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- PDB-6jl5: Crystal structure of aspartate transcarbamoylase from Trypanosoma... -

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Basic information

Entry
Database: PDB / ID: 6jl5
TitleCrystal structure of aspartate transcarbamoylase from Trypanosoma cruzi in complex with aspartate (Asp) and 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 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
ASPARTIC ACID / PHOSPHATE ION / aspartate carbamoyltransferase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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

Downloads & links

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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)220,28024
Polymers218,3596
Non-polymers1,92118
Water9,440524
1
A: Aspartate carbamoyltransferase
B: Aspartate carbamoyltransferase
C: Aspartate carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,14012
Polymers109,1793
Non-polymers9619
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8650 Å2
ΔGint-46 kcal/mol
Surface area32910 Å2
MethodPISA
2
D: Aspartate carbamoyltransferase
E: Aspartate carbamoyltransferase
F: Aspartate carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,14012
Polymers109,1793
Non-polymers9619
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8720 Å2
ΔGint-45 kcal/mol
Surface area32590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.696, 158.017, 88.901
Angle α, β, γ (deg.)90.00, 119.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Aspartate carbamoyltransferase / Putative aspartate carbamoyltransferase


Mass: 36393.125 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H7NO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 524 / 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: 2.49 Å3/Da / Density % sol: 50.54 %
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: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 20, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 133035 / % possible obs: 97.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 6.6
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 2 / Num. unique obs: 11182 / % possible all: 94.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JKQ

6jkq


Resolution: 2.05→29.55 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 8.618 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.161 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21596 6539 5.1 %RANDOM
Rwork0.17482 ---
obs0.17689 122813 97.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 22.865 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.05→29.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14687 0 120 524 15331
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02215040
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.97920324
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.34651893
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.15523.468620
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.21152733
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.13115121
X-RAY DIFFRACTIONr_chiral_restr0.10.22406
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110979
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.7881.59507
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.44215333
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4435533
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8864.54989
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 482 -
Rwork0.226 8783 -
obs--94.96 %
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)
10.6080.31530.0090.22760.0120.1583-0.0226-0.0880.0147-0.0363-0.02620.05140.01950.0580.04870.03810.01650.01650.04370.03570.080132.1011-40.569866.8409
20.4450.00090.15330.0719-0.06870.5891-0.07830.10280.02360.0120.0361-0.04420.0503-0.0440.04220.0702-0.03010.00520.0485-0.01530.04226.5596-44.123935.0016
30.6264-0.0397-0.4610.06630.07990.5041-0.0076-0.05060.032-0.03810.0029-0.0160.0292-0.04880.00470.0494-0.02010.03040.0759-0.00710.0304-8.6716-42.550673.0414
40.65170.0977-0.12020.043-0.00710.1052-0.0156-0.0292-0.0408-0.0125-0.0023-0.0359-0.0239-0.04690.01790.04280.0082-0.01440.0410.00330.08-31.5873-2.402245.7633
50.3709-0.0723-0.19420.13550.11430.5491-0.04310.0882-0.02660.0120.03940.0413-0.0260.01890.00380.0718-0.03-0.01010.05560.00760.0316-6.34542.215714.0877
60.2881-0.07990.22370.1941-0.11880.4771-0.0001-0.0214-0.017-0.02770.02270.0418-0.01660.0788-0.02250.0561-0.0108-0.02210.0408-0.00290.058.9516-1.7551.9943
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 501
2X-RAY DIFFRACTION2B0 - 501
3X-RAY DIFFRACTION3C2 - 501
4X-RAY DIFFRACTION4D-1 - 501
5X-RAY DIFFRACTION5E-3 - 501
6X-RAY DIFFRACTION6F3 - 501

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