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- PDB-4dbc: Substrate Activation in Aspartate Aminotransferase -

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Basic information

Entry
Database: PDB / ID: 4dbc
TitleSubstrate Activation in Aspartate Aminotransferase
ComponentsAspartate aminotransferase
KeywordsTRANSFERASE / 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
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 / Resolution: 1.5 Å
AuthorsToney, M.D. / Fisher, A.J. / Griswold, W.R.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: Ground-state electronic destabilization via hyperconjugation in aspartate aminotransferase.
Authors: Griswold, W.R. / Castro, J.N. / Fisher, A.J. / Toney, M.D.
History
DepositionJan 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen / entity_src_nat / Item: _entity.src_method
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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 aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3697
Polymers43,5611
Non-polymers8086
Water8,053447
1
A: Aspartate aminotransferase
hetero molecules

A: Aspartate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,73714
Polymers87,1222
Non-polymers1,61512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area8060 Å2
ΔGint-91 kcal/mol
Surface area29760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.290, 155.250, 77.960
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-649-

HOH

21A-800-

HOH

31A-945-

HOH

41A-1033-

HOH

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Components

#1: Protein Aspartate aminotransferase / AspAT / Transaminase A


Mass: 43561.109 Da / Num. of mol.: 1 / Mutation: K258A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / References: UniProt: P00509, aspartate transaminase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 447 / 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: 2.93 Å3/Da / Density % sol: 57.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / 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), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.033
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.5→28.617 Å / Num. all: 81931 / Num. obs: 80890 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.24 % / Rmerge(I) obs: 0.038 / Rsym value: 0.038 / Net I/σ(I): 17.7
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 2.73 % / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 2.03 / Rsym value: 0.543 / % possible all: 93.9

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Processing

Software
NameVersionClassification
MOLREPphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
DENZOdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→28.617 Å / SU ML: 0.43 / σ(F): 1.35 / Phase error: 20.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1935 4061 5.02 %
Rwork0.1692 --
obs0.1704 80854 98.74 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.448 Å2 / ksol: 0.361 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.3233 Å2-0 Å2-0 Å2
2---0.8079 Å2-0 Å2
3----0.5153 Å2
Refinement stepCycle: LAST / Resolution: 1.5→28.617 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3065 0 48 447 3560
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0163199
X-RAY DIFFRACTIONf_angle_d1.6074343
X-RAY DIFFRACTIONf_dihedral_angle_d12.8661158
X-RAY DIFFRACTIONf_chiral_restr0.115474
X-RAY DIFFRACTIONf_plane_restr0.01570
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.51770.3631110.3682464X-RAY DIFFRACTION92
1.5177-1.53620.32031140.32312510X-RAY DIFFRACTION94
1.5362-1.55560.29391180.29752568X-RAY DIFFRACTION95
1.5556-1.57610.2861470.2652610X-RAY DIFFRACTION100
1.5761-1.59770.2911560.25512665X-RAY DIFFRACTION100
1.5977-1.62050.30781340.24262643X-RAY DIFFRACTION100
1.6205-1.64470.25491460.23532646X-RAY DIFFRACTION100
1.6447-1.67040.21641470.20782656X-RAY DIFFRACTION100
1.6704-1.69780.24821400.20792649X-RAY DIFFRACTION100
1.6978-1.7270.2481450.20942653X-RAY DIFFRACTION100
1.727-1.75840.22561410.19842655X-RAY DIFFRACTION100
1.7584-1.79220.24481350.18872659X-RAY DIFFRACTION100
1.7922-1.82880.22531260.18422659X-RAY DIFFRACTION99
1.8288-1.86860.24541510.18472648X-RAY DIFFRACTION100
1.8686-1.9120.18411320.17792647X-RAY DIFFRACTION99
1.912-1.95980.19491580.17432629X-RAY DIFFRACTION99
1.9598-2.01280.23011480.17332658X-RAY DIFFRACTION99
2.0128-2.0720.20691500.16712628X-RAY DIFFRACTION99
2.072-2.13890.21561470.15872652X-RAY DIFFRACTION99
2.1389-2.21530.1731370.1622672X-RAY DIFFRACTION99
2.2153-2.3040.1941300.15812625X-RAY DIFFRACTION98
2.304-2.40880.2031360.16322658X-RAY DIFFRACTION99
2.4088-2.53570.18161430.1652670X-RAY DIFFRACTION99
2.5357-2.69450.20641830.16672648X-RAY DIFFRACTION100
2.6945-2.90230.17871410.16712705X-RAY DIFFRACTION100
2.9023-3.1940.18481370.16292705X-RAY DIFFRACTION100
3.194-3.65540.17641380.15612730X-RAY DIFFRACTION99
3.6554-4.60230.15621330.13612747X-RAY DIFFRACTION99
4.6023-28.62180.17241370.16922734X-RAY DIFFRACTION95
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)
10.02860.04250.05690.03850.0730.1010.11880.2159-0.081-0.10710.0476-0.0260.18710.34230.00140.26140.0068-0.07290.31330.0150.2865-20.665625.5643-14.5209
20.66690.03050.16760.59770.08170.7433-0.0024-0.1512-0.00470.0444-0.00540.047-0.0255-0.0885-00.14370.01080.00390.16790.00970.148-46.18226.0212-4.2125
30.2745-0.0821-0.11440.3570.33940.29840.0887-0.1544-0.13150.22260.0514-0.19580.07240.11350.0070.26-0.0164-0.07270.24080.05090.2414-25.184517.41545.5927
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 13:43)
2X-RAY DIFFRACTION2chain 'A' and (resseq 44:312)
3X-RAY DIFFRACTION3chain 'A' and (resseq 313:408)

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