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- PDB-6jkq: Crystal structure of aspartate transcarbamoylase from Trypanosoma... -

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Basic information

Entry
Database: PDB / ID: 6jkq
TitleCrystal structure of aspartate transcarbamoylase from Trypanosoma cruzi (Ligand-free form)
ComponentsAspartate carbamoyltransferase
KeywordsTRANSFERASE / ATCase / Pyrimidine metabolism
Function / homology
Function and homology information


aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / amino acid metabolic process / amino acid binding / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process
Similarity search - Function
Aspartate carbamoyltransferase / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
aspartate carbamoyltransferase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsMatoba, K. / Shiba, T. / Nara, T. / Aoki, T. / Nagasaki, S. / Hayamizu, R. / Honma, T. / Tanaka, A. / Inoue, M. / Matsuoka, S. ...Matoba, K. / Shiba, T. / Nara, T. / Aoki, T. / Nagasaki, S. / Hayamizu, R. / Honma, T. / Tanaka, A. / Inoue, M. / Matsuoka, S. / Balogun, E.O. / Inaoka, D.K. / Kita, K. / Harada, S.
CitationJournal: To Be Published
Title: Crystallographic snapshots of Trypanosoma cruzi aspartate transcarbamoylase revealed an ordered Bi-Bi reaction mechanism
Authors: Matoba, K. / Shiba, T. / Nara, T. / Aoki, T. / Nagasaki, S. / Hayamizu, R. / Honma, T. / Tanaka, A. / Inoue, M. / Matsuoka, S. / Balogun, E.O. / Inaoka, D.K. / Kita, K. / Harada, S.
History
DepositionMar 1, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aspartate carbamoyltransferase
B: Aspartate carbamoyltransferase
C: Aspartate carbamoyltransferase
D: Aspartate carbamoyltransferase
E: Aspartate carbamoyltransferase
F: Aspartate carbamoyltransferase


Theoretical massNumber of molelcules
Total (without water)216,4916
Polymers216,4916
Non-polymers00
Water00
1
A: Aspartate carbamoyltransferase
B: Aspartate carbamoyltransferase
C: Aspartate carbamoyltransferase


Theoretical massNumber of molelcules
Total (without water)108,2453
Polymers108,2453
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-19 kcal/mol
Surface area34230 Å2
MethodPISA
2
D: Aspartate carbamoyltransferase
E: Aspartate carbamoyltransferase
F: Aspartate carbamoyltransferase


Theoretical massNumber of molelcules
Total (without water)108,2453
Polymers108,2453
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-16 kcal/mol
Surface area33690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.419, 79.282, 92.016
Angle α, β, γ (deg.)69.56, 82.90, 63.25
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Aspartate carbamoyltransferase / Putative aspartate carbamoyltransferase


Mass: 36081.766 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: C3747_31g124 / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / References: UniProt: O15636, aspartate carbamoyltransferase

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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: 2.21 Å3/Da / Density % sol: 44.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 10% PEG 3350, 0.1 M acetate buffer pH 4.6, 0.2 M ammonium acetate, 0.01 M cobalt chloride and 3% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: IMAGE PLATE / Date: May 22, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 44850 / % possible obs: 97.7 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 15.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 4436 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ML4

1ml4


Resolution: 2.81→29.51 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.88 / SU B: 15.011 / SU ML: 0.3 / Cross valid method: THROUGHOUT / ESU R Free: 0.446 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26547 2205 5.1 %RANDOM
Rwork0.1778 ---
obs0.18214 41411 96.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 54.247 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å2-0.14 Å20.09 Å2
2---0.03 Å20.12 Å2
3----0.46 Å2
Refinement stepCycle: 1 / Resolution: 2.81→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13949 0 0 0 13949
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01914175
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214113
X-RAY DIFFRACTIONr_angle_refined_deg1.5591.97419163
X-RAY DIFFRACTIONr_angle_other_deg1.01332377
X-RAY DIFFRACTIONr_dihedral_angle_1_deg751785
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.69623.322578
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.87152570
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.05615114
X-RAY DIFFRACTIONr_chiral_restr0.0810.22293
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02115671
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023091
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_it3.2235.2677194
X-RAY DIFFRACTIONr_mcbond_other3.2215.2677193
X-RAY DIFFRACTIONr_mcangle_it5.0697.8888961
X-RAY DIFFRACTIONr_mcangle_other5.0697.8888962
X-RAY DIFFRACTIONr_scbond_it3.2075.6336981
X-RAY DIFFRACTIONr_scbond_other3.2065.6336981
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2338.31910202
X-RAY DIFFRACTIONr_long_range_B_refined7.36340.40914813
X-RAY DIFFRACTIONr_long_range_B_other7.36340.4114814
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.808→2.88 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 139 -
Rwork0.198 2678 -
obs--85.49 %

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