PDB-8wqj: Crystal Structure of Transaminase from Shimia marina

ID or keywords:

Entry

Database: PDB / ID: 8wqj

Title

Crystal Structure of Transaminase from Shimia marina

Components

Transaminase from Shimia marina

Keywords

TRANSFERASE / transaminase

Function / homology

PYRIDOXAL-5'-PHOSPHATE

Function and homology information

Biological species

Shimia marina (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.14 Å

Authors

Heo, Y.S.

Funding support

1items

Citation

Journal: To Be Published
Title: Crystal Structure of Transaminase from Shimia marina
Authors: Heo, Y.S.

History

Deposition	Oct 11, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 10, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8wqj.cif.gz	372.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8wqj.ent.gz	303.8 KB	Display	PDB format
PDBx/mmJSON format	8wqj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8wqj_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	8wqj_full_validation.pdf.gz	1.1 MB	Display
Data in XML	8wqj_validation.xml.gz	39.3 KB	Display
Data in CIF	8wqj_validation.cif.gz	57.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wq/8wqj ftp://data.pdbj.org/pub/pdb/validation_reports/wq/8wqj	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Transaminase from Shimia marina

B: Transaminase from Shimia marina

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	64.710, 73.440, 184.900
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Transaminase from Shimia marina Mass: 54000.965 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shimia marina (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 533 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.03 Å³/Da / Density % sol: 39.27 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M BIS-TRIS pH 6.5 25% w/v Polyethylene glycol 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97949 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 31, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97949 Å / Relative weight: 1
Reflection	Resolution: 2.14→29.61 Å / Num. obs: 49439 / % possible obs: 99.81 % / Redundancy: 9 % / CC_1/2: 0.994 / Net I/σ(I): 10.95
Reflection shell	Resolution: 2.14→2.216 Å / Num. unique obs: 4867 / CC_1/2: 0.763

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Processing

Software

Name	Version	Classification
PHENIX	(1.20_4459: ???)	refinement
XDS		data reduction
XDS		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.14→29.61 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.28 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2159	2469	5 %
R_work	0.1759	-	-
obs	0.1778	49429	99.86 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.14→29.61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7184	0	17	533	7734

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	7365
X-RAY DIFFRACTION	f_angle_d	0.9	10015
X-RAY DIFFRACTION	f_dihedral_angle_d	8.637	1006
X-RAY DIFFRACTION	f_chiral_restr	0.053	1103
X-RAY DIFFRACTION	f_plane_restr	0.008	1313

