PDB-4f5h: Intercoversion of Substrate Specificity: E. coli Aspatate Aminotr...

ID or keywords:

Entry

Database: PDB / ID: 4f5h

Title

Intercoversion of Substrate Specificity: E. coli Aspatate Aminotransferase to Tyrosine Aminotransferase: Chimera P3.

Components

Aspartate aminotransferase

Keywords

TRANSFERASE / Aminotransferase

Function / homology

Function and homology information

L-phenylalanine biosynthetic process from chorismate via phenylpyruvate / L-tyrosine-2-oxoglutarate transaminase activity / L-phenylalanine biosynthetic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / pyridoxal phosphate binding / protein homodimerization activity / identical protein binding / cytosol / cytoplasm
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Addington, T.A. / Fisher, A.J. / Toney, M.D.

Citation

Journal: J.Mol.Biol. / Year: 2013
Title: Janus: prediction and ranking of mutations required for functional interconversion of enzymes.
Authors: Addington, T.A. / Mertz, R.W. / Siegel, J.B. / Thompson, J.M. / Fisher, A.J. / Filkov, V. / Fleischman, N.M. / Suen, A.A. / Zhang, C. / Toney, M.D.

History

Deposition	May 13, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 13, 2013	Provider: repository / Type: Initial release
Revision 1.1	Feb 27, 2013	Group: Database references
Revision 1.2	Apr 24, 2013	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4f5h.cif.gz	338.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4f5h.ent.gz	287.2 KB	Display	PDB format
PDBx/mmJSON format	4f5h.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4f5h_validation.pdf.gz	442 KB	Display	wwPDB validaton report
Full document	4f5h_full_validation.pdf.gz	449.2 KB	Display
Data in XML	4f5h_validation.xml.gz	40.9 KB	Display
Data in CIF	4f5h_validation.cif.gz	62.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f5/4f5h ftp://data.pdbj.org/pub/pdb/validation_reports/f5/4f5h	HTTPS FTP

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Related structure data

Related structure data	4f5fC 4f5gC 4f5iC 4f5jC 4f5kC 4f5mC 4f5l C: citing same article (ref.)
Similar structure data	4f5j-d 1g4v-1 1g7x-1 1ars-1 1toe-1 3qn6-1 4f5k-d 1aaw-1 5ax8-1 1czc-1 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

Deposited unit

A: Aspartate aminotransferase

B: Aspartate aminotransferase

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	58.129, 109.785, 141.673
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Aspartate aminotransferase / AspAT / Transaminase A Mass: 44845.383 Da / Num. of mol.: 2 Mutation: I39V, N40D, L56M, N74T, I78L, I81L, T114S, S145A, V146I, I197A, F220I, A228G, N295S, M331L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: AAT, aspC, b0928, JW0911 / Plasmid: pET45b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00509, aspartate transaminase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 968 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Aspartate aminotransferase / AspAT / Transaminase A

Mass: 44845.383 Da / Num. of mol.: 2
Mutation: I39V, N40D, L56M, N74T, I78L, I81L, T114S, S145A, V146I, I197A, F220I, A228G, N295S, M331L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli (E. coli) / Strain: K12 / Gene: AAT, aspC, b0928, JW0911 / Plasmid: pET45b / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00509, aspartate transaminase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 968 / 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: 2.52 Å³/Da / Density % sol: 51.19 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 8% PEG 4000, 0.1 M Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97946 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 11, 2010
Radiation	Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97946 Å / Relative weight: 1
Reflection	Resolution: 1.6→50 Å / Num. all: 119994 / Num. obs: 118914 / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / B_iso Wilson estimate: 18.16 Å² / R_merge(I) obs: 0.052 / R_sym value: 0.052 / Net I/σ(I): 9.9
Reflection shell	Resolution: 1.6→1.64 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.367 / Mean I/σ(I) obs: 2.6 / Num. unique all: 8625 / R_sym value: 0.367 / % possible all: 98.6

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Processing

Software

Name	Version	Classification
Blu-Ice		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.7.1_743)	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.6→19.955 Å / SU ML: 0.41 / σ(F): 1.34 / Phase error: 15.85 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1869	5936	5 %
R_work	0.1611	-	-
obs	0.1624	118766	98.91 %

Solvent computation

Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 45.318 Å² / k_sol: 0.35 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.2325 Å²	0 Å²	0 Å²
2-	-	0.0861 Å²	0 Å²
3-	-	-	0.1464 Å²

