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

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Basic information

Entry
Database: PDB / ID: 7zid
TitleCrystal Structure of truncated aspartate transcarbamoylase from Plasmodium falciparum in complex with BDA-14
ComponentsAspartate carbamoyltransferase
KeywordsTRANSFERASE / Aspartate transcarbamoylase / Plasmodium falciparum / fragment-based screening / inhibitor.
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-EIZ / aspartate carbamoyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsWang, C. / Zhang, B.
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
DepositionApr 7, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 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 1.2Nov 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 1.3Jan 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)121,7918
Polymers121,0523
Non-polymers7395
Water46826
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)119.260, 90.016, 136.942
Angle α, β, γ (deg.)90.000, 108.866, 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:

Beg auth comp-ID: ASP / Beg label comp-ID: ASP

Dom-IDComponent-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PROPROAA49 - 38113 - 345
221ALAALABB49 - 37713 - 341
332GLNGLNAA49 - 38213 - 346
442GLNGLNCC49 - 38213 - 346
553ALAALABB47 - 37711 - 341
663SERSERCC47 - 37911 - 343

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

#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
#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-EIZ / tert-butyl N-[3-(2-hydroxyethylcarbamoyl)-5-phenyl-thiophen-2-yl]carbamate / (2S)-2-[[(2S)-4-methyl-2-(phenylmethoxycarbonylamino)pentanoyl]amino]-1-oxidanyl-hexane-1-sulfonic acid


Type: Peptide-like / Class: Inhibitor / Mass: 362.443 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H22N2O4S / Feature type: SUBJECT OF INVESTIGATION / References: BIRD: PRD_002386
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
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: 2.87 Å3/Da / Density % sol: 57.19 %
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: Feb 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.55→45.599 Å / Num. obs: 43972 / % possible obs: 98.1 % / Redundancy: 1.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.045 / Rrim(I) all: 0.063 / Net I/σ(I): 9.4
Reflection shellResolution: 2.55→2.65 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.045 / Num. unique obs: 43972 / CC1/2: 0.609 / Rpim(I) all: 0.045 / Rrim(I) all: 0.063

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Processing

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

5ilq


Resolution: 2.55→45.599 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.247 / WRfactor Rwork: 0.202 / SU B: 32.499 / SU ML: 0.292 / Average fsc free: 0.8519 / Average fsc work: 0.8707 / Cross valid method: FREE R-VALUE / ESU R: 0.458 / ESU R Free: 0.277
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.244 2205 5.015 %
Rwork0.1991 41766 -
all0.201 --
obs-43971 97.994 %
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: 76.47 Å2
Baniso -1Baniso -2Baniso -3
1-2.141 Å2-0 Å2-5.08 Å2
2---0.872 Å20 Å2
3---1.785 Å2
Refinement stepCycle: LAST / Resolution: 2.55→45.599 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7824 0 47 26 7897
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0138007
X-RAY DIFFRACTIONr_bond_other_d0.0010.0157668
X-RAY DIFFRACTIONr_angle_refined_deg1.7791.64210812
X-RAY DIFFRACTIONr_angle_other_deg1.2691.58717703
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8915963
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.79323.878410
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.644151485
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4451532
X-RAY DIFFRACTIONr_chiral_restr0.0830.21086
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028920
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021792
X-RAY DIFFRACTIONr_nbd_refined0.2220.21709
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.27504
X-RAY DIFFRACTIONr_nbtor_refined0.1690.23935
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.24087
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2162
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1540.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1640.216
X-RAY DIFFRACTIONr_nbd_other0.2680.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0560.22
X-RAY DIFFRACTIONr_mcbond_it2.2173.3113873
X-RAY DIFFRACTIONr_mcbond_other2.2163.313872
X-RAY DIFFRACTIONr_mcangle_it3.6834.9544829
X-RAY DIFFRACTIONr_mcangle_other3.6824.9564830
X-RAY DIFFRACTIONr_scbond_it2.0383.4914134
X-RAY DIFFRACTIONr_scbond_other1.9873.4864127
X-RAY DIFFRACTIONr_scangle_it3.3615.1585983
X-RAY DIFFRACTIONr_scangle_other3.2975.155972
X-RAY DIFFRACTIONr_lrange_it5.95238.88775
X-RAY DIFFRACTIONr_lrange_other5.92538.7998775
X-RAY DIFFRACTIONr_ncsr_local_group_10.0990.0510241
X-RAY DIFFRACTIONr_ncsr_local_group_20.0980.0510218
X-RAY DIFFRACTIONr_ncsr_local_group_30.1020.0510206
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.099280.05008
12BX-RAY DIFFRACTIONLocal ncs0.099280.05008
23AX-RAY DIFFRACTIONLocal ncs0.098020.05008
24CX-RAY DIFFRACTIONLocal ncs0.098020.05008
35BX-RAY DIFFRACTIONLocal ncs0.102010.05008
36CX-RAY DIFFRACTIONLocal ncs0.102010.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.6160.3511450.3293105X-RAY DIFFRACTION98.8443
2.616-2.6880.3521400.3313041X-RAY DIFFRACTION98.9117
2.688-2.7660.3561740.3292907X-RAY DIFFRACTION98.6236
2.766-2.8510.3561580.3052840X-RAY DIFFRACTION98.7158
2.851-2.9440.341590.2872744X-RAY DIFFRACTION98.6744
2.944-3.0470.2911410.2742694X-RAY DIFFRACTION98.9184
3.047-3.1620.2621330.2392542X-RAY DIFFRACTION97.8062
3.162-3.2910.2561260.2192423X-RAY DIFFRACTION96.1524
3.291-3.4380.2671090.2112256X-RAY DIFFRACTION92.0592
3.438-3.6050.2461300.2072238X-RAY DIFFRACTION97.4486
3.605-3.80.2511180.1982190X-RAY DIFFRACTION99.5257
3.8-4.030.231040.1832046X-RAY DIFFRACTION98.8506
4.03-4.3080.231060.1811941X-RAY DIFFRACTION98.8411
4.308-4.6520.229850.1511794X-RAY DIFFRACTION97.7627
4.652-5.0950.1751080.1421637X-RAY DIFFRACTION98.2545
5.095-5.6950.239880.181512X-RAY DIFFRACTION98.5829
5.695-6.5730.262700.1931322X-RAY DIFFRACTION98.2357
6.573-8.0420.229540.1791147X-RAY DIFFRACTION98.362
8.042-11.3380.188400.142888X-RAY DIFFRACTION98.2011
11.338-45.5990.199170.234499X-RAY DIFFRACTION94.8529
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)
11.1870.36850.67112.7789-1.14254.5090.10170.084-0.0733-0.66750.05490.19960.28650.1498-0.15660.2561-0.0324-0.1770.433-0.04380.465920.284237.7586-17.0591
22.27771.0221.82992.172-0.35493.27050.020.0179-0.04290.0908-0.1538-0.1076-0.11620.32790.13380.0198-0.08930.01910.5487-0.07490.341145.39649.711516.5335
31.25690.66550.58394.56480.03921.25580.2169-0.2454-0.5189-0.06050.01270.13190.5838-0.0628-0.22950.4822-0.0956-0.20580.65280.15550.610728.57439.85615.3854
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA49 - 383
2X-RAY DIFFRACTION1ALLA401
3X-RAY DIFFRACTION2ALLB47 - 377
4X-RAY DIFFRACTION3ALLC47 - 382

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