PDB-4emy: Crystal structure of aminotransferase from anaerococcus prevotii ...

ID or keywords:

Entry

Database: PDB / ID: 4emy

Title

Crystal structure of aminotransferase from anaerococcus prevotii dsm 20548.

Components

Aminotransferase class I and II

Keywords

TRANSFERASE / PSI-BIOLOGY / MCSG / MIDWEST CENTER FOR STRUCTURAL GENOMICS / aminotransferase class I / PYRIDOXAL- 5'-PHOSPHATE BINDING

Function / homology

Function and homology information

amino acid metabolic process /

transaminase activity / biosynthetic process /

pyridoxal phosphate binding
Similarity search - Function

Biological species

Anaerococcus prevotii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.86 Å

Authors

Chang, C. / Tesar, C. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: TO BE PUBLISHED
Title: Crystal structure of aminotransferase from anaerococcus prevotii dsm 20548.
Authors: Chang, C. / Tesar, C. / Bearden, J. / Joachimiak, A.

History

Deposition	Apr 12, 2012	Deposition site: RCSB / Processing site: RCSB
Supersession	May 9, 2012	ID: 3T18
Revision 1.0	May 9, 2012	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4emy.cif.gz	642.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4emy.ent.gz	562.4 KB	Display	PDB format
PDBx/mmJSON format	4emy.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/em/4emy ftp://data.pdbj.org/pub/pdb/validation_reports/em/4emy	HTTPS FTP

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Related structure data

Similar structure data	2jgt-d 3dc1-2 3cy0-1 2zyj-d 5xmr-2 5yg3-1 5xms-1 2xh1-d 5yg1-1 5xmp-1 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
Other databases	TargetTrack: MCSG-APC100368 TargetTrack: APC100368

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Aminotransferase class I and II

B: Aminotransferase class I and II

C: Aminotransferase class I and II

D: Aminotransferase class I and II

hetero molecules

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

1

A: Aminotransferase class I and II

B: Aminotransferase class I and II

hetero molecules

defined by author&software
94 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Aminotransferase class I and II

D: Aminotransferase class I and II

hetero molecules

defined by author&software
94 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	64.297, 131.178, 239.913
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Details

AS IS, A+B AND C+D

#1: Protein	Aminotransferase class I and II Mass: 46766.875 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anaerococcus prevotii (bacteria) / Strain: DSM 20548 / Gene: Apre_1502 / Plasmid: PMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)MAGIC / References: UniProt: C7REB0
#2: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.7 Å³/Da / Density % sol: 54.52 %
Crystal grow	Temperature: 297 K / pH: 6.5 Details: 0.2 M SODIUM CITRATE, 20% PEG 3350, PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 297K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2010
Radiation	Monochromator: SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97924 Å / Relative weight: 1
Reflection	Resolution: 2.85→50 Å / Num. obs: 48027 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.6 % / R_merge(I) obs: 0.126 / Net I/σ(I): 24.3
Reflection shell	Resolution: 2.85→2.9 Å / Redundancy: 9.9 % / R_merge(I) obs: 0.633 / Mean I/σ(I) obs: 3.86 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.6.0117	refinement
PDB_EXTRACT	3.11	data extraction
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
MLPHARE		phasing
DM		phasing
SHELXDE		phasing
RESOLVE		phasing
ARP/wARP		model building
Coot		model building

Refinement

Method to determine structure:

SAD / Resolution: 2.86→50 Å / Cor.coef. F_o:F_c: 0.916 / Cor.coef. F_o:F_c free: 0.887 / Occupancy max: 1 / Occupancy min: 1 / SU B: 45.415 / SU ML: 0.401 / Cross valid method: THROUGHOUT / ESU R Free: 0.453
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.29015	2420	5.1 %	RANDOM
R_work	0.24479	-	-	-
obs	0.24711	45488	99.39 %	-
all	-	47908	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 75.976 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	9.56 Å²	0 Å²	0 Å²
2-	-	-4.55 Å²	0 Å²
3-	-	-	-5.01 Å²

Refinement step

Cycle: LAST / Resolution: 2.86→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12963	0	64	28	13055

