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- PDB-3dyd: Human Tyrosine Aminotransferase -

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Basic information

Entry
Database: PDB / ID: 3dyd
TitleHuman Tyrosine Aminotransferase
ComponentsTyrosine aminotransferase
KeywordsTRANSFERASE / PLP / TYROSINE / SGC / Structural Genomics / Structural Genomics Consortium / Aminotransferase / Disease mutation / Phenylalanine catabolism / Pyridoxal phosphate / Tyrosine catabolism
Function / homology
Function and homology information


tyrosine transaminase / Tyrosine catabolism / glutamate metabolic process / L-tyrosine-2-oxoglutarate transaminase activity / response to mercury ion / L-tyrosine catabolic process / 2-oxoglutarate metabolic process / L-phenylalanine catabolic process / amino acid binding / biosynthetic process ...tyrosine transaminase / Tyrosine catabolism / glutamate metabolic process / L-tyrosine-2-oxoglutarate transaminase activity / response to mercury ion / L-tyrosine catabolic process / 2-oxoglutarate metabolic process / L-phenylalanine catabolic process / amino acid binding / biosynthetic process / response to dexamethasone / pyridoxal phosphate binding / response to oxidative stress / identical protein binding / cytosol
Similarity search - Function
Tyrosine aminotransferase ubiquitination region / Aminotransferase ubiquitination site / Tyrosine aminotransferase / Tyrosine/nicotianamine 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 ...Tyrosine aminotransferase ubiquitination region / Aminotransferase ubiquitination site / Tyrosine aminotransferase / Tyrosine/nicotianamine 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
PYRIDOXAL-5'-PHOSPHATE / Tyrosine aminotransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKarlberg, T. / Moche, M. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. ...Karlberg, T. / Moche, M. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Kotenyova, T. / Lehtio, L. / Nilsson, M.E. / Nordlund, P. / Nyman, T. / Olesen, K. / Persson, C. / Sagemark, J. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Wikstrom, M. / Wisniewska, M. / Schuler, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Human Tyrosine Aminotransferase
Authors: Karlberg, T. / Moche, M. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / ...Authors: Karlberg, T. / Moche, M. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Kotenyova, T. / Lehtio, L. / Nilsson, M.E. / Nordlund, P. / Nyman, T. / Olesen, K. / Persson, C. / Sagemark, J. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Wikstrom, M. / Wisniewska, M. / Schuler, H. / Structural Genomics Consortium (SGC)
History
DepositionJul 27, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Aug 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_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_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: Tyrosine aminotransferase
B: Tyrosine aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,9604
Polymers95,4662
Non-polymers4942
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-32 kcal/mol
Surface area29410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.420, 91.590, 75.570
Angle α, β, γ (deg.)90.00, 106.18, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Tyrosine aminotransferase / L-tyrosine:2-oxoglutarate aminotransferase / TAT


Mass: 47733.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAT / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) R3 pRARE / References: UniProt: P17735, tyrosine transaminase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.69 Å3/Da / Density % sol: 54.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 30% MPD, 0.1M Na-Acetate pH 4.6, 3mM PLP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 25, 2008
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. all: 44821 / Num. obs: 44821 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.115 / Rsym value: 0.157 / Net I/σ(I): 10.7
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 3.3 / Num. unique all: 5284 / Rsym value: 0.55 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.5.0035refinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BW0

1bw0


Resolution: 2.3→36.91 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.89 / SU B: 16.384 / SU ML: 0.177 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.31 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26088 2241 5 %RANDOM
Rwork0.21949 ---
obs0.22158 42574 100 %-
all-42574 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.102 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20.14 Å2
2---0.61 Å20 Å2
3---0.79 Å2
Refinement stepCycle: LAST / Resolution: 2.3→36.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6043 0 30 206 6279
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226248
X-RAY DIFFRACTIONr_bond_other_d0.0010.024245
X-RAY DIFFRACTIONr_angle_refined_deg1.1551.9868506
X-RAY DIFFRACTIONr_angle_other_deg0.85310403
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.285779
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.60224.208259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.77151050
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1471534
X-RAY DIFFRACTIONr_chiral_restr0.0680.2955
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216878
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021194
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3111.53900
X-RAY DIFFRACTIONr_mcbond_other0.0581.51547
X-RAY DIFFRACTIONr_mcangle_it0.60526337
X-RAY DIFFRACTIONr_scbond_it0.97532348
X-RAY DIFFRACTIONr_scangle_it1.5814.52168
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 163 -
Rwork0.277 3103 -
obs--100 %
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)
12.49211.6833-0.31192.0892-0.31250.2880.2561-0.37480.24540.4563-0.23840.2308-0.0922-0.0192-0.01760.1428-0.02310.00750.1036-0.02940.080420.302189.991213.351
21.31630.60360.19061.15530.02050.41110.0857-0.1585-0.02140.1919-0.0920.05480.06110.02940.00630.06950.00340.01950.0654-0.00420.010257.047480.429112.9704
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA41 - 44424 - 427
2X-RAY DIFFRACTION2BB41 - 44424 - 427

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