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- PDB-6jl6: Crystal structure of aspartate transcarbamoylase from Trypanosoma... -

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Basic information

Entry
Database: PDB / ID: 6jl6
TitleCrystal structure of aspartate transcarbamoylase from Trypanosoma cruzi in complex with phosphate (Pi).
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/ornithine carbamoyltransferase / Aspartate 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
ASPARTIC ACID / PHOSPHATE ION / aspartate carbamoyltransferase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 4, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,7198
Polymers216,4916
Non-polymers2282
Water7,819434
1
A: Aspartate carbamoyltransferase
B: Aspartate carbamoyltransferase
C: Aspartate carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,3784
Polymers108,2453
Non-polymers1331
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-19 kcal/mol
Surface area33670 Å2
MethodPISA
2
D: Aspartate carbamoyltransferase
E: Aspartate carbamoyltransferase
F: Aspartate carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,3404
Polymers108,2453
Non-polymers951
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-27 kcal/mol
Surface area34520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.420, 158.607, 89.200
Angle α, β, γ (deg.)90.00, 119.69, 90.00
Int Tables number4
Space group name H-MP1211

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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
#2: Chemical ChemComp-ASP / ASPARTIC ACID / Aspartic acid


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO4
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 434 / 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: 2.5 Å3/Da / Density % sol: 50.9 %
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, 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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 20, 2017
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→50 Å / Num. obs: 143565 / % possible obs: 99.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 9.1
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 7167 / % possible all: 100

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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: 6JKQ

6jkq


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.133 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.158 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2226 6710 5 %RANDOM
Rwork0.18504 ---
obs0.18691 127417 93.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.803 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å2-0.11 Å2
2--0.84 Å20 Å2
3----0.31 Å2
Refinement stepCycle: 1 / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14344 0 14 434 14792
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01914579
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214510
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.97419705
X-RAY DIFFRACTIONr_angle_other_deg0.954333301
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.30651837
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.47723.406596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.479152653
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.71315116
X-RAY DIFFRACTIONr_chiral_restr0.0770.22354
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216126
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023170
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_it1.5172.6437399
X-RAY DIFFRACTIONr_mcbond_other1.5172.6437398
X-RAY DIFFRACTIONr_mcangle_it2.4633.9459219
X-RAY DIFFRACTIONr_mcangle_other2.4633.9459220
X-RAY DIFFRACTIONr_scbond_it1.792.9197180
X-RAY DIFFRACTIONr_scbond_other1.792.9197180
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9784.27810486
X-RAY DIFFRACTIONr_long_range_B_refined4.57320.71115637
X-RAY DIFFRACTIONr_long_range_B_other4.56120.67615552
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 358 -
Rwork0.233 7209 -
obs--72.03 %

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