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- PDB-4w5k: Structure of a mitochondrial aspartate aminotransferase from Tryp... -

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Basic information

Entry
Database: PDB / ID: 4w5k
TitleStructure of a mitochondrial aspartate aminotransferase from Trypanosoma brucei, K237A mutant
ComponentsAspartate aminotransferase, mitochondrial
KeywordsTRANSFERASE / SSGCID / Aspartate aminotransferase / mitochondrial / Trypanosoma brucei / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


L-alanine:2-oxoglutarate aminotransferase activity / L-methionine salvage from methylthioadenosine / L-aspartate:2-oxoglutarate aminotransferase activity / ciliary plasm / nuclear lumen / 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
D-MALATE / PYRIDOXAL-5'-PHOSPHATE / Transaminase A
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr.,Sect.F / 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
DepositionAug 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2May 20, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Advisory / Derived calculations ...Advisory / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_close_contact / software / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein
Revision 2.0Dec 25, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / pdbx_distant_solvent_atoms ...atom_site / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.occupancy / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_site_gen.auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aspartate aminotransferase, mitochondrial
B: Aspartate aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,5258
Polymers87,6382
Non-polymers8876
Water14,304794
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-26 kcal/mol
Surface area28680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.390, 96.660, 81.610
Angle α, β, γ (deg.)90.000, 111.030, 90.000
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is a dimer, the same as asymmetric unit

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Components

#1: Protein Aspartate aminotransferase, mitochondrial


Mass: 43819.129 Da / Num. of mol.: 2 / Mutation: K237A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / Gene: Tb11.02.2740 / Plasmid: TrbrA.01471.a.B13 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q385Q9, aspartate 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: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 794 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.63 Å3/Da / Density % sol: 53.07 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Rigaku Reagents JCSG+ G8: 20% PEG 3350, 150mM Na2 DL-malic acid; TrbrA.01471.a.B13.PS01760 at 28.8 mg/ml, tray 243596g8, puck qjb3-4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 3, 2013
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 97248 / Num. obs: 97248 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 20.86 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.047 / Rrim(I) all: 0.055 / Χ2: 1.012 / Net I/σ(I): 16.09 / Num. measured all: 372563
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.7-1.743.90.9110.5172.9127701732771080.59997
1.74-1.790.9390.4033.6926985712269210.46897.2
1.79-1.840.9570.3064.6226290694867500.35597.2
1.84-1.90.9690.2555.525592676665720.29697.1
1.9-1.960.9820.1936.8724769651263610.22497.7
1.96-2.030.9890.1419.0123919630861550.16497.6
2.03-2.110.9920.11411.0723197611959890.13297.9
2.11-2.190.9940.09213.222304588757650.10797.9
2.19-2.290.9950.07615.5321309563655290.08998.1
2.29-2.40.9960.06817.220388540053060.07998.3
2.4-2.530.9960.05820.1819270511050410.06898.6
2.53-2.690.9970.0522.6618225487148010.05998.6
2.69-2.870.9980.04325.6716953456945060.0598.6
2.87-3.10.9980.03829.415724424941990.04498.8
3.1-3.40.9980.03332.6214419392338740.03998.8
3.4-3.80.9990.02935.1312923354735050.03498.8
3.8-4.390.9990.02737.1111519315631140.03198.7
4.39-5.380.9990.02537.829681265026170.02998.8
5.38-7.60.9990.02637.747600208420520.03198.5
7.60.9990.02437.873795116810830.02992.7

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(phenix.refine: dev_1769)refinement
Cootmodel building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EU1, native structure