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.02	13306
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.043	1.963	17974
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.26	5	1624
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.839	24.373	638
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.217	15	2303
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.09	15	76
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	1935
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	10133
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.855→2.93 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.377	157	-
R_work	0.344	2971	-
obs	-	-	95.98 %

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	6.8161	-6.2535	3.1031	9.9393	-2.0787	1.5775	0.3766	-0.3145	-1.2189	0.2843	0.0201	1.3347	0.3332	-0.1197	-0.3968	0.5454	0.0211	0.1826	0.6446	0.1271	0.7484	34.7554	68.7573	180.9672
2	0.9745	-0.4452	0.0935	1.7771	0.1878	0.4792	0.0048	0.1556	0.0136	-0.0951	0.1229	-0.3465	0.189	0.1271	-0.1278	0.1465	-0.009	-0.0541	0.4165	-0.0317	0.5331	59.9785	67.0706	163.0232
3	2.118	-0.0846	0.5373	2.5319	-0.3009	2.1419	0.0845	0.1159	-0.1891	-0.1437	0.0254	0.1929	0.3905	-0.2988	-0.1099	0.2272	-0.0485	-0.0397	0.4395	-0.015	0.4503	36.8761	59.2316	156.6792
4	10.4326	-0.7152	4.2238	2.2976	0.0425	2.7926	-0.2769	0.4893	0.0626	-0.3392	0.173	-0.1129	0.0915	0.0597	0.1039	0.3388	-0.1175	-0.0337	0.3419	0.0469	0.3801	44.0249	61.6432	150.868
5	13.1636	8.105	0.9809	4.9917	0.5974	0.1098	-0.2118	0.1975	-0.1394	-0.1837	0.1401	-0.095	0.133	0.1201	0.0717	0.8787	0.2179	0.17	0.5789	-0.0122	0.4915	46.538	60.9997	143.3573
6	0.7968	0.1224	-0.4571	2.8042	1.1082	0.7688	0.0122	0.184	0.1487	-0.5982	-0.0233	0.0639	-0.2196	-0.1338	0.0111	0.3013	-0.0185	-0.013	0.455	0.0435	0.4695	43.9629	72.2046	152.2305
7	0.8534	-0.3954	0.6201	4.3336	-0.8578	1.663	0.0604	0.1055	-0.1879	-0.0511	0.0092	-0.469	0.3838	0.1729	-0.0696	0.1782	0.0037	-0.0736	0.4199	-0.0404	0.4895	57.1739	57.4086	160.2746
8	1.6638	-0.3842	1.4656	2.8655	-0.2708	1.8197	0.3075	0.1573	-0.3534	0.3775	-0.0685	-0.4875	0.0256	-0.135	-0.239	0.5117	0.0527	-0.1726	0.4239	-0.0204	0.6101	56.7887	43.8225	171.4225
9	1.6907	6.1293	-1.3244	22.6095	-4.839	1.0682	-0.1858	0.3879	0.6441	0.0832	0.9369	2.1019	-0.0086	-0.2116	-0.7511	0.2286	-0.1877	-0.103	0.5618	0.0298	0.9868	31.8737	81.9473	154.9099
10	0.537	0.1969	0.2719	2.4899	0.2144	1.4799	-0.0474	0.1108	0.0472	0.2697	0.1264	-0.5642	-0.0199	0.1239	-0.079	0.0392	0.0042	-0.0813	0.1218	-0.0059	0.2333	58.6744	88.2476	169.0217
11	0.8874	0.4407	0.0471	2.1861	-0.3262	1.3832	0.0301	0.1054	0.0005	0.347	0.0375	0.1768	-0.1711	-0.1634	-0.0676	0.096	0.0448	-0.0042	0.1489	-0.0215	0.1503	35.725	92.1252	178.7874
12	8.0222	-0.7338	-2.753	0.1263	0.0011	2.1353	-0.678	-0.3145	0.4675	0.1479	0.1075	-0.1741	0.0396	-0.081	0.5705	0.3645	0.1339	-0.0528	0.0916	-0.0893	0.4924	43.9352	91.071	183.5631
13	11.5323	0.7003	-19.9037	0.1404	-1.4385	34.9031	-0.873	-1.4792	-0.3882	0.3315	-0.0115	-0.1294	0.5464	2.226	0.8845	1.5713	0.5381	-0.3743	0.4675	-0.1161	0.1444	47.5473	92.3722	190.4661
14	2.3283	-1.779	-1.5459	3.0593	1.4903	1.0859	0.108	0.076	-0.1596	0.8029	-0.1454	-0.1874	0.0754	-0.0772	0.0374	0.5081	0.0107	-0.1498	0.2109	-0.0037	0.0897	45.5415	80.7018	182.0541
