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

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Basic information

Entry
Database: PDB / ID: 3qpg
TitleCrystal Structures of Escherichia coli Aspartate Aminotransferase Reconstituted with 1-Deaza-Pyridoxal 5'-Phosphate: Internal Aldimine and Stable L-Aspartate External Aldimine
ComponentsAspartate transaminase
KeywordsTRANSFERASE / 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
Aspartate/other aminotransferase / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain ...Aspartate/other aminotransferase / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-3QP / : / Aspartate aminotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.79 Å
AuthorsGriswold, W.R.
CitationJournal: 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
DepositionFeb 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aspartate transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,03315
Polymers43,6191
Non-polymers1,41314
Water5,819323
1
A: Aspartate transaminase
hetero molecules

A: Aspartate transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,06530
Polymers87,2382
Non-polymers2,82728
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area10900 Å2
ΔGint-182 kcal/mol
Surface area29410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.785, 154.834, 77.799
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-583-

HOH

21A-636-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Aspartate transaminase


Mass: 43619.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / Strain (production host): MG204
References: UniProt: C9QZE8, UniProt: P00509*PLUS, aspartate transaminase

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Non-polymers , 5 types, 337 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / 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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-3QP / (E)-N-{2-hydroxy-3-methyl-6-[(phosphonooxy)methyl]benzylidene}-L-aspartic acid


Type: peptide-like / Mass: 361.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H16NO9P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.47 %
Crystal growTemperature: 293 K / pH: 7.5
Details: 2 uL of protein solution(15-20 mg/ml, 50 mM TEA, pH 7.5, 100 mM KCL, 2 mM DTT, 10 mM deaza-PLP, 50 mM L-aspartate) mixed with 2 uL reservoir buffer (53-60% saturated ammonium sulfate and 50 ...Details: 2 uL of protein solution(15-20 mg/ml, 50 mM TEA, pH 7.5, 100 mM KCL, 2 mM DTT, 10 mM deaza-PLP, 50 mM L-aspartate) mixed with 2 uL reservoir buffer (53-60% saturated ammonium sulfate and 50 mM TEA, pH 7.5), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.79→28.5 Å / Num. obs: 46701 / % possible obs: 98.2 % / Redundancy: 3.4 % / Rsym value: 0.059 / Net I/σ(I): 17.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 35.27 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å38.36 Å
Translation2.5 Å38.36 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALAdata scaling
PHASER2.1.4phasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→28.5 Å / Occupancy max: 1 / Occupancy min: 0.22 / SU ML: 0.16 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.179 2368 5.07 %
Rwork0.148 --
obs0.149 46680 97.4 %
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.66 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 36.66 Å2
Baniso -1Baniso -2Baniso -3
1-3.2294 Å2-0 Å20 Å2
2---4.8843 Å2-0 Å2
3---1.6549 Å2
Refinement stepCycle: LAST / Resolution: 1.79→28.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3056 0 81 323 3460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0163390
X-RAY DIFFRACTIONf_angle_d1.5184616
X-RAY DIFFRACTIONf_dihedral_angle_d13.471260
X-RAY DIFFRACTIONf_chiral_restr0.114494
X-RAY DIFFRACTIONf_plane_restr0.008613
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7911-1.85510.2542090.19834028X-RAY DIFFRACTION90
1.8551-1.92940.22442360.18014409X-RAY DIFFRACTION98
1.9294-2.01710.23532510.16544399X-RAY DIFFRACTION98
2.0171-2.12350.17832480.14484426X-RAY DIFFRACTION98
2.1235-2.25640.19092240.14444475X-RAY DIFFRACTION98
2.2564-2.43060.19222290.14414459X-RAY DIFFRACTION99
2.4306-2.6750.19822770.15064463X-RAY DIFFRACTION99
2.675-3.06170.18592320.14844511X-RAY DIFFRACTION99
3.0617-3.85590.16542310.14324556X-RAY DIFFRACTION99
3.8559-28.50910.15492310.1434586X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.04660.04280.04760.03820.03150.04830.05630.1568-0.0719-0.11570.0325-0.07450.18580.2411-00.2860.0125-0.05950.38440.01260.3424-22.622321.6407-11.798
20.7932-0.03350.1740.5844-0.01380.91050.0049-0.18960.02140.07870.00280.0402-0.004-0.11200.1820.01710.01290.21670.00610.1901-46.251825.3144-3.73
30.24060.0770.08390.06220.14380.37150.0009-0.288-0.08870.24440.1043-0.29280.12940.1259-0.00010.3184-0.0077-0.0770.36160.00860.3509-20.246220.04546.57
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 13:54)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 55:330)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 331:408)

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