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- PDB-5iln: Crystal structure of Aspartate Transcarbamoylase from Plasmodium ... -

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Basic information

Entry
Database: PDB / ID: 5iln
TitleCrystal structure of Aspartate Transcarbamoylase from Plasmodium falciparum (PfATC) with bound citrate
ComponentsAspartate carbamoyltransferase
KeywordsTRANSFERASE / Plasmodium / Malaria / Aspartate / Pyrimidine Biosynthesis
Function / homology
Function and homology information


: / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / amino acid metabolic process / amino acid binding / membrane => GO:0016020 / 'de novo' pyrimidine nucleobase biosynthetic process / cytosol / cytoplasm
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
CITRATE ANION / PHOSPHATE ION / Aspartate carbamoyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsLunev, S. / Bosch, S.S. / Batista, F.D.A. / Wrenger, C. / Groves, M.R.
CitationJournal: To be published
Title: Crystal structure of truncated Aspartate Transcarbamoylase from Plasmodium falciparum
Authors: Lunev, S. / Bosch, S.S. / Batista, F.D.A. / Wrenger, C. / Groves, M.R.
History
DepositionMar 4, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.2May 1, 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,45911
Polymers133,6173
Non-polymers8428
Water2,990166
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.450, 107.290, 87.320
Angle α, β, γ (deg.)90.00, 117.46, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A55 - 102
2114B55 - 102
3114C55 - 102
1214A110 - 129
2214B110 - 129
3214C110 - 129
1314A140 - 156
2314B140 - 156
3314C140 - 156
1414A166 - 182
2414B166 - 182
3414C166 - 182
1514A186 - 218
2514B186 - 218
3514C186 - 218
1614A231 - 242
2614B231 - 242
3614C231 - 242
1714A257 - 269
2714B257 - 269
3714C257 - 269
1814A287 - 297
2814B287 - 297
3814C287 - 297
1914A314 - 374
2914B314 - 374
3914C314 - 374
1124A32 - 55
2124B32 - 55

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.493063, -0.362417, -0.790913), (0.032468, 0.900803, -0.433012), (0.869388, -0.239181, -0.432386)1.20684, 3.54681, 14.86001
3given(-0.47952, 0.017638, 0.877353), (-0.403608, 0.883339, -0.238352), (-0.779205, -0.468402, -0.41646)-12.82825, 0.54525, 8.14231
4given(1), (1), (1)
5given(-0.449219, -0.36004, -0.817663), (0.045766, 0.904729, -0.423522), (0.892249, -0.227676, -0.389944)2.65028, 3.15495, 14.90471

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Components

#1: Protein Aspartate carbamoyltransferase


Mass: 44539.012 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Gene: atcasE, MAL13P1.221 / Plasmid: pASK-IBA3-PfATC-full / Details (production host): full length pfATC / Cell line (production host): Rosetta 2(DE3) pLysS / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q8IDP8, aspartate carbamoyltransferase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Potassium citrate tribasic monohydrate, 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Oxford Cryostream - 700 series
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 2, 2015
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 2.21→45.1 Å / Num. obs: 69115 / % possible obs: 97.7 % / Redundancy: 2.9 % / CC1/2: 0.984 / Rmerge(I) obs: 0.108 / Rsym value: 0.112 / Net I/σ(I): 5
Reflection shellResolution: 2.21→2.29 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 0.8 / % possible all: 83.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
Cootmodel building
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PfATC-Met3

Resolution: 2.21→45.1 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.943 / SU B: 13.546 / SU ML: 0.18 / Cross valid method: FREE R-VALUE / ESU R: 0.209 / ESU R Free: 0.19 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23398 3470 5 %RANDOM
Rwork0.17957 ---
obs0.18224 65645 97.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 51.616 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.01 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.21→45.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8200 0 52 166 8418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.028390
X-RAY DIFFRACTIONr_bond_other_d0.0060.028094
X-RAY DIFFRACTIONr_angle_refined_deg2.2481.97411314
X-RAY DIFFRACTIONr_angle_other_deg1.188318678
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.33851004
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.18125.241395
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.153151575
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.891532
X-RAY DIFFRACTIONr_chiral_restr0.1320.21295
X-RAY DIFFRACTIONr_gen_planes_refined0.010.029294
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021872
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_it3.8634.8914031
X-RAY DIFFRACTIONr_mcbond_other3.8574.894030
X-RAY DIFFRACTIONr_mcangle_it5.7197.3225030
X-RAY DIFFRACTIONr_mcangle_other5.7187.3235031
X-RAY DIFFRACTIONr_scbond_it4.5615.344359
X-RAY DIFFRACTIONr_scbond_other4.5155.3374347
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.9367.7836267
X-RAY DIFFRACTIONr_long_range_B_refined8.94838.3489496
X-RAY DIFFRACTIONr_long_range_B_other8.94638.3489496
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A3736medium positional0.50.5
11B3736medium positional0.520.5
11C3736medium positional0.640.5
22A422medium positional0.960.5
11A3736medium thermal7.912
11B3736medium thermal4.152
11C3736medium thermal6.392
22A422medium thermal4.592
LS refinement shellResolution: 2.21→2.267 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 208 -
Rwork0.346 4032 -
obs--81.6 %
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDOrigin x (Å)Origin y (Å)Origin z (Å)
10.3506-30.5316-2.5612
2-10.1944-21.8888-17.9987
3-16.6502-25.783922.5691
4-23.8137-8.687535.9788
521.2896-27.23724.5608
622.794-7.384218.0922
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 148
2X-RAY DIFFRACTION2A149 - 338
3X-RAY DIFFRACTION3B31 - 165
4X-RAY DIFFRACTION4B166 - 337
5X-RAY DIFFRACTION5C32 - 102
6X-RAY DIFFRACTION6C103 - 339

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