PDB-4f5l: A Theoretical Optimized Mutant for the Conversion of Substrate Sp...

ID or keywords:

Entry

Database: PDB / ID: 4f5l

Title

A Theoretical Optimized Mutant for the Conversion of Substrate Specificity and Activity of Aspartate Aminotransferase to Tyrosine Aminotransferase: Chimera P7.

Components

Aspartate aminotransferase

Keywords

TRANSFERASE / Aminotransferase

Function / homology

Function and homology information

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

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.4 Å

Authors

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

Citation

Journal: To be Published
Title: Janus: an algorithm for ranking functional importance of residues from protein sequence alignments.
Authors: Addington, T.A. / Mertz, R.W. / Siegel, J.B. / Thompson, J.M. / Fisher, A.J. / Filkov, V. / Fleischman, N. / Suen, A. / Zhang, C. / Toney, M.D.

History

Deposition	May 13, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 15, 2013	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4f5l.cif.gz	347.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4f5l.ent.gz	293.5 KB	Display	PDB format
PDBx/mmJSON format	4f5l.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4f5l_validation.pdf.gz	456.7 KB	Display	wwPDB validaton report
Full document	4f5l_full_validation.pdf.gz	463.1 KB	Display
Data in XML	4f5l_validation.xml.gz	43.7 KB	Display
Data in CIF	4f5l_validation.cif.gz	68.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f5/4f5l ftp://data.pdbj.org/pub/pdb/validation_reports/f5/4f5l	HTTPS FTP

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Related structure data

Related structure data	4f5f 4f5g 4f5h 4f5i 4f5j 4f5k 4f5m
Similar structure data	4f5j-d 1ars-1 1tat-d 3pd6-1 3r1r-9 4h51-d 3qn6-1 3r1r-2 1aia-d 1r1r-2 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

hetero molecules

90.4 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)	59.736, 102.990, 139.304
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: 44783.402 Da / Num. of mol.: 2 Mutation: I39V, N40D, I43V, L56M, N74T, I78L, I81L, T114S, S139T, S145A, V146I, I197A, F220I, F222I, A228G, Y254C, N295S, V385I 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: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1237 / 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: 2.39 Å³/Da / Density % sol: 48.58 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 8% PEG 4000, 0.1 M Sodium Acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 1, 2010 / Details: Si 111
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97946 Å / Relative weight: 1
Reflection	Resolution: 1.4→60 Å / Num. all: 167501 / Num. obs: 167317 / % possible obs: 98.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / B_iso Wilson estimate: 13.82 Å² / R_merge(I) obs: 0.049 / R_sym value: 0.049 / Net I/σ(I): 12.6
Reflection shell	Resolution: 1.4→1.44 Å / Redundancy: 2.6 % / R_merge(I) obs: 0.336 / Mean I/σ(I) obs: 2.4 / Num. unique all: 11171 / R_sym value: 0.336 / % possible all: 90.3

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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: 1.4→33.333 Å / SU ML: 0.36 / σ(F): 1.34 / Phase error: 16.13 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1808	8382	5.01 %
R_work	0.1608	-	-
obs	0.1618	167227	98.8 %

Solvent computation

Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 51.8 Å² / k_sol: 0.364 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.0667 Å²	0 Å²	0 Å²
2-	-	0.0749 Å²	0 Å²
3-	-	-	-0.0082 Å²

Refine analyze

Luzzati sigma a obs: 0.36 Å

Refinement step

Cycle: LAST / Resolution: 1.4→33.333 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6168	0	51	1237	7456

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	6645
X-RAY DIFFRACTION	f_angle_d	1.133	9036
X-RAY DIFFRACTION	f_dihedral_angle_d	11.983	2452
X-RAY DIFFRACTION	f_chiral_restr	0.075	996
X-RAY DIFFRACTION	f_plane_restr	0.006	1200

