378 / Mean I/σ(I) obs: 1 / Num. unique obs: 2182 / CC_1/2: 0.652 / R_pim(I) all: 0.818 / % possible all: 94.2

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Processing

Software

Name	Version	Classification
PHENIX	1.16_3549	refinement
xia2		data reduction
DIALS		data reduction
pointless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.93→105 Å / SU ML: 0.198 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.646

	R_factor	Num. reflection	% reflection
R_free	0.212	2333	5.06 %
R_work	0.175	-	-
obs	0.177	46116	97.9 %

Solvent computation

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

Displacement parameters

B_iso mean: 37.68 Å²

Refinement step

Cycle: LAST / Resolution: 1.93→105 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3826	0	204	372	4402

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	4395
X-RAY DIFFRACTION	f_angle_d	0.91	6034
X-RAY DIFFRACTION	f_dihedral_angle_d	19.047	2527
X-RAY DIFFRACTION	f_chiral_restr	0.053	664
X-RAY DIFFRACTION	f_plane_restr	0.005	781

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 (%)
1.93-1.97	0.3916	124	0.3041	2455	X-RAY DIFFRACTION	94
1.97-2.01	0.293	137	0.2566	2468	X-RAY DIFFRACTION	97
2.01-2.06	0.2604	120	0.2394	2520	X-RAY DIFFRACTION	97
2.06-2.11	0.2543	143	0.2173	2526	X-RAY DIFFRACTION	97
2.11-2.17	0.2271	128	0.2027	2515	X-RAY DIFFRACTION	97
2.17-2.23	0.2307	160	0.1926	2521	X-RAY DIFFRACTION	98
2.23-2.3	0.2068	140	0.188	2529	X-RAY DIFFRACTION	98
2.3-2.38	0.2545	132	0.189	2537	X-RAY DIFFRACTION	98
2.38-2.48	0.2209	120	0.1818	2601	X-RAY DIFFRACTION	98
2.48-2.59	0.1981	150	0.1752	2522	X-RAY DIFFRACTION	98
2.59-2.73	0.2099	142	0.1737	2565	X-RAY DIFFRACTION	98
2.73-2.9	0.261	132	0.1783	2604	X-RAY DIFFRACTION	99
2.9-3.12	0.2037	121	0.1642	2612	X-RAY DIFFRACTION	99
3.12-3.44	0.1777	151	0.16	2612	X-RAY DIFFRACTION	99
3.44-3.94	0.1903	149	0.1443	2670	X-RAY DIFFRACTION	99
3.94-4.96	0.1563	139	0.1313	2701	X-RAY DIFFRACTION	99
4.96-105	0.2314	145	0.1971	2825	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	4.5185	0.1526	0.8788	3.1989	0.6409	5.3869	-0.0598	-0.5034	-0.386	0.3216	-0.04	0.2379	0.2067	0.0806	0.0792	0.2158	0.0083	0.071	0.269	0.08	0.2238	12.2165	29.6536	26.4551
2	7.1414	-0.0938	-4.6003	7.3992	-1.5639	5.0248	0.051	0.3988	0.3672	-0.3506	-0.1053	0.0355	0.2326	-0.2544	0.0359	0.1763	0.0179	-0.0569	0.3422	0.0263	0.2368	10.9604	42.473	17.052
3	1.3109	1.949	0.1078	9.3738	2.2838	0.7935	-0.1046	0.048	0.1117	-0.2899	0.1381	0.1616	0.0138	-0.0164	-0.0249	0.1952	0.0043	-0.0092	0.269	-0.003	0.2535	4.1967	38.8568	16.0862
4	4.1651	1.1838	1.2534	2.5681	1.5412	2.6782	-0.1443	-0.0745	-0.2107	-0.0815	0.0377	0.0014	-0.0604	0.0043	0.0845	0.2199	-0.0025	0.0429	0.1889	0.0565	0.1266	18.8828	30.4953	18.2668
5	5.891	2.3815	1.8869	8.4919	5.6201	3.7381	-0.1472	0.9255	-0.4568	-0.9064	-0.2889	0.0144	-0.6114	-0.4426	0.2643	0.4461	-0.0292	0.0325	0.4612	-0.0481	0.3552	15.6962	26.129	0.5621
6	4.17	-1.2329	-3.6556	1.921	1.7273	3.4859	-0.0543	-0.061	0.201	0.0329	0.0151	0.1806	0.0726	-0.1317	0.0597	0.18	0.0037	-0.0115	0.2552	0.0219	0.1983	15.962	39.0373	23.6446
7	2.8633	-2.8905	-1.3979	3.0818	1.746	2.0389	-0.3773	0.3168	0.0134	-0.7454	0.1565	0.2916	-0.2352	0.0742	0.1447	0.2628	-0.0341	-0.0075	0.2938	-0.0088	0.1806	22.1458	33.2772	4.5578
8	2.9915	2.8233	-0.966	3.9009	-0.2373	2.4085	0.3869	-0.2534	-0.869	0.1877	-0.1341	-0.5466	0.5753	0.0475	-0.229	0.3109	0.0038	-0.0606	0.1782	0.0222	0.4751	-10.2712	14.6743	19.0287
