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

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Basic information

Entry
Database: PDB / ID: 7zea
TitleCrystal Structure of truncated aspartate transcarbamoylase from Plasmodium falciparum with bound inhibitor O-benzylhydroxylamine
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
O-benzylhydroxylamine / aspartate carbamoyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.448 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
DepositionMar 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2022Group: Refinement description / Category: struct_ncs_ens / Item: _struct_ncs_ens.details
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)121,5148
Polymers121,0523
Non-polymers4615
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-80 kcal/mol
Surface area39080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.025, 104.507, 87.301
Angle α, β, γ (deg.)90.000, 117.470, 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 - A to B
2Local NCS retraints between domains - A to C
3Local NCS retraints between domains - B to C

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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-OBZ / O-benzylhydroxylamine


Mass: 123.152 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H9NO / Feature type: SUBJECT OF INVESTIGATION
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.91 Å3/Da / Density % sol: 57.73 %
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: 2.448→45.278 Å / Num. obs: 50829 / % possible obs: 99.4 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.048 / Rrim(I) all: 0.07 / Net I/σ(I): 11.3
Reflection shellResolution: 2.45→2.52 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.464 / Num. unique obs: 4363 / CC1/2: 0.852 / Rpim(I) all: 0.443 / Rrim(I) all: 0.643

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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: 2.448→45.278 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 19.309 / SU ML: 0.199 / Cross valid method: FREE R-VALUE / ESU R: 0.335 / ESU R Free: 0.23
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2231 2430 4.783 %
Rwork0.1821 48379 -
all0.184 --
obs-50809 99.306 %
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: 53.665 Å2
Baniso -1Baniso -2Baniso -3
1--1.472 Å20 Å20.097 Å2
2--4.451 Å20 Å2
3----1.999 Å2
Refinement stepCycle: LAST / Resolution: 2.448→45.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8117 0 29 134 8280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0138299
X-RAY DIFFRACTIONr_bond_other_d0.0010.0157918
X-RAY DIFFRACTIONr_angle_refined_deg1.871.6411210
X-RAY DIFFRACTIONr_angle_other_deg1.3471.58618279
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0375996
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.33324.048420
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.603151532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1321530
X-RAY DIFFRACTIONr_chiral_restr0.0890.21122
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029249
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021883
X-RAY DIFFRACTIONr_nbd_refined0.220.21663
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.27571
X-RAY DIFFRACTIONr_nbtor_refined0.1730.24116
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.23951
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2197
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1160.26
X-RAY DIFFRACTIONr_metal_ion_refined0.0990.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4860.222
X-RAY DIFFRACTIONr_nbd_other0.4430.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1380.22
X-RAY DIFFRACTIONr_mcbond_it2.5163.6564002
X-RAY DIFFRACTIONr_mcbond_other2.5143.6564001
X-RAY DIFFRACTIONr_mcangle_it3.9495.4794992
X-RAY DIFFRACTIONr_mcangle_other3.9495.4794993
X-RAY DIFFRACTIONr_scbond_it2.7553.9164297
X-RAY DIFFRACTIONr_scbond_other2.7133.9134290
X-RAY DIFFRACTIONr_scangle_it4.2925.7556218
X-RAY DIFFRACTIONr_scangle_other4.2735.756207
X-RAY DIFFRACTIONr_lrange_it6.42342.2839098
X-RAY DIFFRACTIONr_lrange_other6.38342.2419079
X-RAY DIFFRACTIONr_ncsr_local_group_10.0950.0510580
X-RAY DIFFRACTIONr_ncsr_local_group_20.0860.0510735
X-RAY DIFFRACTIONr_ncsr_local_group_30.1050.0510829
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.094790.05008
12BX-RAY DIFFRACTIONLocal ncs0.094790.05008
23AX-RAY DIFFRACTIONLocal ncs0.086410.05008
24CX-RAY DIFFRACTIONLocal ncs0.086410.05008
35BX-RAY DIFFRACTIONLocal ncs0.10460.05008
36CX-RAY DIFFRACTIONLocal ncs0.10460.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.448-2.5120.3091410.2983579X-RAY DIFFRACTION98.1271
2.512-2.5810.2991620.2793450X-RAY DIFFRACTION99.3126
2.581-2.6560.2742050.2583364X-RAY DIFFRACTION99.5259
2.656-2.7370.2961540.2423308X-RAY DIFFRACTION99.2546
2.737-2.8270.2541950.2163175X-RAY DIFFRACTION99.6747
2.827-2.9260.3031470.2183050X-RAY DIFFRACTION99.595
2.926-3.0360.2711550.2062974X-RAY DIFFRACTION99.745
3.036-3.160.2321410.1922893X-RAY DIFFRACTION99.508
3.16-3.3010.2191060.1822751X-RAY DIFFRACTION99.6512
3.301-3.4620.2261130.1912670X-RAY DIFFRACTION99.3929
3.462-3.6490.233910.1872539X-RAY DIFFRACTION99.7345
3.649-3.870.2021210.1812370X-RAY DIFFRACTION99.6002
3.87-4.1360.2121330.1592220X-RAY DIFFRACTION99.3246
4.136-4.4670.1891020.1312044X-RAY DIFFRACTION99.3979
4.467-4.8930.1521020.1211904X-RAY DIFFRACTION99.1597
4.893-5.4690.2041090.1581728X-RAY DIFFRACTION99.5125
5.469-6.3120.2221050.1811505X-RAY DIFFRACTION99.6904
6.312-7.7230.269630.1671291X-RAY DIFFRACTION98.9043
7.723-10.8930.138510.1331011X-RAY DIFFRACTION97.7001
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)
13.9079-1.0337-0.21940.89030.09741.6821-0.05930.1337-0.1387-0.00220.0608-0.02890.1560.1796-0.00150.0365-0.0140.00650.1834-0.00150.015150.8130.177313.3849
22.09280.0667-0.85921.1715-1.22042.9604-0.06430.0252-0.15660.03070.0260.09440.2284-0.05880.03830.051-0.0270.02160.064-0.00480.024421.6359-4.721945.7057
31.79620.33750.83590.9537-0.23063.6411-0.03360.33070.0089-0.13170.05890.2320.0263-0.1719-0.02530.0218-0.0131-0.02310.26260.03290.11798.82279.23786.59
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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