15	1.4217	-0.5641	0.6809	2.8311	-0.937	1.194	-0.0574	0.0899	0.1387	0.365	-0.0913	-0.3257	-0.1942	0.0368	0.1487	0.0775	0.0132	-0.0771	0.0731	-0.0032	0.1053	54.6487	97.3811	172.1409
16	3.8192	-1.6314	0.7024	0.8277	-0.6842	1.5175	-0.1126	0.0128	0.3858	-0.0193	-0.0174	-0.186	-0.06	-0.0151	0.13	0.2478	-0.0085	-0.0485	0.0515	0.0129	0.2633	50.2991	110.5054	161.2911
17	15.424	11.7955	6.9721	9.6937	2.7298	18.992	2.0142	0.1623	-2.3431	0.7953	0.3942	-1.2195	0.2273	0.0851	-2.4084	2.2779	0.0813	-0.1623	1.0166	-0.1916	1.6003	47.4202	56.6637	120.5197
18	1.9448	-0.7711	1.4623	0.5396	-0.9944	2.684	0.1247	-0.3138	0.0218	0.2962	-0.031	-0.2264	0.2116	0.6978	-0.0937	1.5412	0.1573	-0.4672	1.0702	-0.1124	0.8311	74.6429	61.407	106.9921
19	0.6894	0.0007	-0.0822	0.5287	0.0414	4.3522	-0.0933	-0.1943	-0.351	0.8302	0.0783	-0.0103	0.8645	0.2978	0.015	1.6533	-0.0379	0.0094	0.7448	0.0588	0.5771	57.6686	43.8955	100.335
20	14.8698	0.9837	8.1688	3.948	3.3819	7.0991	-0.2371	0.8284	0.1109	1.4541	0.3296	-0.6505	1.001	0.4556	-0.0925	1.5777	0.0343	-0.2751	0.7167	0.0817	0.4179	63.5123	47.46	94.5009
21	0.4874	-2.7884	-2.2316	16.2318	13.0523	10.509	-0.0093	-0.2183	0.1596	-0.4657	1.1664	-1.2761	-0.4122	0.96	-1.1571	2.0081	0.2463	-0.3921	0.8575	-0.0179	0.8015	68.462	46.4783	88.3785
22	0.0928	-0.5379	0.0795	7.4298	2.0711	3.6258	0.0471	-0.0851	0.0459	1.3562	-0.1291	-0.1567	1.0437	0.3621	0.0821	1.3595	-0.1357	-0.0324	0.6778	0.0134	0.3373	60.2552	57.5442	93.385
23	1.4557	-1.8018	1.6185	3.3546	-2.6919	2.3478	-0.0692	-0.3987	-0.1379	0.4119	-0.0245	-0.5496	-0.0443	0.1917	0.0937	1.7743	0.1811	-0.3077	1.1981	-0.1759	0.8334	76.0853	50.9757	106.6178
24	8.5198	2.0525	-1.5016	0.5494	-0.4592	0.5137	-0.8407	0.4021	-0.3418	-0.0703	0.1881	-0.3429	0.1621	0.1639	0.6526	1.8183	0.5032	-0.3713	1.5754	-0.012	1.318	78.3645	41.0732	120.9758
25	11.3022	1.682	-7.6639	1.26	-3.3241	10.1191	0.4153	0.3712	1.0708	0.056	0.0915	0.2924	0.1672	-0.3164	-0.5068	1.7827	-0.5048	0.5496	1.031	-0.2833	0.9781	44.9359	62.3512	91.8052
26	0.4989	-0.5104	-0.2384	0.7083	0.4685	1.8716	-0.013	-0.2588	0.1687	0.4269	0.2341	-0.3987	0.2613	0.2516	-0.2211	1.1262	-0.1652	-0.1923	0.9267	-0.0834	0.7604	64.9763	80.736	106.9476
27	1.1852	0.0007	-0.5221	0.2195	0.6881	2.8312	-0.1766	-0.2087	-0.0928	0.248	-0.0526	0.1601	0.3887	-0.3622	0.2292	1.3271	-0.1835	0.4355	0.8495	-0.1333	0.8301	40.71	78.0073	112.3785
28	6.6035	2.8707	1.9563	1.5822	0.8027	0.6219	-0.0079	-1.289	1.7634	0.4076	-0.3872	1.2383	-0.2421	-0.261	0.3951	1.7333	-0.4276	0.6528	1.0959	-0.2433	1.1947	47.5631	80.9496	118.2053
29	18.9468	-8.3346	6.2397	3.7188	-2.4852	3.8862	-1.5769	-3.9652	0.1823	0.7638	1.9175	-0.2107	1.297	-0.1279	-0.3406	3.655	0.6969	0.2691	1.938	-0.4566	0.795	49.1574	84.8123	125.0179
30	3.442	-0.1019	-2.2122	0.2372	0.7331	3.425	-0.1868	-0.3808	-0.3748	-0.0296	0.0931	-0.0125	-0.2544	0.2974	0.0937	1.2981	0.0414	0.0435	0.9736	-0.0499	0.7142	52.915	71.7698	119.7803
31	1.2431	0.396	-0.1667	5.0199	1.1618	2.4037	0.2377	-0.1817	0.3731	1.3145	-0.2889	0.0857	0.0954	0.1723	0.0511	0.8766	-0.1171	0.1538	0.7926	-0.1334	0.5241	57.574	88.6858	106.7794
32	2.3661	-0.1493	-1.5059	5.6787	2.7275	6.9327	0.2703	0.0192	0.6769	0.0713	-0.4221	0.8521	-0.6986	-0.4538	0.1518	0.4521	-0.0001	0.0975	0.6958	-0.1366	0.7549	51.6459	96.4424	92.2584

