PDB-3qn6: Crystal Structures of Escherichia coli Aspartate Aminotransferase...

ID or keywords:

Entry

Database: PDB / ID: 3qn6

Title

Crystal Structures of Escherichia coli Aspartate Aminotransferase Reconstituted with 1-Deaza-Pyridoxal 5'-Phosphate: Internal Aldimine and Stable L-Aspartate External Aldimine

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 aminotransferase 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 /

molecular replacement / Resolution: 1.79 Å

Authors

Griswold, W.R.

Citation

Journal: Biochemistry / Year: 2011
Title: Crystal Structures of Aspartate Aminotransferase Reconstituted with 1-Deazapyridoxal 5'-Phosphate: Internal Aldimine and Stable l-Aspartate External Aldimine.
Authors: Griswold, W.R. / Fisher, A.J. / Toney, M.D.

History

Deposition	Feb 8, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 15, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Jul 20, 2011	Group: Database references
Revision 2.0	Nov 15, 2023	Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_close_contact / struct_conn / struct_site Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _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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PDBx/mmCIF format	3qn6.cif.gz	181.5 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3qn6_validation.pdf.gz	456.2 KB	Display	wwPDB validaton report
Full document	3qn6_full_validation.pdf.gz	460.3 KB	Display
Data in XML	3qn6_validation.xml.gz	21.2 KB	Display
Data in CIF	3qn6_validation.cif.gz	32.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qn/3qn6 ftp://data.pdbj.org/pub/pdb/validation_reports/qn/3qn6	HTTPS FTP

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Related structure data

Related structure data	3qpgC C: citing same article (ref.)
Similar structure data	5vwq-2 1toe-1 1g4x-1 1aaw-1 1g4v-1 2d66-1 1ix7-1 1b4x-1 4f5h-d 2d7y-1 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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Aspartate aminotransferase

hetero molecules

44.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Aspartate aminotransferase

hetero molecules

A: Aspartate aminotransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	84.749, 154.678, 79.147
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-747- HOH

#1: Protein	Aspartate aminotransferase / AspAT / Transaminase A Mass: 43846.344 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: aspC, b0928, JW0911 / Production host: Escherichia coli (E. coli) / Strain (production host): MG204 / References: UniProt: P00509, aspartate transaminase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.98 Å³/Da / Density % sol: 58.77 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2 L of protein (15-20 mg/ml, 50 mM TEA, pH 7.5, 100 mM KCL, 2 mM DTT, 10 M deaza-PLP) mixed with 2 L reservoir buffer (53-60% saturated ammonium sulfate and 50 mM TEA, pH 7.5), VAPOR ...Details: 2 L of protein (15-20 mg/ml, 50 mM TEA, pH 7.5, 100 mM KCL, 2 mM DTT, 10 M deaza-PLP) mixed with 2 L reservoir buffer (53-60% saturated ammonium sulfate and 50 mM TEA, pH 7.5), VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal

Density Matthews: 2.98 Å³/Da / Density % sol: 58.77 %

Crystal grow

Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2 L of protein (15-20 mg/ml, 50 mM TEA, pH 7.5, 100 mM KCL, 2 mM DTT, 10 M deaza-PLP) mixed with 2 L reservoir buffer (53-60% saturated ammonium sulfate and 50 mM TEA, pH 7.5), VAPOR ...

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Data collection

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL9-2

Detector

Type: MARMOSAIC 325 mm CCD / Detector: CCD

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Relative weight: 1

Reflection

Redundancy: 3.4 % / Av σ(I) over netI: 8.6 / Number: 167956 / R_sym value: 0.056 / D res high: 1.79 Å / D res low: 39.574 Å / Num. obs: 48807 / % possible obs: 99.1

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	R_sym value	Redundancy
8.01	39.57	79.7	1	0.024	0.024	2.9
5.66	8.01	99	1	0.026	0.026	3.5
4.62	5.66	94.9	1	0.033	0.033	3.4
4	4.62	94.4	1	0.032	0.032	3.2
3.58	4	98.3	1	0.033	0.033	3.3
3.27	3.58	98.5	1	0.04	0.04	3.5
3.03	3.27	99.3	1	0.044	0.044	3.4
2.83	3.03	99.7	1	0.052	0.052	3.5
2.67	2.83	99.8	1	0.06	0.06	3.5
2.53	2.67	99.7	1	0.068	0.068	3.5
2.41	2.53	99.8	1	0.082	0.082	3.5
2.31	2.41	99.9	1	0.092	0.092	3.5
2.22	2.31	99.8	1	0.108	0.108	3.5
2.14	2.22	99.9	1	0.124	0.124	3.5
2.07	2.14	99.9	1	0.15	0.15	3.5
2	2.07	99.9	1	0.174	0.174	3.5
1.94	2	99.8	1	0.214	0.214	3.4
1.89	1.94	99.6	1	0.279	0.279	3.4
1.84	1.89	99.6	1	0.325	0.325	3.4
1.79	1.84	99.7	1	0.428	0.428	3.3

