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- PDB-7zst: Crystal Structure of truncated aspartate transcarbamoylase from P... -

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Basic information

Entry
Database: PDB / ID: 7zst
TitleCrystal Structure of truncated aspartate transcarbamoylase from Plasmodium falciparum in complex with FLA-01
ComponentsAspartate carbamoyltransferase
KeywordsTRANSFERASE / Aspartate transcarbamoylase / Plasmodium falciparum / fragment-based screening / inhibitor / malaria
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
Chem-JUF / aspartate carbamoyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWang, C. / Zhang, B. / Groves, M.R.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Scholarship Council China
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Discovery of Small-Molecule Allosteric Inhibitors of Pf ATC as Antimalarials.
Authors: Wang, C. / Zhang, B. / Kruger, A. / Du, X. / Visser, L. / Domling, A.S.S. / Wrenger, C. / Groves, M.R.
History
DepositionMay 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2022Group: Structure summary / Category: struct_keywords / Item: _struct_keywords.text
Revision 1.2Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 2, 2022Group: 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 1.4Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)121,7289
Polymers121,0523
Non-polymers6766
Water79344
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.284, 89.735, 137.052
Angle α, β, γ (deg.)90.000, 109.215, 90.000
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
32A
42C
53B
63C

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPPROPROAA47 - 38111 - 345
221ASPASPALAALABB47 - 37711 - 341
332ASPASPSERSERAA47 - 37211 - 336
442ASPASPSERSERCC47 - 37211 - 336
553ILEILESERSERBB46 - 37310 - 337
663ILEILESERSERCC46 - 37310 - 337

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Aspartate carbamoyltransferase


Mass: 40350.762 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Strain: isolate 3D7 / Gene: PF3D7_1344800 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A5K1K910, aspartate carbamoyltransferase

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Non-polymers , 5 types, 50 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-JUF / 2-azanyl-~{N}-(2-methoxyethyl)-5-phenyl-thiophene-3-carboxamide


Mass: 276.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H16N2O2S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.86 Å3/Da / Density % sol: 57.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 200mM NaCl, 15%(w/v)PEG3350, 100mM bis-tris propane, 2%(v/v)DMSO

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Data collection

DiffractionMean temperature: 291 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.5→49.504 Å / Num. obs: 47374 / % possible obs: 99.9 % / Redundancy: 2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.032 / Rpim(I) all: 0.032 / Rrim(I) all: 0.045 / Net I/σ(I): 13.3
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2 % / Rmerge(I) obs: 0.012 / Num. unique obs: 4608 / CC1/2: 0.878 / Rpim(I) all: 0.012 / Rrim(I) all: 0.016