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 (%)
1.4-1.4159	0.3123	253	0.2743	4735	X-RAY DIFFRACTION	89
1.4159-1.4326	0.2768	242	0.2616	4848	X-RAY DIFFRACTION	91
1.4326-1.45	0.2602	245	0.2429	4959	X-RAY DIFFRACTION	93
1.45-1.4684	0.2236	260	0.2217	5155	X-RAY DIFFRACTION	97
1.4684-1.4877	0.2156	275	0.207	5301	X-RAY DIFFRACTION	100
1.4877-1.5081	0.2153	271	0.1966	5305	X-RAY DIFFRACTION	100
1.5081-1.5296	0.2035	285	0.1854	5350	X-RAY DIFFRACTION	100
1.5296-1.5525	0.207	233	0.1753	5293	X-RAY DIFFRACTION	100
1.5525-1.5767	0.1863	295	0.1724	5345	X-RAY DIFFRACTION	100
1.5767-1.6026	0.1997	258	0.1642	5267	X-RAY DIFFRACTION	100
1.6026-1.6302	0.1987	295	0.1654	5339	X-RAY DIFFRACTION	100
1.6302-1.6599	0.1806	305	0.157	5322	X-RAY DIFFRACTION	100
1.6599-1.6918	0.1864	294	0.1498	5265	X-RAY DIFFRACTION	100
1.6918-1.7263	0.168	256	0.1478	5373	X-RAY DIFFRACTION	100
1.7263-1.7639	0.1678	275	0.1523	5344	X-RAY DIFFRACTION	100
1.7639-1.8049	0.1826	290	0.1519	5330	X-RAY DIFFRACTION	100
1.8049-1.85	0.1735	325	0.1488	5282	X-RAY DIFFRACTION	100
1.85-1.9	0.1533	328	0.1503	5256	X-RAY DIFFRACTION	100
1.9-1.9559	0.1663	282	0.1491	5353	X-RAY DIFFRACTION	100
1.9559-2.0191	0.1658	269	0.1538	5403	X-RAY DIFFRACTION	100
2.0191-2.0912	0.1775	300	0.1514	5302	X-RAY DIFFRACTION	100
2.0912-2.1749	0.1767	291	0.1497	5340	X-RAY DIFFRACTION	100
2.1749-2.2739	0.1555	284	0.1398	5374	X-RAY DIFFRACTION	100
2.2739-2.3937	0.1659	260	0.1472	5443	X-RAY DIFFRACTION	100
2.3937-2.5437	0.1846	278	0.1533	5372	X-RAY DIFFRACTION	100
2.5437-2.74	0.1715	278	0.1545	5424	X-RAY DIFFRACTION	100
2.74-3.0156	0.1911	272	0.1606	5419	X-RAY DIFFRACTION	100
3.0156-3.4515	0.1695	304	0.1565	5434	X-RAY DIFFRACTION	100
3.4515-4.347	0.1679	279	0.1443	5441	X-RAY DIFFRACTION	99
4.347-33.3422	0.1908	300	0.1805	5471	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	0.0384	-0.2417	0.5952	0.2488	-0.4759	1.3906	-0.0355	-0.0355	0.1709	0.2653	-0.1399	-0.1712	-0.6057	0.4581	0.1128	0.2324	-0.075	-0.0518	0.2737	0.0238	0.1936	32.388	9.0689	35.6099
2	0.5668	0.063	0.0194	0.2049	0.0577	0.6416	0.0033	0.0273	-0.0887	0.0211	-0.0101	-0.0256	0.151	0.0528	0.026	0.0998	0.0118	-0.0037	0.0654	-0.0054	0.102	26.3845	-19.2104	23.7334
3	0.312	0.0647	-0.2909	0.4617	-0.1457	1.5699	-0.0341	-0.0445	0.0515	0.0543	0.0048	0.0825	-0.0645	-0.1752	0.0315	0.0975	0.014	0.0079	0.1165	-0.0166	0.1223	9.4982	-7.4831	39.7896
