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- PDB-1bw0: CRYSTAL STRUCTURE OF TYROSINE AMINOTRANSFERASE FROM TRYPANOSOMA CRUZI -

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Basic information

Entry
Database: PDB / ID: 1bw0
TitleCRYSTAL STRUCTURE OF TYROSINE AMINOTRANSFERASE FROM TRYPANOSOMA CRUZI
ComponentsPROTEIN (TYROSINE AMINOTRANSFERASE)
KeywordsTRANSFERASE / TYROSINE CATABOLISM / AMINOTRANSFERASE / PYRIDOXAL-5'-PHOSPHATE / PLP
Function / homology
Function and homology information


tyrosine transaminase / L-tyrosine-2-oxoglutarate transaminase activity / L-tyrosine catabolic process / L-phenylalanine catabolic process / biosynthetic process / pyridoxal phosphate binding / mitochondrion
Similarity search - Function
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) ...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
Tyrosine aminotransferase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBlankenfeldt, W. / Montemartini, M. / Hunter, G.R. / Kalisz, H.M. / Nowicki, C. / Hecht, H.J.
Citation
Journal: Protein Sci. / Year: 1999
Title: Crystal structure of Trypanosoma cruzi tyrosine aminotransferase: substrate specificity is influenced by cofactor binding mode.
Authors: Blankenfeldt, W. / Nowicki, C. / Montemartini-Kalisz, M. / Kalisz, H.M. / Hecht, H.J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallization and Preliminary X-Ray Analysis of Tyrosine Aminotransferase from Trypanosoma Cruzi Epimastigotes
Authors: Nowicki, C. / Montemartini, M. / Hunter, G.R. / Blankenfeldt, W. / Hecht, H.J.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: Aromatic Amino Acid Transamination and Methionine Recycling in Trypanosomatids
Authors: Berger, B.J. / Dai, W.W. / Wang, H. / Stark, R.E. / Cerami, A.
#3: Journal: Fems Microbiol.Lett. / Year: 1994
Title: Production of Aromatic Alpha-Hydroxyacids by Epimastigotes of Trypanosoma Cruzi, and its Possible Role in Nadh Reoxidation
Authors: Montemartini, M. / Santome, J.A. / Cazzulo, J.J. / Nowicki, C.
History
DepositionSep 28, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 27, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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
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
Revision 1.4Nov 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

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Assembly

Deposited unit
A: PROTEIN (TYROSINE AMINOTRANSFERASE)
B: PROTEIN (TYROSINE AMINOTRANSFERASE)


Theoretical massNumber of molelcules
Total (without water)92,9002
Polymers92,9002
Non-polymers00
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6450 Å2
ΔGint-45 kcal/mol
Surface area29340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.600, 102.200, 77.900
Angle α, β, γ (deg.)90.00, 110.30, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.57939, 0.761052, 0.291731), (0.766816, -0.630292, 0.121344), (0.276225, 0.153399, -0.948772)
Vector: 5.682, -10.995, -1.489)

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Components

#1: Protein PROTEIN (TYROSINE AMINOTRANSFERASE) / E.C.2.6.1.5 TRANSFERASE / TAT


Mass: 46449.988 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THE PROTEIN WAS PURIFIED FROM TRYPANOSOMA CRUZI EPIMASTIGOTES.
Source: (natural) Trypanosoma cruzi (eukaryote) / Strain: TUL 0 / References: UniProt: P33447, tyrosine transaminase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 5

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 51 %
Crystal growpH: 7
Details: DIALYSIS OF 2.6 MG/ML PROTEIN AGAINST 25 % (W/W) PEG 8000, 5 MM PLP, 0.1 M PHOSPHATE/CITRATE, PH 7.0, 285 K
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 285 K / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 %(w/w)PEG800011
25 mMPLP11
30.1 Mcitrate/phosphate11

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Data collection

DiffractionMean temperature: 285 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS X1000 / Detector: AREA DETECTOR / Date: Jun 15, 1996 / Details: COLLIMATOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→10 Å / Num. obs: 24668 / % possible obs: 78.4 % / Redundancy: 1.7 % / Biso Wilson estimate: 30.17 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 17
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.096 / Mean I/σ(I) obs: 6 / % possible all: 47
Reflection shell
*PLUS
% possible obs: 47 %

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
X-GENdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ART

1art


Resolution: 2.5→10 Å / SU B: 5.63 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.31
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1264 5 %RANDOM
Rwork0.157 ---
obs-24668 78.4 %-
Displacement parametersBiso mean: 25.19 Å2
Baniso -1Baniso -2Baniso -3
1-7.54 Å20 Å22.74 Å2
2---0.76 Å20 Å2
3----6.75 Å2
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6472 0 0 118 6590
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0060.02
X-RAY DIFFRACTIONp_angle_d0.0230.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.020.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.7212
X-RAY DIFFRACTIONp_mcangle_it1.3073
X-RAY DIFFRACTIONp_scbond_it0.7382
X-RAY DIFFRACTIONp_scangle_it1.2873
X-RAY DIFFRACTIONp_plane_restr0.01430.03
X-RAY DIFFRACTIONp_chiral_restr0.0810.15
X-RAY DIFFRACTIONp_singtor_nbd0.1780.3
X-RAY DIFFRACTIONp_multtor_nbd0.2420.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1390.3
X-RAY DIFFRACTIONp_planar_tor2.77
X-RAY DIFFRACTIONp_staggered_tor16.615
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor30.720
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.157
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.04
X-RAY DIFFRACTIONp_planar_d0.050.02
X-RAY DIFFRACTIONp_plane_restr0.03
X-RAY DIFFRACTIONp_chiral_restr0.15
LS refinement shell
*PLUS
Highest resolution: 2.51 Å / Lowest resolution: 2.6 Å / Rfactor Rfree: 0.294 / Rfactor obs: 0.211

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