PDB-5g2g: Crystal structure of ketosteroid isomerase containing M116K mutat...

ID or keywords:

Entry

Database: PDB / ID: 5g2g

Title

Crystal structure of ketosteroid isomerase containing M116K mutation in the equilenin-bound form

Components

STEROID DELTA-ISOMERASE

Keywords

ISOMERASE / KETOSTEROID ISOMERASE / CATALYSIS / STABILITY / STRUCTURAL ANALYSIS / CONSERVED MET112

Function / homology

Function and homology information

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

Biological species

PSEUDOMONAS PUTIDA (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.599 Å

Authors

Cha, H.J. / Jeong, J.H.

Citation

Journal: Biochim.Biophys.Acta / Year: 2016
Title: Role of Conserved met112 Residue in the Catalytic Activity and Stability of Ketosteroid Isomerase.
Authors: Cha, H.J. / Jang, D.S. / Jeong, J.H. / Hong, B.H. / Yun, Y.S. / Shin, E.J. / Choi, K.Y.

History

Deposition	Apr 8, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 13, 2016	Provider: repository / Type: Initial release
Revision 1.1	Aug 31, 2016	Group: Database references
Revision 1.2	Mar 29, 2017	Group: Other
Revision 1.3	Jan 10, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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	5g2g.cif.gz	114.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5g2g.ent.gz	90.3 KB	Display	PDB format
PDBx/mmJSON format	5g2g.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5g2g_validation.pdf.gz	978 KB	Display	wwPDB validaton report
Full document	5g2g_full_validation.pdf.gz	969.9 KB	Display
Data in XML	5g2g_validation.xml.gz	13.5 KB	Display
Data in CIF	5g2g_validation.cif.gz	17.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/g2/5g2g ftp://data.pdbj.org/pub/pdb/validation_reports/g2/5g2g	HTTPS FTP

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Related structure data

Related structure data	4k1uS S: Starting model for refinement
Similar structure data	5kp1-1 6ubq-d 3ipt-2 5kp3-1 3ipt-1 1gs3-1 4k1v-1 5d83-d 1ogx-d 1e3v-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

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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: STEROID DELTA-ISOMERASE

B: STEROID DELTA-ISOMERASE

hetero molecules

28.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	35.525, 73.582, 95.214
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	STEROID DELTA-ISOMERASE / DELTA(5)-3-KETOSTEROID ISOMERASE / KETOSTEROID ISOMERASE Mass: 14060.929 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS PUTIDA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P07445
#2: Chemical	ChemComp-EQU / EQUILENIN Mass: 266.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₈H₁₈O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.23 Å³/Da / Density % sol: 44.88 % / Description: NONE
Crystal grow	pH: 5.5 / Details: BIS-TRIS, MAGNESIUM CHLORIDE, PEG 3350, PH 5.50

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1
Detector	Detector: CCD / Details: MIRRORS
Radiation	Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.6→50 Å / Num. obs: 33850 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 8.6 % / B_iso Wilson estimate: 17.12 Å² / R_merge(I) obs: 0.07 / Net I/σ(I): 36.37
Reflection shell	Resolution: 1.6→1.63 Å / Redundancy: 4.8 % / R_merge(I) obs: 0.33 / Mean I/σ(I) obs: 2.86 / % possible all: 94.2

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4K1U

4k1u

Resolution: 1.599→39.971 Å / SU ML: 0.21 / σ(F): 1.49 / Phase error: 23.92 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2297	1999	6 %
R_work	0.1978	-	-
obs	0.1997	33492	99.08 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.599→39.971 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1960	0	40	85	2085

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	2048
X-RAY DIFFRACTION	f_angle_d	1.057	2787
X-RAY DIFFRACTION	f_dihedral_angle_d	14.161	1201
X-RAY DIFFRACTION	f_chiral_restr	0.064	293
X-RAY DIFFRACTION	f_plane_restr	0.007	370

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 (%)
1.5995-1.6395	0.3805	133	0.3375	2085	X-RAY DIFFRACTION	94
1.6395-1.6838	0.329	139	0.3257	2212	X-RAY DIFFRACTION	99
1.6838-1.7334	0.3433	139	0.3072	2194	X-RAY DIFFRACTION	99
1.7334-1.7893	0.2955	143	0.2713	2242	X-RAY DIFFRACTION	99
1.7893-1.8533	0.3004	139	0.2425	2209	X-RAY DIFFRACTION	99
1.8533-1.9275	0.2483	142	0.2138	2220	X-RAY DIFFRACTION	100
1.9275-2.0152	0.2258	142	0.2067	2229	X-RAY DIFFRACTION	100
2.0152-2.1214	0.2161	143	0.1989	2259	X-RAY DIFFRACTION	100
2.1214-2.2543	0.241	143	0.1834	2262	X-RAY DIFFRACTION	100
2.2543-2.4284	0.2235	143	0.1789	2252	X-RAY DIFFRACTION	100
2.4284-2.6727	0.201	145	0.1854	2274	X-RAY DIFFRACTION	100
2.6727-3.0593	0.2289	146	0.2044	2292	X-RAY DIFFRACTION	100
3.0593-3.8539	0.2156	147	0.1791	2319	X-RAY DIFFRACTION	100
3.8539-39.9831	0.187	155	0.157	2444	X-RAY DIFFRACTION	100