4	0.5424	0.0235	0.0885	0.5247	0.0378	1.0079	0.0069	-0.0427	-0.0419	0.0757	-0.0219	0.0541	0.1665	-0.0974	0.0151	0.1288	-0.0168	0.0184	0.0901	-0.0006	0.1017	13.8227	-20.403	39.3652
5	0.4392	-0.0412	0.1857	0.2061	0.0937	0.7601	-0.012	0.0233	-0.0226	0.0246	-0.0163	0.0306	0.0876	-0.029	0.0223	0.0847	-0.0024	0.0026	0.0734	-0.0071	0.0909	20.6414	-17.0393	22.6994
6	0.9707	-0.5242	-0.3341	1.9115	1.3658	2.9887	-0.0394	-0.1662	-0.0294	0.268	0.0699	-0.0874	0.456	0.2024	-0.0231	0.1192	0.0425	-0.0097	0.0859	0.0288	0.0971	34.9221	-21.4	44.5324
7	1.2133	0.3996	0.2405	1.1719	0.4507	1.3611	-0.0414	-0.2105	0.2066	0.232	0.0611	-0.0332	0.0317	0.145	-0.0143	0.1443	0.0176	-0.0171	0.1732	-0.0407	0.1568	31.709	-4.8656	53.9025
8	0.1011	0.225	0.0256	0.027	0.1228	0.1222	-0.0686	-0.0026	-0.0909	-0.0015	-0.0138	0.0194	0.1542	-0.0962	0.0084	0.107	0.0007	0.0422	0.116	-0.0143	0.1191	15.3133	-19.7936	3.0074
9	-0.006	-0.0143	-0.012	0.1219	-0.1902	0.2509	-0.0149	0.0027	0.0032	0.0025	0.0096	-0.0258	0.0171	0.2015	-0.0021	0.0634	0.0221	-0.0056	0.1466	-0.0132	0.1011	40.6452	-11.4229	13.8296
10	0.0369	0.055	0.0053	0.0795	-0.0023	0.1623	-0.0596	-0.0687	0.0054	-0.0015	-0.0004	-0.2348	-0.0527	0.4128	-0.0165	0.1091	-0.0761	-0.0316	0.129	-0.0182	0.1127	40.7811	10.1694	15.3292
11	0.1595	-0.0067	0.0295	0.2458	0.1464	0.7575	-0.0135	0.011	0.0174	-0.0218	-0.0274	0.0283	-0.1454	-0.0486	-0.0243	0.1024	0.0118	-0.0148	0.0695	-0.0021	0.0896	21.4092	8.5817	3.2521
12	0.2296	-0.081	0.0851	0.0622	0.0618	0.4312	-0.0221	0.0111	0.019	-0.0161	0.0045	0.0116	-0.0957	0.0713	-0.0171	0.0913	-0.0143	-0.0073	0.0735	-0.004	0.0807	32.4982	4.8668	13.1003
13	0.3663	0.1285	-0.1754	-0.0228	-0.0139	0.1564	0.0139	0.1184	-0.0317	-0.1429	0.0239	-0.051	-0.0882	0.3757	-0.0006	0.0547	-0.0104	0.0174	0.1624	-0.0063	0.0971	41.9335	-6.5235	-5.5702
14	0.1264	0.1351	-0.0279	0.4208	-0.1553	0.4593	-0.0182	0.105	-0.016	-0.0362	0.0312	0.0938	0.0065	-0.0025	0	0.0838	0.004	-0.0117	0.1008	-0.0146	0.1104	25.5195	-11.2189	-14.6188

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESSEQ 8:42)
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 8:42)
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESSEQ 43:81)
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESSEQ 82:104)
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESSEQ 105:214)
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESSEQ 215:310)
13	X-RAY DIFFRACTION	13	CHAIN B AND (RESSEQ 311:341)
14	X-RAY DIFFRACTION	14	CHAIN B AND (RESSEQ 342:406)

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