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 (%)
2.14-2.18	0.2557	135	0.2223	2574	X-RAY DIFFRACTION	100
2.18-2.23	0.2707	137	0.2203	2608	X-RAY DIFFRACTION	100
2.23-2.27	0.2646	133	0.2065	2522	X-RAY DIFFRACTION	100
2.27-2.33	0.2475	136	0.1993	2582	X-RAY DIFFRACTION	100
2.33-2.39	0.2236	135	0.1952	2563	X-RAY DIFFRACTION	100
2.39-2.45	0.2194	136	0.2006	2586	X-RAY DIFFRACTION	100
2.45-2.52	0.255	136	0.1894	2582	X-RAY DIFFRACTION	100
2.52-2.6	0.2441	135	0.1906	2572	X-RAY DIFFRACTION	100
2.6-2.7	0.2231	137	0.1898	2590	X-RAY DIFFRACTION	100
2.7-2.8	0.2328	136	0.1839	2615	X-RAY DIFFRACTION	100
2.8-2.93	0.2386	136	0.1853	2580	X-RAY DIFFRACTION	100
2.93-3.09	0.2241	137	0.181	2600	X-RAY DIFFRACTION	100
3.09-3.28	0.2046	136	0.1804	2602	X-RAY DIFFRACTION	100
3.28-3.53	0.2324	137	0.1676	2613	X-RAY DIFFRACTION	100
3.53-3.89	0.2048	139	0.157	2641	X-RAY DIFFRACTION	100
3.89-4.45	0.1684	139	0.1444	2646	X-RAY DIFFRACTION	100
4.45-5.6	0.1729	141	0.1555	2673	X-RAY DIFFRACTION	100
5.6-29.61	0.2205	148	0.1741	2811	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	0.7631	-0.3534	0.3269	0.94	0.1252	1.1168	-0.0124	-0.1024	0.0222	0.1229	-0.0379	-0.1662	-0.0017	0.1559	0.0472	0.2071	-0.0071	-0.0118	0.2226	0.0078	0.2494	36.9276	50.104	127.3299
2	0.9391	0.7788	0.3203	1.8301	-0.0304	0.2257	0.1966	-0.2073	0.0931	0.4111	-0.1774	0.0823	0.1137	-0.0286	0.018	0.3212	0.0369	0.0383	0.237	-0.0366	0.2359	17.0375	55.2366	133.2817
3	0.3169	0.3276	-0.0818	0.3302	-0.1662	0.9085	-0.0276	-0.0537	-0.0016	-0.0304	-0.0015	0.207	-0.0161	-0.0653	0.0213	0.1876	0.0181	0.0206	0.2083	-0.0275	0.2488	4.5333	51.8297	116.5093
4	0.503	0.0584	0.0658	0.9883	0.1446	0.8129	0.0086	0.103	0.0664	-0.2834	-0.0485	0.0406	-0.0765	0.0559	0.0464	0.2448	0.0054	-0.0123	0.2158	0.004	0.1798	19.2359	63.5136	100.1729
5	0.1529	-0.0075	-0.1836	0.6229	-0.0997	0.3919	0.0082	0.0248	0.011	-0.0409	0.0022	0.1866	0.0036	-0.0263	-0.0012	0.2086	0.0291	-0.0296	0.2193	-0.0311	0.227	8.9897	61.6693	112.1138
6	1.1601	0.1281	-0.3067	1.2052	-0.0188	0.881	-0.0416	-0.1431	0.242	-0.0938	-0.0408	0.2212	-0.2191	-0.0084	0.0781	0.2246	-0.0182	-0.0326	0.1763	-0.0317	0.1937	18.2219	70.4978	127.7174
7	1.9537	-0.1576	-0.3517	0.9304	0.1538	1.2134	0.0094	-0.2062	-0.0097	-0.0965	-0.0848	-0.0999	0.1345	0.4638	0.091	0.2321	0.0041	-0.0125	0.3396	0.0289	0.2218	37.942	71.9555	112.8451
8	1.1032	0.2038	-0.4195	0.6558	-0.2976	1.5823	0.0456	-0.1544	0.0697	0.0264	-0.1353	-0.2189	-0.2197	0.5875	0.0718	0.2161	-0.0466	-0.0225	0.2744	0.0166	0.2738	39.2432	72.4558	117.138
9	0.9069	-0.3002	-0.239	0.9377	-0.0565	0.9788	-0.136	-0.2389	-0.0234	0.2235	0.0201	0.4025	-0.021	-0.1851	0.1542	0.2617	0.029	0.0737	0.3327	-0.0625	0.3683	-3.9917	44.729	126.6131
10	0.747	0.784	-0.3336	2.1777	0.0228	0.3735	0.1387	-0.1709	0.0258	0.643	-0.0812	0.1468	0.0273	-0.0443	-0.0127	0.3746	0.0037	0.069	0.2671	-0.0147	0.22	15.7747	40.2133	133.895
11	0.289	0.1114	0.1943	0.7158	0.0855	0.3495	0.006	0.0289	-0.0701	-0.0586	-0.0005	-0.0139	0.0397	0.0464	-0.0049	0.1804	0.0354	0.0111	0.1743	-0.002	0.1675	21.7907	33.1661	109.7152
12	0.9714	0.4702	0.1998	1.6317	0.0506	0.5452	0.0316	-0.1734	-0.2779	0.1676	-0.0953	-0.0093	0.1891	-0.0056	0.0789	0.2842	-0.0068	0.052	0.2472	0.0156	0.2336	14.6266	24.517	129.5024
13	1.9196	-0.4743	0.1473	1.1276	-0.3176	1.0713	0.0567	0.0464	0.2241	-0.0886	-0.0248	0.5793	-0.0181	-0.2884	-0.0335	0.2212	-0.0225	0.0067	0.3108	0.0147	0.3996	-4.1828	22.0394	113.4872
14	1.5524	0.0863	-0.0412	1.2316	-0.2814	1.1277	0.0564	-0.1682	-0.0207	0.0696	-0.0693	0.5295	0.1297	-0.6655	0.027	0.2379	-0.0593	0.0668	0.34	-0.0347	0.4595	-5.0437	23.5153	121.6018
15	3.836	-6.256	-4.2465	2.0001	8.6734	4.9716	0.1529	-0.0373	0.1046	-0.12	0.0852	-0.2619	-0.0031	0.0739	-0.2254	0.2529	0.0004	0.0637	0.2433	-0.0246	0.1676	13.292	37.5665	115.1523
16	2.3427	-2.2379	3.7804	2	-5.2293	6.2822	0.0941	-0.0144	-0.046	-0.0599	0.1097	0.2614	-0.0102	-0.0741	-0.2451	0.2844	-0.0222	0.0935	0.3457	-0.0026	0.242	20.2316	56.2823	114.5577

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 59 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 60 through 84 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 85 through 140 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 141 through 241 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 242 through 327 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 328 through 367 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 368 through 413 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 414 through 473 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 2 through 59 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 60 through 84 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 85 through 327 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 328 through 367 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 368 through 412 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 413 through 463 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 501 through 501)
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 501 through 501)

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