[English] 日本語
Yorodumi
- PDB-1bw0: CRYSTAL STRUCTURE OF TYROSINE AMINOTRANSFERASE FROM TRYPANOSOMA CRUZI -

+
Open data


ID or keywords:

Loading...

-
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 / tyrosine catabolic process / L-tyrosine-2-oxoglutarate transaminase activity / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

-
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

-
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 %

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more