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- PDB-6jl4: Crystal structure of aspartate transcarbamoylase from Trypanosoma... -

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Basic information

Entry
Database: PDB / ID: 6jl4
TitleCrystal structure of aspartate transcarbamoylase from Trypanosoma cruzi in complex with carbamoyl aspartate (CA) 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 / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER / N-CARBAMOYL-L-ASPARTATE / PHOSPHATE ION / aspartate carbamoyltransferase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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)217,94818
Polymers216,4916
Non-polymers1,45812
Water7,710428
1
A: Aspartate carbamoyltransferase
B: Aspartate carbamoyltransferase
C: Aspartate carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,0199
Polymers108,2453
Non-polymers7736
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8360 Å2
ΔGint-42 kcal/mol
Surface area32940 Å2
MethodPISA
2
D: Aspartate carbamoyltransferase
E: Aspartate carbamoyltransferase
F: Aspartate carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,9309
Polymers108,2453
Non-polymers6846
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7870 Å2
ΔGint-43 kcal/mol
Surface area32710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.992, 156.983, 88.302
Angle α, β, γ (deg.)90.00, 119.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 6 molecules ABCDEF

#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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Non-polymers , 5 types, 440 molecules

#2: Chemical ChemComp-NCD / N-CARBAMOYL-L-ASPARTATE


Mass: 176.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8N2O5
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H7NO4
#5: Chemical ChemComp-CP / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER


Mass: 141.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4NO5P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 2.44 Å3/Da / Density % sol: 49.56 %
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: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jan 22, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 81396 / % possible obs: 99.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 5.5
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4068 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JKQ

6jkq


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.898 / SU B: 18.16 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.483 / ESU R Free: 0.283 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24989 3869 5 %RANDOM
Rwork0.17564 ---
obs0.17937 73258 95.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.152 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å20.1 Å2
2---1.04 Å2-0 Å2
3---0.99 Å2
Refinement stepCycle: 1 / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14687 0 90 428 15205
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01914993
X-RAY DIFFRACTIONr_bond_other_d0.0010.0214872
X-RAY DIFFRACTIONr_angle_refined_deg1.5851.97820269
X-RAY DIFFRACTIONr_angle_other_deg0.826334140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.95551888
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62923.539616
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.141152725
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.77115118
X-RAY DIFFRACTIONr_chiral_restr0.0810.22409
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02116647
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023260
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 210 -
Rwork0.224 3933 -
obs--69.32 %
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)
10.50930.0784-0.30730.0362-0.00340.3702-0.00510.06040.00610.02260.00010.01360.01460.03630.0050.06660.0060.0220.1195-0.0070.009430.551738.4491-34.7407
20.4963-0.18040.04140.0805-0.02130.0899-0.01030.07390.0220.0207-0.0059-0.01150.0188-0.03060.01610.0707-0.0190.03110.0912-0.02250.0285-10.067440.7929-28.2144
30.234-0.09150.12630.14880.10580.5065-0.0896-0.0883-0.03080.02170.06750.04490.01510.03620.02210.08650.02930.01710.10160.01120.019215.809636.76413.6127
40.36450.1158-0.06010.0477-0.0120.0831-0.0127-0.0271-0.0327-0.01160.0092-0.0202-0.0135-0.03960.00350.06680.00310.01260.0950.00710.0324-53.9629-0.34886.8971
50.44040.0252-0.22170.14440.1560.4713-0.05860.1026-0.00410.02250.04520.03570.00220.03090.01340.0734-0.03020.0040.10230.00670.0189-28.32354.4134-24.5922
60.2678-0.13160.23320.1559-0.00250.38040.0031-0.0158-0.0151-0.01580.01990.014-0.0060.0515-0.0230.0669-0.0081-0.00040.11360.00030.012-13.35851.380713.5424
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 501
2X-RAY DIFFRACTION2B0 - 501
3X-RAY DIFFRACTION3C0 - 501
4X-RAY DIFFRACTION4D0 - 501
5X-RAY DIFFRACTION5E0 - 501
6X-RAY DIFFRACTION6F1 - 501

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