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

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Basic information

Entry
Database: PDB / ID: 6jkt
TitleCrystal structure of aspartate transcarbamoylase from Trypanosoma cruzi in complex with N-(PHOSPHONACETYL)-L-ASPARTIC ACID (PALA).
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
N-(PHOSPHONACETYL)-L-ASPARTIC ACID / aspartate carbamoyltransferase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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

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)218,91618
Polymers216,8336
Non-polymers2,08312
Water7,566420
1
A: Aspartate carbamoyltransferase
B: Aspartate carbamoyltransferase
C: Aspartate carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,4589
Polymers108,4163
Non-polymers1,0426
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9620 Å2
ΔGint-37 kcal/mol
Surface area32270 Å2
MethodPISA
2
D: Aspartate carbamoyltransferase
E: Aspartate carbamoyltransferase
F: Aspartate carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,4589
Polymers108,4163
Non-polymers1,0426
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8960 Å2
ΔGint-37 kcal/mol
Surface area33220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.289, 157.262, 88.725
Angle α, β, γ (deg.)90.00, 119.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Aspartate carbamoyltransferase / Putative aspartate carbamoyltransferase


Mass: 36138.820 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-PAL / N-(PHOSPHONACETYL)-L-ASPARTIC ACID


Mass: 255.119 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H10NO8P
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 420 / 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: 2.46 Å3/Da / Density % sol: 50.07 %
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: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 24, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 92925 / % possible obs: 99.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 8.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 9274 / % possible all: 100

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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: 2.3→29.44 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.911 / SU B: 12.962 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.295 / ESU R Free: 0.216 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22145 4640 5 %RANDOM
Rwork0.16848 ---
obs0.17112 88009 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 22.712 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.3→29.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14629 0 132 420 15181
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02215008
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4811.97820283
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15151884
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.07123.355617
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.209152717
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.39415122
X-RAY DIFFRACTIONr_chiral_restr0.1660.22403
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110965
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_it0.611.59424
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.208215208
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.23135584
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6244.55072
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: 2.301→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 340 -
Rwork0.186 6384 -
obs--98.56 %
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)
10.61660.1043-0.04880.0662-0.00010.1726-0.0138-0.0333-0.0072-0.00630.0036-0.0154-0.0005-0.04060.01020.03930.0069-0.0070.01860.00390.0596-9.441719.03157.1676
20.30970.0035-0.13350.08280.0440.6127-0.04960.1033-0.0080.00120.05270.0216-0.0206-0.0091-0.00310.051-0.0277-0.01130.06730.01320.014215.550523.4724-24.4717
30.3146-0.02160.17670.1166-0.05990.43980.0052-0.0131-0.01260.00430.00920.0319-0.01380.0631-0.01430.0499-0.0057-0.01790.01880.00110.042730.891619.641613.4157
40.63560.1781-0.02810.07250.01660.1549-0.0252-0.073-0.0087-0.0125-0.00790.02590.00160.05290.03320.03170.01750.00720.03580.03030.061453.8388-18.503628.2519
50.3141-0.0090.06280.0677-0.05420.6014-0.04960.07430.0014-0.00340.0152-0.0380.0392-0.03580.03450.0501-0.02140.0040.0253-0.00720.038628.4293-22.4822-3.4333
60.69140.0514-0.39470.03140.02870.4875-0.0185-0.04640.0204-0.022-0.0043-0.00450.0259-0.04350.02280.0454-0.01720.01530.0336-0.0080.034513.0984-20.926735.1682
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 401
2X-RAY DIFFRACTION2B-1 - 401
3X-RAY DIFFRACTION3C4 - 401
4X-RAY DIFFRACTION4D0 - 401
5X-RAY DIFFRACTION5E0 - 401
6X-RAY DIFFRACTION6F3 - 401

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