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	3.1003	-2.2695	-0.8751	8.7197	1.9834	4.9795	-0.0677	0.0216	-0.1469	0.5882	0.1707	-0.1579	1.5083	-0.5373	0.0065	0.3114	-0.0298	-0.0484	0.1017	0.0218	0.1427	2.8706	-26.8769	-11.9094
2	5.5159	-6.4498	-5.5929	7.5231	6.5277	5.6851	-0.1748	-0.8715	-0.1927	0.2873	0.282	0.1781	0.2778	0.3219	-0.1039	0.1816	-0.0104	0.0209	0.2474	0.0022	0.1701	4.7999	-19.983	-1.7466
3	1.8715	1.0273	-0.3267	5.2025	-3.4212	7.4116	0.0051	0.2043	0.2005	0.1659	-0.2107	-0.2824	-0.5254	1.0479	0.2157	0.2247	-0.0636	-0.0286	0.2128	0.0179	0.188	14.0525	-13.27	-11.6183
4	5.0667	-3.4772	2.9582	7.2636	-0.888	6.5124	-0.3476	-0.4094	0.8025	0.9387	0.0128	-0.2909	-0.4438	-0.3059	0.3067	0.2468	0.0245	-0.0333	0.1624	-0.0168	0.1319	8.5998	-11.7398	-3.3107
5	5.4842	2.421	3.5069	6.7798	6.2567	6.2552	-0.5621	-1.4048	0.6751	0.129	-0.7459	1.4211	-0.5968	-1.6902	1.0623	0.2961	0.1724	-0.0367	0.6085	-0.0992	0.3032	-6.1424	-13.2774	-8.6258
6	2.6177	-0.246	0.6306	3.1045	-0.0184	3.6964	-0.1901	0.3458	-0.1318	0.0937	0.1799	-0.1799	0.5764	0.1719	0.0317	0.1741	0.0003	-0.0305	0.1239	-0.0549	0.1613	4.2329	-26.9623	-21.96
7	2.6394	-2.6917	-1.7591	4.994	2.6833	3.8356	0.4388	0.3317	0.5431	-0.1512	-0.2943	0.1428	-0.9331	-0.4621	-0.0076	0.3756	0.0594	0.0649	0.2031	0.0221	0.3127	-3.0602	-11.2541	-15.1754
8	5.3981	-0.4347	-1.3636	3.9186	1.6813	4.948	-0.0495	-0.0034	0.1125	0.3424	0.0315	0.4259	-0.4352	-0.3448	0.0393	0.1695	0.0266	0.0289	0.1107	-0.0021	0.1268	1.3552	-14.098	-16.309
9	2.7259	-1.8686	0.9519	2.8761	-0.7134	3.9901	0.4775	-0.0444	-0.0241	1.0765	0.0132	-1.2328	1.1416	1.2259	-0.2519	0.6359	0.2277	-0.1271	0.224	-0.0093	0.3238	14.8436	-29.3125	-8.4388
10	2.3705	-0.4461	0.0099	4.2961	-0.3072	3.1564	0.0481	0.329	0.3522	0.0459	-0.1944	0.2701	-0.8765	-0.0294	0.0113	0.2853	0.0689	-0.004	0.0977	-0.0108	0.1919	2.8744	-10.0135	-18.1078
11	2.9803	1.0551	0.4216	6.6134	4.0746	7.2686	0.0197	0.0506	0.2647	-0.7222	-0.2388	0.0735	-1.1721	-0.3531	0.1644	0.3046	-0.0274	-0.0362	0.185	0.0561	0.158	3.596	-10.4526	-36.0206
12	3.8103	-0.5498	-1.1861	3.4245	-0.8033	6.3151	0.0162	0.3786	0.0126	-0.2476	-0.1047	-0.3152	0.3427	1.3766	0.0816	0.249	0.0253	0.0376	0.4586	-0.0365	0.1906	13.942	-20.3801	-37.8317
13	3.9256	-0.9908	-1.8257	3.1944	0.4864	5.3744	-0.1911	0.726	-0.3259	-0.4599	-0.0593	0.1102	0.4819	-0.1206	0.2063	0.2383	0.0121	0.0109	0.2718	-0.0026	0.14	6.0422	-20.0594	-37.3876
14	2.8382	0.7677	0.7054	7.3397	1.7637	4.1035	-0.0738	0.36	-0.3576	-0.4096	-0.0154	0.2284	0.504	-0.2695	0.0323	0.2364	-0.0685	0.001	0.2233	-0.0423	0.1657	1.5531	-24.7051	-32.7546
15	3.4752	-0.1064	-0.004	6.6513	0.0598	5.4782	-0.0755	0.244	0.3172	-0.4311	0.0051	-0.764	-0.5811	1.2341	0.0219	0.2242	-0.0952	0.0319	0.3567	-0.005	0.2088	13.866	-13.3888	-33.5133
16	3.8112	3.5085	0.0256	7.222	1.7128	3.9935	0.3338	0.1233	0.0252	-0.0959	-0.4388	0.559	1.1284	-0.6388	-0.1047	0.4848	-0.113	-0.0501	0.2313	-0.0651	0.2449	-0.3223	-32.6614	-29.1667

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 2 THROUGH 22 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 23 THROUGH 31 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 32 THROUGH 49 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 50 THROUGH 61 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 62 THROUGH 70 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 71 THROUGH 80 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 81 THROUGH 94 )
8	X-RAY DIFFRACTION	8	CHAIN 'A' AND (RESID 95 THROUGH 107 )
9	X-RAY DIFFRACTION	9	CHAIN 'A' AND (RESID 108 THROUGH 112 )
10	X-RAY DIFFRACTION	10	CHAIN 'A' AND (RESID 113 THROUGH 128 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 3 THROUGH 22 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 23 THROUGH 49 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 50 THROUGH 80 )
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESID 81 THROUGH 107 )
15	X-RAY DIFFRACTION	15	CHAIN 'B' AND (RESID 108 THROUGH 119 )
16	X-RAY DIFFRACTION	16	CHAIN 'B' AND (RESID 120 THROUGH 128 )

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