Reflection

Resolution: 1.79→39.574 Å / Num. all: 48807 / Num. obs: 48807 / % possible obs: 99.1 % / Redundancy: 3.4 % / R_sym value: 0.056 / Net I/σ(I): 10.7

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
1.79-1.84	3.3	0.428	1.7	11977	3603	0.428	99.7
1.84-1.89	3.4	0.325	2.2	11726	3497	0.325	99.6
1.89-1.94	3.4	0.279	2.2	11502	3398	0.279	99.6
1.94-2	3.4	0.214	3.3	11459	3324	0.214	99.8
2-2.07	3.5	0.174	4	11223	3218	0.174	99.9
2.07-2.14	3.5	0.15	3.2	11005	3119	0.15	99.9
2.14-2.22	3.5	0.124	5.4	10606	3008	0.124	99.9
2.22-2.31	3.5	0.108	6.1	10224	2900	0.108	99.8
2.31-2.41	3.5	0.092	6.8	9921	2808	0.092	99.9
2.41-2.53	3.5	0.082	7.6	9316	2654	0.082	99.8
2.53-2.67	3.5	0.068	8.9	8897	2534	0.068	99.7
2.67-2.83	3.5	0.06	10.2	8447	2421	0.06	99.8
2.83-3.03	3.5	0.052	10.8	7804	2257	0.052	99.7
3.03-3.27	3.4	0.044	13.2	7200	2100	0.044	99.3
3.27-3.58	3.5	0.04	14.4	6674	1912	0.04	98.5
3.58-4	3.3	0.033	15.9	5843	1759	0.033	98.3
4-4.62	3.2	0.032	15.9	4666	1475	0.032	94.4
4.62-5.66	3.4	0.033	16.4	4417	1290	0.033	94.9
5.66-8.01	3.5	0.026	21.5	3639	1043	0.026	99
8.01-39.574	2.9	0.024	26.4	1410	487	0.024	79.7

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA	3.3.15	data scaling
MOLREP		phasing
PHENIX	1.6.4_486	refinement
PDB_EXTRACT	3.1	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.79→35.229 Å / Occupancy max: 1 / Occupancy min: 0.26 / FOM work R set: 0.8969 / SU ML: 0.18 / σ(F): 1.34 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.188	2471	5.07 %
R_work	0.1515	-	-
obs	0.1533	48759	98.87 %

Solvent computation

Shrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 55.804 Å² / k_sol: 0.421 e/Å³

Displacement parameters

B_iso max: 93.76 Å² / B_iso mean: 32.4028 Å² / B_iso min: 11.96 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.1514 Å²	-0 Å²	-0 Å²
2-	-	-2.4448 Å²	0 Å²
3-	-	-	-0.7065 Å²

Refinement step

Cycle: LAST / Resolution: 1.79→35.229 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3067	0	41	396	3504

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.017	3292
X-RAY DIFFRACTION	f_angle_d	1.486	4472
X-RAY DIFFRACTION	f_chiral_restr	0.112	483
X-RAY DIFFRACTION	f_plane_restr	0.007	591
X-RAY DIFFRACTION	f_dihedral_angle_d	13.901	1216

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.79-1.854	0.3066	235	0.2596	4611	4846	100
1.854-1.9282	0.2559	242	0.2128	4618	4860	100
1.9282-2.0159	0.2229	256	0.1816	4616	4872	100
2.0159-2.1222	0.2052	272	0.1546	4582	4854	100
2.1222-2.2552	0.1765	245	0.1424	4655	4900	100
2.2552-2.4292	0.178	231	0.1392	4649	4880	100
2.4292-2.6736	0.1944	276	0.1349	4635	4911	100
2.6736-3.0603	0.1763	258	0.1384	4671	4929	100
3.0603-3.8549	0.1805	231	0.1397	4663	4894	98
3.8549-35.2362	0.1682	225	0.1526	4588	4813	93

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	0.0325	-0.0533	0.0239	0.0911	-0.0652	0.0377	-0.0313	0.0725	0.133	-0.0787	0.1424	-0.0951	-0.0925	0.1272	0.0157	0.2401	-0.096	-0.0153	0.3026	-0.012	0.2644	-21.4575	22.607	-13.8582
2	0.5956	-0.1042	0.1041	0.8408	0.1545	0.837	0.0167	-0.1088	0.072	0.0646	0.016	0.0232	-0.094	-0.0758	-0	0.1549	0.0063	0.0209	0.1711	0.0001	0.158	-45.042	25.0705	-3.7423
3	0.2447	0.2064	0.0207	0.2536	0.183	0.3198	0.0489	-0.2862	-0.1119	0.0977	-0.0192	-0.39	-0.0768	0.0866	0	0.2576	-0.0355	-0.083	0.2602	-0.0162	0.3082	-18.26	19.7802	5.4868

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(chain A and resid 13:54)	A	13 - 54
2	X-RAY DIFFRACTION	2	(chain A and resid 55:330)	A	55 - 330
3	X-RAY DIFFRACTION	3	(chain A and resid 331:408)	A	331 - 408

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