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 15
2	X-RAY DIFFRACTION	2	A	16 - 97
3	X-RAY DIFFRACTION	3	A	98 - 210
4	X-RAY DIFFRACTION	4	A	211 - 234
5	X-RAY DIFFRACTION	5	A	235 - 242
6	X-RAY DIFFRACTION	6	A	243 - 289
7	X-RAY DIFFRACTION	7	A	290 - 371
8	X-RAY DIFFRACTION	8	A	372 - 409
9	X-RAY DIFFRACTION	9	B	1 - 15
10	X-RAY DIFFRACTION	10	B	16 - 97
11	X-RAY DIFFRACTION	11	B	98 - 210
12	X-RAY DIFFRACTION	12	B	211 - 234
13	X-RAY DIFFRACTION	13	B	235 - 242
14	X-RAY DIFFRACTION	14	B	243 - 289
15	X-RAY DIFFRACTION	15	B	290 - 371
16	X-RAY DIFFRACTION	16	B	372 - 409
17	X-RAY DIFFRACTION	17	C	1 - 15
18	X-RAY DIFFRACTION	18	C	16 - 97
19	X-RAY DIFFRACTION	19	C	98 - 210
20	X-RAY DIFFRACTION	20	C	211 - 234
21	X-RAY DIFFRACTION	21	C	235 - 242
22	X-RAY DIFFRACTION	22	C	243 - 289
23	X-RAY DIFFRACTION	23	C	290 - 371
24	X-RAY DIFFRACTION	24	C	372 - 409
25	X-RAY DIFFRACTION	25	D	1 - 15
26	X-RAY DIFFRACTION	26	D	16 - 97
27	X-RAY DIFFRACTION	27	D	98 - 210
28	X-RAY DIFFRACTION	28	D	211 - 234
29	X-RAY DIFFRACTION	29	D	235 - 242
30	X-RAY DIFFRACTION	30	D	243 - 289
31	X-RAY DIFFRACTION	31	D	290 - 371
32	X-RAY DIFFRACTION	32	D	372 - 409

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Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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-Related structure data

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-Experimental details

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-Sample preparation

-Data collection

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+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

-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

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Basic information

-
Structure visualization

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Downloads & links

-
Download

-
Validation report

-
Related structure data

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Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

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Sample preparation

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Data collection

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Processing

+
About Yorodumi

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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