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- PDB-4eu1: Structure of a mitochondrial aspartate aminotransferase from Tryp... -

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Basic information

Entry
Database: PDB / ID: 4eu1
TitleStructure of a mitochondrial aspartate aminotransferase from Trypanosoma brucei
ComponentsMitochondrial aspartate aminotransferase
KeywordsTRANSFERASE / SSGCID / Aspartate aminotransferase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / pyridoxalphosphate lysine / mitochondrial
Function / homology
Function and homology information


L-alanine:2-oxoglutarate aminotransferase activity / L-methionine salvage from methylthioadenosine / aspartate transaminase / nuclear lumen / L-aspartate:2-oxoglutarate aminotransferase activity / ciliary plasm / biosynthetic process / pyridoxal phosphate binding / mitochondrion / cytoplasm
Similarity search - Function
Aspartate/other aminotransferase / 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 ...Aspartate/other aminotransferase / 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
Aspartate aminotransferase, mitochondrial / Aspartate transaminase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: Structures of aspartate aminotransferases from Trypanosoma brucei, Leishmania major and Giardia lamblia.
Authors: Abendroth, J. / Choi, R. / Wall, A. / Clifton, M.C. / Lukacs, C.M. / Staker, B.L. / Van Voorhis, W. / Myler, P. / Lorimer, D.D. / Edwards, T.E.
History
DepositionApr 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2May 13, 2015Group: Database references
Revision 1.3May 20, 2015Group: Database references
Revision 1.4Sep 13, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 6, 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: Mitochondrial aspartate aminotransferase
B: Mitochondrial aspartate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,14510
Polymers90,7812
Non-polymers3638
Water6,557364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-55 kcal/mol
Surface area28890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.260, 96.250, 81.320
Angle α, β, γ (deg.)90.000, 111.620, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 0 / Auth seq-ID: 8 - 387 / Label seq-ID: 29 - 408

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Mitochondrial aspartate aminotransferase


Mass: 45390.719 Da / Num. of mol.: 2 / Fragment: UNP residues 1-388
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Strain: TREU927 / Gene: Tb11.02.2740 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q964F0, UniProt: Q385Q9*PLUS, aspartate transaminase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 2.51 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: EmeraldBio Wizard classic 3/4 B7: 20% PEG 3350, 200mM ammonium nitrate, TrbrA.34891.a.A1 PW34891 at 27.7 mg/ml, tray 232857g1, pH 7.5, vapor diffusion, sitting drop, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 6, 2012
RadiationMonochromator: RIGAKU VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 39748 / Num. obs: 38947 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 35.39 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 12.82
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.3-2.363.80.5323.110489280096.5
2.36-2.423.80.3534.3510497279397.7
2.42-2.493.80.3024.9710337274597.4
2.49-2.573.80.2565.849846260898.1
2.57-2.663.80.2266.359636255898.1
2.66-2.753.80.1817.629345247898.1
2.75-2.853.80.1558.619111241398.3
2.85-2.973.80.1339.968750231598.5
2.97-3.13.80.10911.738440222298.4
3.1-3.253.80.08713.928016211398.9
3.25-3.433.80.07915.467724203998.4
3.43-3.643.70.07817.466888188398.4
3.64-3.893.50.06222.076232177295.6
3.89-4.23.80.05222.866279166097.7
4.2-4.63.80.04426.285834154598.6
4.6-5.143.80.04625.365368141599.3
5.14-5.943.80.04623.554746124799
5.94-7.273.80.04324.054008105798.9
7.27-10.293.70.0330.94311583699.1
10.29-503.60.02536.62160244895.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å19.87 Å
Translation3.5 Å19.87 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
JDirectordata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4EFF modified with CCP4 program chainsaw

4eff


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.901 / WRfactor Rfree: 0.2206 / WRfactor Rwork: 0.1749 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8463 / SU B: 11.506 / SU ML: 0.152 / SU R Cruickshank DPI: 0.3332 / SU Rfree: 0.2368 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.333 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2447 1963 5 %RANDOM
Rwork0.196 ---
obs0.1984 38947 98.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.44 Å2 / Biso mean: 29.3858 Å2 / Biso min: 9.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å2-0 Å20.26 Å2
2--0.16 Å2-0 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5844 0 17 364 6225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196011
X-RAY DIFFRACTIONr_bond_other_d0.0040.023993
X-RAY DIFFRACTIONr_angle_refined_deg1.3751.9648175
X-RAY DIFFRACTIONr_angle_other_deg1.08139718
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6545768
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46123.463257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.46715939
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3321541
X-RAY DIFFRACTIONr_chiral_restr0.0770.2911
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216784
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021231
Refine LS restraints NCS

Ens-ID: 1 / Number: 13085 / Refine-ID: X-RAY DIFFRACTION / Rms: 0.09 / Type: LOCAL / Weight: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 129 -
Rwork0.3 2612 -
all-2741 -
obs--96.55 %
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)
10.52610.0435-0.36140.32480.21892.21520.02720.0524-0.00250.00130.0590.01620.0168-0.0077-0.08620.21180.01410.09180.04020.0060.04938.58328.3352.15
20.6146-0.0147-0.62280.66170.0822.40120.0373-0.01150.0758-0.04910.04990.0027-0.0139-0.1034-0.08720.14660.01050.08120.02970.00830.051820.93926.82985.459
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 388
2X-RAY DIFFRACTION2B8 - 388

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