4eu1


Resolution: 1.7→38.088 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1829 4844 4.99 %
Rwork0.1526 92310 -
obs0.1542 97154 97.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.93 Å2 / Biso mean: 29.5852 Å2 / Biso min: 11.41 Å2
Refinement stepCycle: final / Resolution: 1.7→38.088 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5772 0 50 794 6616
Biso mean--27.22 36.26 -
Num. residues----760
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016057
X-RAY DIFFRACTIONf_angle_d1.1558261
X-RAY DIFFRACTIONf_chiral_restr0.055925
X-RAY DIFFRACTIONf_plane_restr0.0061078
X-RAY DIFFRACTIONf_dihedral_angle_d14.342201
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.71930.221470.21173036318397
1.7193-1.73950.23351580.20783051320997
1.7395-1.76080.26461690.19983008317797
1.7608-1.7830.24071480.20183082323097
1.783-1.80650.22951460.19023047319397
1.8065-1.83130.2211540.18273062321697
1.8313-1.85740.18971590.16843010316997
1.8574-1.88510.20781500.17523066321698
1.8851-1.91460.22021730.17343010318397
1.9146-1.9460.21191780.17343081325997
1.946-1.97950.20451460.16993059320598
1.9795-2.01550.20461530.16293069322298
2.0155-2.05430.17761560.1563067322398
2.0543-2.09620.20691550.15823043319898
2.0962-2.14180.19071750.1543090326598
2.1418-2.19160.16491790.14773061324098
2.1916-2.24640.18341540.1453064321898
2.2464-2.30720.1921710.15073091326298
2.3072-2.3750.16921600.14833060322098
2.375-2.45170.17621480.14463105325399
2.4517-2.53930.17381830.1513099328299
2.5393-2.64090.22351670.15353082324999
2.6409-2.76110.21541450.1573135328099
2.7611-2.90660.16911520.15793110326299
2.9066-3.08870.20031700.16353123329399
3.0887-3.3270.16951770.15493111328899
3.327-3.66160.2111680.15253110327899
3.6616-4.19080.14251490.13383139328899
4.1908-5.27780.14771870.12443122330999
5.2778-38.09790.16431670.14593117328497
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)
12.51040.0757-0.41571.3859-0.30142.6522-0.39180.0893-0.1141-0.02660.21560.16681.1094-1.09930.01070.4703-0.1880.03880.3628-0.03370.266229.236712.073450.3633
20.9121-0.6019-0.54350.87520.29552.4049-0.0094-0.1927-0.05020.03410.0206-0.22770.14920.5659-0.01920.15170.036-0.02690.2382-0.0110.217446.968427.738969.6622
30.69780.2433-0.08071.00360.17761.81590.07150.02540.1950.0049-0.01470.0305-0.5349-0.1592-0.08350.24560.04470.03230.1250.02680.187435.007242.197658.6294
40.909-0.2239-0.48980.66040.18672.05420.21780.15640.1762-0.12640.02290.1094-0.6594-0.3541-0.14640.26050.060.01080.2060.03370.192532.41238.811347.3911
51.1643-0.0177-0.560.62940.08712.51680.10120.04920.1567-0.08070.0325-0.1084-0.26450.2349-0.08760.162-0.01110.03140.1134-0.01360.180344.767935.927552.0136
61.7673-0.1537-0.56151.17-0.05781.950.0551-0.12330.07950.11230.0056-0.009-0.00490.365-0.08140.20710.0187-0.0070.182-0.00340.143441.511431.27172.2584
71.729-0.21121.15410.8809-0.13864.4190.03870.1501-0.2014-0.14140.0398-0.08580.96250.3703-0.13960.37640.04690.04430.1782-0.03630.237143.974114.022645.1919
80.7737-0.00180.34940.3970.36892.2258-0.05410.2781-0.09070.08330.03280.22730.9811-1.01560.00560.2999-0.2162-0.00230.5162-0.01990.23129.036819.150435.4979
90.6694-0.4079-1.02950.53820.06272.7454-0.0916-0.1616-0.0057-0.03660.1141-0.11250.27350.6055-0.040.17820.00890.01120.21770.0060.224836.342419.247384.3977
101.9334-0.54431.06750.7098-0.11720.696-0.05240.1909-0.342-0.17340.13520.49110.31-0.9396-0.11230.2219-0.1227-0.06430.43190.02230.293510.484718.016274.1219
110.7992-0.0474-0.93161.03550.07072.81480.08210.15240.1185-0.02170.03920.1365-0.1618-0.5594-0.0520.09190.0433-0.02340.20510.03560.195116.38331.063181.2427
121.10721.15050.72933.06782.68894.5578-0.0059-0.1021-0.06860.1239-0.04650.02340.488-0.12850.00350.19040.0174-0.00170.13020.02560.184325.960114.783396.5719
131.9482-0.4918-0.26760.8050.39462.37670.1093-0.27330.2350.11560.0676-0.2739-0.09620.6593-0.13470.1501-0.0281-0.01390.3205-0.05390.220834.30430.1284104.4945
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 44 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 90 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 91 through 120 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 121 through 148 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 149 through 255 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 256 through 291 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 292 through 323 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 324 through 388 )A0
9X-RAY DIFFRACTION9chain 'B' and (resid 9 through 60 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 61 through 83 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 84 through 291 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 292 through 322 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 323 through 388 )B0

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