9	4.0164	0.5882	2.8942	2.0444	-0.7581	8.2395	-0.0456	0.5204	-0.1218	-0.005	0.1142	-0.093	0.0214	0.0819	-0.0469	0.215	-0.0312	0.0463	0.317	-0.0426	0.3336	-7.3318	22.4758	8.4098
10	2.2431	2.212	2.1278	4.1183	4.6722	5.4536	-0.3911	0.6814	0.081	-0.3871	0.1386	-0.2118	-0.1155	0.2721	0.3076	0.2727	-0.0462	0.0255	0.3989	-0.0255	0.276	-4.0902	26.5063	6.5177
11	4.2257	2.3634	0.8588	7.7888	1.7035	1.714	0.1079	-0.1549	-0.3067	0.3024	0.0149	-0.1623	0.1662	0.0427	-0.117	0.2295	0.0013	-0.0318	0.1965	0.0303	0.2394	-15.8625	23.1755	18.1455
12	4.6983	5.1714	-1.2929	5.7045	-1.5089	1.0951	0.0542	-0.0028	1.4168	0.438	0.228	1.2809	-0.4003	-0.1306	-0.3093	0.3195	0.0416	0.0117	0.2706	-0.0446	0.4866	-15.6113	39.8098	21.0886
13	8.7051	-5.2538	-2.1973	4.1578	3.1127	3.9924	0.0788	0.4998	-0.7207	0.2231	-0.0595	-0.1108	0.3192	0.1057	-0.0842	0.2322	-0.0276	-0.0016	0.2185	-0.0481	0.3626	-14.0776	16.776	9.0983
14	6.7361	-3.0655	-1.5088	3.3398	4.1747	6.5884	-0.3122	-0.3028	0.8826	-0.2346	0.1424	-0.1088	-0.5608	0.0394	-0.0621	0.2972	-0.0073	-0.0143	0.1939	0.009	0.353	-22.6376	35.4563	15.1259
15	1.9827	-0.245	0.3307	3.5999	1.0822	2.8571	0.0271	0.208	0.0257	-0.1719	0.1588	-0.457	-0.1506	0.2268	-0.1629	0.1773	-0.0056	0.027	0.2177	0.001	0.2508	-0.207	58.8012	22.4678
16	7.2164	2.365	2.3273	8.3055	1.1607	2.5661	-0.1575	0.3686	0.3521	-0.4127	0.1165	-0.7711	-0.2743	0.2289	0.0272	0.3044	0.0008	0.0685	0.251	-0.0261	0.3046	2.8295	53.6816	12.8701
17	3.6623	0.3671	-0.8207	2.824	-0.5596	2.6781	-0.2379	0.167	0.0787	-0.3233	0.2399	-0.347	0.152	0.1142	-0.0056	0.2268	-0.0326	0.0123	0.2324	0.001	0.166	-0.6548	68.1088	20.8036
18	3.0382	1.2913	1.5134	2.8296	-0.4909	1.3361	-0.0409	0.7899	0.7825	-0.648	0.1672	-0.5648	-0.1822	0.0762	-0.317	0.3245	-0.0556	0.0639	0.4201	0.0364	0.4085	7.6147	75.9511	8.6768
19	2.4947	-0.8776	0.5383	7.2691	-5.4542	7.2141	0.0538	0.1927	-0.1228	-0.0178	-0.0324	0.1509	0.2084	0.0709	0.0123	0.1709	-0.0145	0.0132	0.2245	-0.004	0.1888	-7.1945	58.6589	21.3362
20	2.0066	2.0536	-1.6498	3.1517	-1.2525	6.4324	-0.3524	0.6754	0.4873	-0.1855	0.5391	-0.0946	-0.5929	0.2678	-0.0731	0.3346	-0.0483	0.041	0.3363	0.0625	0.2862	-1.6064	76.4905	9.9695
21	8.0081	4.0262	-2.7912	3.2914	-3.0484	5.3557	0.3455	-0.1366	0.4721	0.4492	-0.286	0.9698	-0.0759	0.0504	-0.168	0.2666	0.0146	0.1001	0.1952	-0.0456	0.474	-36.5842	25.1569	8.7985
22	7.8702	-1.6251	2.3252	6.6968	-0.0887	4.2109	0.4697	0.2616	-1.0486	-0.1897	-0.0038	0.897	0.5538	0.0541	-0.4656	0.3746	-0.0156	-0.1049	0.2931	-0.0567	0.5213	-35.9475	12.9212	3.5777
23	2.6599	-0.3697	0.4829	3.0603	2.8674	7.06	0.3052	0.142	-0.8386	-0.3174	-0.089	0.974	0.3713	-0.3509	-0.0795	0.5164	-0.0085	-0.2477	0.3072	-0.1105	0.8269	-39.2873	8.0325	3.8421
24	4.6691	2.2223	1.6619	5.6912	0.0976	4.1082	0.246	0.059	-0.0206	0.2706	-0.2765	0.2427	-0.0793	0.0689	0.0039	0.1958	0.0547	0.0573	0.1381	-0.004	0.2784	-30.5092	23.0575	12.2121
25	4.4909	3.7788	-1.9471	4.5956	-3.0964	2.3587	0.1657	-0.1937	-0.463	0.2169	-0.211	0.2919	0.6204	-0.1711	0.187	0.5386	-0.1159	0.0794	0.2661	0.0137	0.4753	-35.4427	11.01	20.0255
26	2.5275	-1.4599	2.9938	8.351	-5.5507	9.1429	0.3315	0.2589	-0.4212	-0.4311	-0.226	0.2684	0.2507	0.1351	-0.0888	0.24	0.0393	0.0021	0.2307	-0.0494	0.2972	-29.2185	18.5838	4.3447
27	4.5234	-1.2275	-0.8879	6.7195	-1.5732	6.1747	-0.1643	-0.5417	-1.1878	1.0726	-0.4728	0.406	0.0809	0.0882	-0.2922	0.5082	-0.1117	0.0179	0.2735	0.0946	0.6457	-26.5073	7.1792	20.9674