Refine analyze

Luzzati sigma a obs: 0.41 Å

Refinement step

Cycle: LAST / Resolution: 1.6→19.955 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6177	0	0	968	7145

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	6440
X-RAY DIFFRACTION	f_angle_d	1.083	8755
X-RAY DIFFRACTION	f_dihedral_angle_d	12.83	2357
X-RAY DIFFRACTION	f_chiral_restr	0.073	963
X-RAY DIFFRACTION	f_plane_restr	0.005	1160

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 (%)
1.6-1.6182	0.2748	207	0.2417	3682	X-RAY DIFFRACTION	98
1.6182-1.6372	0.2864	193	0.2378	3667	X-RAY DIFFRACTION	98
1.6372-1.6572	0.2503	208	0.2132	3710	X-RAY DIFFRACTION	98
1.6572-1.6781	0.2456	175	0.2078	3696	X-RAY DIFFRACTION	98
1.6781-1.7002	0.2265	200	0.1996	3713	X-RAY DIFFRACTION	98
1.7002-1.7235	0.2353	220	0.1966	3700	X-RAY DIFFRACTION	99
1.7235-1.7481	0.2154	191	0.1854	3695	X-RAY DIFFRACTION	98
1.7481-1.7742	0.1978	200	0.1701	3726	X-RAY DIFFRACTION	99
1.7742-1.8019	0.196	191	0.1664	3685	X-RAY DIFFRACTION	99
1.8019-1.8314	0.2035	188	0.1632	3748	X-RAY DIFFRACTION	99
1.8314-1.863	0.2144	201	0.161	3702	X-RAY DIFFRACTION	99
1.863-1.8968	0.2012	200	0.1533	3733	X-RAY DIFFRACTION	99
1.8968-1.9333	0.1829	177	0.1602	3778	X-RAY DIFFRACTION	99
1.9333-1.9727	0.1865	208	0.1531	3726	X-RAY DIFFRACTION	99
1.9727-2.0155	0.1832	224	0.1532	3725	X-RAY DIFFRACTION	99
2.0155-2.0624	0.1761	230	0.1566	3709	X-RAY DIFFRACTION	99
2.0624-2.1139	0.1899	191	0.1567	3764	X-RAY DIFFRACTION	99
2.1139-2.171	0.1854	172	0.1556	3777	X-RAY DIFFRACTION	99
2.171-2.2348	0.1686	197	0.1501	3802	X-RAY DIFFRACTION	99
2.2348-2.3068	0.181	210	0.1507	3757	X-RAY DIFFRACTION	99
2.3068-2.3891	0.1879	231	0.1525	3769	X-RAY DIFFRACTION	100
2.3891-2.4846	0.1767	198	0.1575	3765	X-RAY DIFFRACTION	100
2.4846-2.5975	0.1828	177	0.1607	3838	X-RAY DIFFRACTION	100
2.5975-2.7341	0.1812	211	0.1595	3799	X-RAY DIFFRACTION	100
2.7341-2.9049	0.191	197	0.1619	3850	X-RAY DIFFRACTION	100
2.9049-3.1284	0.1859	190	0.1636	3813	X-RAY DIFFRACTION	100
3.1284-3.4418	0.1658	197	0.1569	3861	X-RAY DIFFRACTION	99
3.4418-3.9365	0.1784	185	0.1442	3741	X-RAY DIFFRACTION	97
3.9365-4.9471	0.1535	186	0.1414	3938	X-RAY DIFFRACTION	100
4.9471-19.9565	0.2	181	0.1805	3961	X-RAY DIFFRACTION	96

