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

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Basic information

Entry
Database: PDB / ID: 7zgs
TitleCrystal Structure of truncated aspartate transcarbamoylase from Plasmodium falciparum with bound inhibitor 2-phenylethan-1-amine
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
3-PHENYLPROPYLAMINE / aspartate carbamoyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.349 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 4, 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)121,6739
Polymers121,0523
Non-polymers6216
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7900 Å2
ΔGint-58 kcal/mol
Surface area38410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.850, 104.368, 87.048
Angle α, β, γ (deg.)90.000, 117.525, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
32A
42C
53B
63C

NCS domain segments:

End auth comp-ID: PHE / End label comp-ID: PHE

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111TYRTYRAA39 - 3833 - 347
211TYRTYRBB39 - 3833 - 347
322TYRTYRAA39 - 3833 - 347
422TYRTYRCC39 - 3833 - 347
533PHEPHEBB38 - 3832 - 347
633PHEPHECC38 - 3832 - 347

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-PRA / 3-PHENYLPROPYLAMINE


Mass: 135.206 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H13N / Feature type: SUBJECT OF INVESTIGATION / Comment: alkaloid*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.86 Å3/Da / Density % sol: 56.98 %
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: Dec 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.349→45.131 Å / Num. obs: 56561 / % possible obs: 98.4 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.04 / Rrim(I) all: 0.058 / Net I/σ(I): 16.4
Reflection shellResolution: 2.35→2.41 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.459 / Num. unique obs: 4298 / CC1/2: 0.824 / Rpim(I) all: 0.448 / Rrim(I) all: 0.642

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Processing

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

5ilq


Resolution: 2.349→45.131 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.901 / WRfactor Rfree: 0.265 / WRfactor Rwork: 0.21 / SU B: 21.436 / SU ML: 0.229 / Average fsc free: 0.8494 / Average fsc work: 0.8693 / Cross valid method: FREE R-VALUE / ESU R: 0.326 / ESU R Free: 0.256
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2723 2711 4.796 %
Rwork0.2167 53820 -
all0.219 --
obs-56531 98.264 %
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: 59.972 Å2
Baniso -1Baniso -2Baniso -3
1--1.848 Å20 Å20.865 Å2
2--3.492 Å20 Å2
3----1.649 Å2
Refinement stepCycle: LAST / Resolution: 2.349→45.131 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8117 0 41 59 8217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0138311
X-RAY DIFFRACTIONr_bond_other_d0.0010.0157939
X-RAY DIFFRACTIONr_angle_refined_deg1.8321.6411223
X-RAY DIFFRACTIONr_angle_other_deg1.2341.58618327
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3495996
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.37424.048420
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.542151532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2561530
X-RAY DIFFRACTIONr_chiral_restr0.0810.21122
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029256
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021888
X-RAY DIFFRACTIONr_nbd_refined0.2230.21757
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.27684
X-RAY DIFFRACTIONr_nbtor_refined0.1710.24008
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.24145
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2186
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0780.21
X-RAY DIFFRACTIONr_metal_ion_refined0.090.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.230.223
X-RAY DIFFRACTIONr_nbd_other0.2750.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.440.25
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1150.21
X-RAY DIFFRACTIONr_mcbond_it2.8554.2814002
X-RAY DIFFRACTIONr_mcbond_other2.8554.2814001
X-RAY DIFFRACTIONr_mcangle_it4.4246.4174992
X-RAY DIFFRACTIONr_mcangle_other4.4246.4174993
X-RAY DIFFRACTIONr_scbond_it2.8754.4954309
X-RAY DIFFRACTIONr_scbond_other2.8444.4934302
X-RAY DIFFRACTIONr_scangle_it4.366.6346231
X-RAY DIFFRACTIONr_scangle_other4.346.6316220
X-RAY DIFFRACTIONr_lrange_it6.69249.7449123
X-RAY DIFFRACTIONr_lrange_other6.67849.7279114
X-RAY DIFFRACTIONr_ncsr_local_group_10.1160.0510329
X-RAY DIFFRACTIONr_ncsr_local_group_20.1160.0510406
X-RAY DIFFRACTIONr_ncsr_local_group_30.1210.0510600
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.116130.05008
12BX-RAY DIFFRACTIONLocal ncs0.116130.05008
23AX-RAY DIFFRACTIONLocal ncs0.11610.05008
24CX-RAY DIFFRACTIONLocal ncs0.11610.05008
35BX-RAY DIFFRACTIONLocal ncs0.120910.05008
36CX-RAY DIFFRACTIONLocal ncs0.120910.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.349-2.410.3711820.3173925X-RAY DIFFRACTION97.0922
2.41-2.4760.3311950.33906X-RAY DIFFRACTION98.6766
2.476-2.5480.3221770.273760X-RAY DIFFRACTION98.4989
2.548-2.6260.3071820.2553656X-RAY DIFFRACTION98.5366
2.626-2.7120.2761800.2573574X-RAY DIFFRACTION98.5819
2.712-2.8070.2831850.2073408X-RAY DIFFRACTION98.6546
2.807-2.9130.2922270.2143270X-RAY DIFFRACTION98.8691
2.913-3.0320.2511720.2083165X-RAY DIFFRACTION99.0208
3.032-3.1660.2851490.2153091X-RAY DIFFRACTION98.6602
3.166-3.3210.2771700.2042904X-RAY DIFFRACTION98.6205
3.321-3.50.2671300.2062802X-RAY DIFFRACTION98.5546
3.5-3.7120.2611120.2052620X-RAY DIFFRACTION97.711
3.712-3.9680.2761220.2112486X-RAY DIFFRACTION97.8245
3.968-4.2860.238830.1912306X-RAY DIFFRACTION98.1512
4.286-4.6940.203800.1822135X-RAY DIFFRACTION97.2344
4.694-5.2470.262850.2031925X-RAY DIFFRACTION97.7626
5.247-6.0560.3051410.2371633X-RAY DIFFRACTION97.419
6.056-7.4110.317670.2311471X-RAY DIFFRACTION98.653
7.411-10.4540.21390.1941140X-RAY DIFFRACTION97.7612
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)
13.9518-0.8209-0.27530.73140.03651.5398-0.03220.1989-0.1427-0.030.0458-0.05690.13920.2165-0.01360.0575-0.00920.01060.1858-0.00310.036150.68170.212113.288
21.9917-0.0484-0.98251.0821-1.12663.0599-0.04780.0261-0.16830.10690.01360.10330.2011-0.09690.03430.0824-0.02710.01880.0241-0.00170.047721.5641-4.724145.4852
31.83950.21960.72941.0145-0.34663.2764-0.02150.41140.0284-0.13190.04840.2770.0517-0.2-0.02680.0217-0.0255-0.02950.30030.03210.1498.82339.21196.5509
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA39 - 383
2X-RAY DIFFRACTION2ALLB38 - 383
3X-RAY DIFFRACTION3ALLC38 - 383

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