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ILQ

5ilq


Resolution: 2.5→49.504 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.899 / SU B: 35.11 / SU ML: 0.341 / Cross valid method: FREE R-VALUE / ESU R: 0.456 / ESU R Free: 0.3
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2824 2448 5.168 %
Rwork0.2359 44924 -
all0.238 --
obs-47372 99.93 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 57.712 Å2
Baniso -1Baniso -2Baniso -3
1-2.637 Å2-0 Å2-4.35 Å2
2--0.688 Å2-0 Å2
3----0.235 Å2
Refinement stepCycle: LAST / Resolution: 2.5→49.504 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7749 0 42 44 7835
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0137923
X-RAY DIFFRACTIONr_bond_other_d0.0010.0157606
X-RAY DIFFRACTIONr_angle_refined_deg1.6711.6410698
X-RAY DIFFRACTIONr_angle_other_deg1.2251.58717557
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7365954
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.04923.97403
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.024101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.952151472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8251531
X-RAY DIFFRACTIONr_chiral_restr0.0750.21076
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028824
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021770
X-RAY DIFFRACTIONr_nbd_refined0.2230.21667
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.27528
X-RAY DIFFRACTIONr_nbtor_refined0.1660.23891
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.23934
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.2205
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1890.210
X-RAY DIFFRACTIONr_metal_ion_refined0.1570.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1820.212
X-RAY DIFFRACTIONr_nbd_other0.2640.241
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3790.23
X-RAY DIFFRACTIONr_mcbond_it1.1932.2383837
X-RAY DIFFRACTIONr_mcbond_other1.1932.2383836
X-RAY DIFFRACTIONr_mcangle_it2.0623.3514784
X-RAY DIFFRACTIONr_mcangle_other2.0623.3514785
X-RAY DIFFRACTIONr_scbond_it0.9732.3314086
X-RAY DIFFRACTIONr_scbond_other0.9382.3254078
X-RAY DIFFRACTIONr_scangle_it1.6313.4555914
X-RAY DIFFRACTIONr_scangle_other1.6053.4475903
X-RAY DIFFRACTIONr_lrange_it4.05626.1778692
X-RAY DIFFRACTIONr_lrange_other4.01426.1678689
X-RAY DIFFRACTIONr_ncsr_local_group_10.0990.0510381
X-RAY DIFFRACTIONr_ncsr_local_group_20.1140.0510115
X-RAY DIFFRACTIONr_ncsr_local_group_30.1090.0510220
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.099170.05008
12BX-RAY DIFFRACTIONLocal ncs0.099170.05008
23AX-RAY DIFFRACTIONLocal ncs0.114470.05008
24CX-RAY DIFFRACTIONLocal ncs0.114470.05008
35BX-RAY DIFFRACTIONLocal ncs0.108820.05008
36CX-RAY DIFFRACTIONLocal ncs0.108820.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.5650.361790.3313329X-RAY DIFFRACTION100
2.565-2.6350.3341550.3083226X-RAY DIFFRACTION99.9704
2.635-2.7120.3581800.3243137X-RAY DIFFRACTION99.9699
2.712-2.7950.3411750.3013008X-RAY DIFFRACTION99.9686
2.795-2.8860.3431540.2872963X-RAY DIFFRACTION99.9679
2.886-2.9880.3691480.2782887X-RAY DIFFRACTION99.9671
2.988-3.10.331550.2782745X-RAY DIFFRACTION100
3.1-3.2270.3061600.2822633X-RAY DIFFRACTION99.9284
3.227-3.370.2981420.2592536X-RAY DIFFRACTION99.8881
3.37-3.5350.2891290.2662434X-RAY DIFFRACTION99.922
3.535-3.7250.3531270.2592334X-RAY DIFFRACTION99.8377
3.725-3.9510.291080.2322202X-RAY DIFFRACTION99.9567
3.951-4.2240.2451140.222047X-RAY DIFFRACTION99.9538
4.224-4.5610.2611190.1991930X-RAY DIFFRACTION99.9512
4.561-4.9960.2351060.1761770X-RAY DIFFRACTION99.9467
4.996-5.5840.245850.211585X-RAY DIFFRACTION99.8207
5.584-6.4440.301810.2161428X-RAY DIFFRACTION99.9338
6.444-7.8850.214650.1991231X-RAY DIFFRACTION100
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)
11.17970.13570.49242.3464-0.90684.12430.07560.0732-0.0407-0.512-0.00440.11510.17450.1225-0.07120.19-0.0443-0.16810.2474-0.04910.438120.199337.7094-16.9284
21.84180.60961.29381.3951-0.23042.5339-0.0009-0.06520.00630.0298-0.0885-0.0442-0.0310.18720.08940.0217-0.0718-0.02990.3449-0.08120.434945.016249.830216.7034
30.94970.3530.43043.491-0.02990.85230.1558-0.1781-0.3933-0.0005-0.01740.06860.4947-0.0135-0.13840.3613-0.0911-0.16830.51080.13140.597628.84389.58915.2734
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA47 - 382
2X-RAY DIFFRACTION1ALLA401
3X-RAY DIFFRACTION2ALLB46 - 377
4X-RAY DIFFRACTION3ALLC44 - 373

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