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- PDB-3bwn: L-tryptophan aminotransferase -

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Basic information

Entry
Database: PDB / ID: 3bwn
TitleL-tryptophan aminotransferase
Components(L-tryptophan ...) x 2
KeywordsTRANSFERASE / aminotransferase / auxin synthesis / tryptophan / pyridoxal-5'-phosphate / indole-3-pyruvate
Function / homology
Function and homology information


tryptophan transaminase / L-tryptophan-pyruvate aminotransferase / indoleacetic acid biosynthetic process / cotyledon vascular tissue pattern formation / L-phenylalanine-pyruvate transaminase activity / L-tryptophan:2-oxoglutarate aminotransferase activity / L-tryptophan:pyruvate aminotransferase activity / L-tyrosine-pyruvate transaminase activity / L-methionine:2-oxoglutarate aminotransferase activity / gynoecium development ...tryptophan transaminase / L-tryptophan-pyruvate aminotransferase / indoleacetic acid biosynthetic process / cotyledon vascular tissue pattern formation / L-phenylalanine-pyruvate transaminase activity / L-tryptophan:2-oxoglutarate aminotransferase activity / L-tryptophan:pyruvate aminotransferase activity / L-tyrosine-pyruvate transaminase activity / L-methionine:2-oxoglutarate aminotransferase activity / gynoecium development / L-phenylalanine-2-oxoglutarate transaminase activity / L-alanine:2-oxoglutarate aminotransferase activity / primary root development / maintenance of root meristem identity / cotyledon development / shoot system development / shade avoidance / carbon-sulfur lyase activity / phloem or xylem histogenesis / response to ethylene / positive gravitropism / leaf development / flower development / auxin polar transport / root development / L-tyrosine-2-oxoglutarate transaminase activity / embryo development ending in seed dormancy / pyridoxal phosphate binding / defense response to bacterium / cytoplasm
Similarity search - Function
Alliinase, C-terminal / Alliinase, N-terminal domain superfamily / Allinase / : / 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 ...Alliinase, C-terminal / Alliinase, N-terminal domain superfamily / Allinase / : / 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
PHENYLALANINE / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PHOSPHATE ION / L-tryptophan--pyruvate aminotransferase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / RIGID BODY / Resolution: 2.25 Å
AuthorsFerrer, J.-L. / Noel, J.P. / Pojer, F. / Bowman, M. / Chory, J. / Tao, Y.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 2008
Title: Rapid synthesis of auxin via a new tryptophan-dependent pathway is required for shade avoidance in plants
Authors: Tao, Y. / Ferrer, J.L. / Ljung, K. / Pojer, F. / Hong, F. / Long, J.A. / Li, L. / Moreno, J.E. / Bowman, M.E. / Ivans, L.J. / Cheng, Y. / Lim, J. / Zhao, Y. / Ballare, C.L. / Sandberg, G. / ...Authors: Tao, Y. / Ferrer, J.L. / Ljung, K. / Pojer, F. / Hong, F. / Long, J.A. / Li, L. / Moreno, J.E. / Bowman, M.E. / Ivans, L.J. / Cheng, Y. / Lim, J. / Zhao, Y. / Ballare, C.L. / Sandberg, G. / Noel, J.P. / Chory, J.
#1: Journal: To be Published
Title: Structural basis for entry of L-TRP into pathway for auxin biosynthesis
Authors: Ferrer, J.-L. / Tao, Y. / Pojer, F. / Bowman, M.E. / Chory, J. / Noel, J.P.
History
DepositionJan 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-tryptophan aminotransferase
B: L-tryptophan aminotransferase
C: L-tryptophan aminotransferase
D: L-tryptophan aminotransferase
E: L-tryptophan aminotransferase
F: L-tryptophan aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)270,66512
Polymers269,4126
Non-polymers1,2536
Water10,665592
1
A: L-tryptophan aminotransferase
B: L-tryptophan aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2244
Polymers89,7282
Non-polymers4962
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-33.8 kcal/mol
Surface area27930 Å2
MethodPISA
2
C: L-tryptophan aminotransferase
D: L-tryptophan aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2043
Polymers89,9562
Non-polymers2481
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-23.1 kcal/mol
Surface area27240 Å2
MethodPISA
3
E: L-tryptophan aminotransferase
F: L-tryptophan aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2365
Polymers89,7282
Non-polymers5083
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-38.5 kcal/mol
Surface area27670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.410, 97.830, 139.460
Angle α, β, γ (deg.)90.00, 104.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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L-tryptophan ... , 2 types, 6 molecules ABDEFC

#1: Protein
L-tryptophan aminotransferase / At1g70560


Mass: 44864.020 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g70560/F5A18_26, F5A18.26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9S7N2
#2: Protein L-tryptophan aminotransferase


Mass: 45092.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g70560/F5A18_26, F5A18.26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9S7N2

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Non-polymers , 4 types, 598 molecules

#3: Chemical
ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H13N2O5P
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 592 / 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: 2.29 Å3/Da / Density % sol: 46.32 %
Crystal growTemperature: 293 K / pH: 7
Details: 13-19% PEG 3350, 0.3M KCl, 100mM MOPSO pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K, pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.97944
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 4, 2006 / Details: MIRRORS + DOUBLE MONOCHROMATOR
RadiationMonochromator: SI (111) DOUBLE MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97944 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 110711 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 2.49 % / Rsym value: 0.56 / Net I/σ(I): 12.5
Reflection shellResolution: 2.25→2.31 Å / Redundancy: 2.41 % / Mean I/σ(I) obs: 2.53 / Rsym value: 0.414 / % possible all: 82.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
Blu-Icedata collection
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: RIGID BODY
Starting model: PDB ENTRY 1LK9

1lk9


Resolution: 2.25→29.66 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.93 / SU B: 19.051 / SU ML: 0.203 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.253 5549 5 %RANDOM
Rwork0.224 ---
obs0.225 105162 95.9 %-
all-105162 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.99 Å2
Baniso -1Baniso -2Baniso -3
1--4.74 Å20 Å2-0.78 Å2
2--6.33 Å20 Å2
3----1.98 Å2
Refinement stepCycle: LAST / Resolution: 2.25→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17464 0 81 592 18137
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02217969
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7341.9524297
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.85152160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.61423.361833
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.547153113
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.18715126
X-RAY DIFFRACTIONr_chiral_restr0.2160.22610
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213562
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2520.29015
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.212183
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.2973
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.280.295
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2760.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4681.511085
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.378217484
X-RAY DIFFRACTIONr_scbond_it2.6237954
X-RAY DIFFRACTIONr_scangle_it3.7894.56813
X-RAY DIFFRACTIONr_rigid_bond_restr1.856319039
X-RAY DIFFRACTIONr_sphericity_free8.6713592
X-RAY DIFFRACTIONr_sphericity_bonded2.112317556
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 410 -
Rwork0.334 7814 -
obs--97.08 %

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