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- PDB-6hl7: Crystal structure of truncated aspartate transcarbamoylase from P... -

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Basic information

Entry
Database: PDB / ID: 6hl7
TitleCrystal structure of truncated aspartate transcarbamoylase from Plasmodium falciparum with mutated active site (R109A/K138A) and N-carbamoyl-L-phosphate bound
ComponentsAspartate transcarbamoylase
KeywordsTRANSFERASE / Falciparum Malaria Pyrimidine biosynthesis Trimer Mutant TRANSFERASE carbamoyl-phospahte
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 / membrane
Similarity search - Function
Aspartate carbamoyltransferase / Aspartate/ornithine carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / 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 ...Aspartate carbamoyltransferase / Aspartate/ornithine carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / 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
PHOSPHORIC ACID MONO(FORMAMIDE)ESTER / aspartate carbamoyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBosch, S.S. / Lunev, S. / Wrenger, C. / Groves, M.R.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation2013/10288-1 Brazil
Sao Paulo Research Foundation2013/17577-9 Brazil
Citation
Journal: Acs Infect Dis. / Year: 2020
Title: Molecular Target Validation of Aspartate Transcarbamoylase fromPlasmodium falciparumby Torin 2.
Authors: Bosch, S.S. / Lunev, S. / Batista, F.A. / Linzke, M. / Kronenberger, T. / Domling, A.S.S. / Groves, M.R. / Wrenger, C.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2016
Title: Crystal structure of truncated aspartate transcarbamoylase from Plasmodium falciparum.
Authors: Lunev, S. / Bosch, S.S. / de Assis Batista, F. / Wrenger, C. / Groves, M.R.
History
DepositionSep 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Mar 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.4May 20, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.5Jan 24, 2024Group: 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 transcarbamoylase
B: Aspartate transcarbamoylase
C: Aspartate transcarbamoylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,6405
Polymers120,3583
Non-polymers2822
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-45 kcal/mol
Surface area38580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.001, 89.715, 121.642
Angle α, β, γ (deg.)90.000, 122.170, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Aspartate transcarbamoylase


Mass: 40119.465 Da / Num. of mol.: 3 / Mutation: R109A, K138A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: ATCase / Production host: Escherichia coli (E. coli) / References: UniProt: O15804, aspartate carbamoyltransferase
#2: Chemical ChemComp-CP / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER


Mass: 141.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH4NO5P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 3.06 Å3/Da / Density % sol: 59.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.2M Potassium citrate tribasic monohydrate 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.5→57.61 Å / Num. obs: 46404 / % possible obs: 97.6 % / Observed criterion σ(I): 1.3 / Redundancy: 3.16 % / CC1/2: 0.999 / Rrim(I) all: 0.066 / Net I/σ(I): 12.95
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.21 % / Num. unique obs: 7154 / CC1/2: 0.619 / Rrim(I) all: 0.957 / % possible all: 94

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
EDNAdata collection
DIMPLEmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ilq

5ilq


Resolution: 2.5→57.61 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.928 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.432 / ESU R Free: 0.283
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2578 2399 5.2 %RANDOM
Rwork0.2042 ---
obs0.207 43356 98.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 163.5 Å2 / Biso mean: 65.452 Å2 / Biso min: 28.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å2-0.02 Å2
2--0.13 Å20 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 2.5→57.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7870 0 16 42 7928
Biso mean--96.34 54.42 -
Num. residues----974
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0138025
X-RAY DIFFRACTIONr_bond_other_d0.0350.0177485
X-RAY DIFFRACTIONr_angle_refined_deg1.9461.64210844
X-RAY DIFFRACTIONr_angle_other_deg2.4121.58117447
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0045967
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93224.24408
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.426151491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7861529
X-RAY DIFFRACTIONr_chiral_restr0.0880.21092
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028772
X-RAY DIFFRACTIONr_gen_planes_other0.010.021583
X-RAY DIFFRACTIONr_mcbond_it3.4216.9563889
X-RAY DIFFRACTIONr_mcbond_other3.426.9553888
X-RAY DIFFRACTIONr_mcangle_it5.47710.4254849
LS refinement shellResolution: 2.502→2.567 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 178 -
Rwork0.379 2969 -
all-3147 -
obs--91.72 %

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