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	0.5942	0.3913	1.3196	0.1613	0.6982	1.9471	-0.1016	-0.0541	0.3252	-0.2221	-0.1086	0.1926	-0.8258	-0.2364	0.0778	0.3551	0.0177	-0.09	0.2895	0.0062	0.2834	23.2615	117.7543	36.9955
2	0.9629	-0.0411	-0.1253	0.4932	-0.1583	0.8871	0.0201	0.0121	-0.0823	-0.0293	-0.0282	0.0549	0.1438	-0.0104	0.0152	0.1032	-0.011	-0.0183	0.0791	0.0107	0.1162	31.7031	90.2709	48.8867
3	1.0324	0.2244	-0.006	0.8774	0.2735	2.9705	-0.0186	0.2451	0.1726	-0.1332	0.0365	-0.0576	-0.2751	0.38	0.054	0.1528	-0.0376	0.0073	0.199	0.0539	0.1394	47.6296	104.4495	33.0008
4	1.4943	0.1244	-0.0453	0.8676	-0.2874	1.7478	0.0056	0.1232	-0.1079	-0.1696	-0.0349	-0.0881	0.1779	0.2259	0.0192	0.154	0.0325	0.0123	0.1558	0.0087	0.1216	44.0289	91.3693	32.8773
5	0.9759	0.1553	0.3109	0.6764	-0.3014	1.1804	0.0306	-0.0305	-0.0489	-0.056	-0.0648	-0.0615	0.0847	0.0818	0.0133	0.0896	0.0026	-0.0081	0.0868	0.0144	0.1095	38.1346	92.5389	49.7693
6	1.4075	0.2742	-0.0089	1.9556	-0.6707	2.0131	0.1205	0.3764	-0.0757	-0.3517	0.0517	0.1356	0.5944	-0.0615	0.0871	0.1852	-0.009	-0.0889	0.142	-0.0461	0.1341	23.3976	89.2049	27.326
7	1.0969	-0.1722	0.3471	0.9937	-0.0052	1.2984	-0.0666	0.5181	0.3574	-0.3058	0.0043	0.1386	-0.1747	-0.0185	0.0221	0.2588	0.0056	-0.0649	0.2923	0.1053	0.234	25.6556	106.311	19.1536
8	-0.0046	-0.0016	-0.37	-0.1473	-1.0815	1.2643	-0.12	0.018	-0.1871	-0.046	-0.0654	-0.1656	0.0819	0.4783	0.1503	0.2357	-0.0762	0.0831	0.2786	-0.0361	0.2096	45.7394	88.9251	67.7672
9	1.0934	-0.0024	1.0406	0.841	-0.4995	2.4503	0.1527	-0.0888	-0.0422	0.0278	0.0023	0.149	0.2971	-0.3028	-0.077	0.1023	-0.0293	0.013	0.1438	0.018	0.142	17.2126	93.255	65.4595
10	0.7406	0.0892	0.313	0.6968	0.1288	1.746	-0.0442	0.0125	0.1455	-0.0117	0.023	0.0874	-0.3826	-0.0779	0.0039	0.1536	0.0129	-0.0001	0.0731	0.0206	0.1377	27.4941	113.9522	58.4278
11	0.908	0.0389	-0.8426	0.5421	0.4844	4.1057	0.0734	-0.1176	0.0293	0.1084	0.0492	-0.1119	-0.1542	0.3432	0.0047	0.1716	-0.0512	-0.0105	0.1626	-0.0229	0.1518	41.6201	112.4468	74.7681
12	1.1516	0.1346	0.1104	1.6955	-0.1843	2.0126	-0.0351	-0.1386	0.326	0.038	-0.0268	0.0757	-0.5852	0.0675	-0.0089	0.2792	-0.032	-0.0028	0.1266	-0.0495	0.1878	34.6378	121.1417	76.6417
13	0.9725	0.2807	-0.1439	0.4592	-0.1485	1.4469	0.0029	-0.0472	0.2092	0.0275	0.0107	0.0838	-0.3295	-0.0833	0.0015	0.1378	0.0227	-0.0017	0.0692	0.0003	0.133	25.6889	113.0924	62.3147
14	1.8902	-0.6673	1.7519	0.6976	-0.3117	3.925	-0.0524	-0.1982	-0.0845	0.0994	0.0972	0.1439	-0.125	-0.4674	-0.0134	0.1332	-0.0111	0.0656	0.152	0.0025	0.1652	17.9073	100.3059	81.0065
15	0.7657	-0.7967	0.2084	1.5758	-0.3868	0.973	-0.0668	-0.098	-0.0013	0.1877	0.043	-0.079	-0.0162	0.0382	0.0269	0.1527	-0.0141	0.0164	0.1329	-0.0057	0.1262	34.9653	95.459	88.196

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESSEQ 10:42)
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESSEQ 43:127)
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESSEQ 128:188)
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESSEQ 189:244)
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESSEQ 245:310)
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESSEQ 311:341)
7	X-RAY DIFFRACTION	7	CHAIN A AND (RESSEQ 342:406)
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESSEQ 7:42)
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESSEQ 43:69)
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESSEQ 70:140)
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESSEQ 141:168)
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESSEQ 169:214)
13	X-RAY DIFFRACTION	13	CHAIN B AND (RESSEQ 215:310)
14	X-RAY DIFFRACTION	14	CHAIN B AND (RESSEQ 311:341)
15	X-RAY DIFFRACTION	15	CHAIN B AND (RESSEQ 342:406)

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