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 1 THROUGH 29 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 30 THROUGH 42 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 43 THROUGH 59 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 60 THROUGH 88 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 89 THROUGH 95 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 96 THROUGH 115 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 116 THROUGH 124 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 2 THROUGH 19 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 20 THROUGH 42 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 43 THROUGH 59 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 60 THROUGH 88 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 89 THROUGH 95 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 96 THROUGH 115 )
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESID 116 THROUGH 125 )
15	X-RAY DIFFRACTION	15	CHAIN 'C' AND (RESID 2 THROUGH 42 )
16	X-RAY DIFFRACTION	16	CHAIN 'C' AND (RESID 43 THROUGH 58 )
17	X-RAY DIFFRACTION	17	CHAIN 'C' AND (RESID 59 THROUGH 88 )
18	X-RAY DIFFRACTION	18	CHAIN 'C' AND (RESID 89 THROUGH 95 )
19	X-RAY DIFFRACTION	19	CHAIN 'C' AND (RESID 96 THROUGH 115 )
20	X-RAY DIFFRACTION	20	CHAIN 'C' AND (RESID 116 THROUGH 126 )
21	X-RAY DIFFRACTION	21	CHAIN 'D' AND (RESID 2 THROUGH 20 )
22	X-RAY DIFFRACTION	22	CHAIN 'D' AND (RESID 21 THROUGH 42 )
23	X-RAY DIFFRACTION	23	CHAIN 'D' AND (RESID 43 THROUGH 60 )
24	X-RAY DIFFRACTION	24	CHAIN 'D' AND (RESID 61 THROUGH 76 )
25	X-RAY DIFFRACTION	25	CHAIN 'D' AND (RESID 77 THROUGH 95 )
26	X-RAY DIFFRACTION	26	CHAIN 'D' AND (RESID 96 THROUGH 115 )
27	X-RAY DIFFRACTION	27	CHAIN 'D' AND (RESID 116 THROUGH 123 )

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Movie

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Structure viewers

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Validation report

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Assembly

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Data collection

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About Yorodumi

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

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Aug 12, 2020. Covid-19 info

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

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Yorodumi