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

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Basic information

Entry
Database: PDB / ID: 7zhi
TitleCrystal Structure of truncated aspartate transcarbamoylase from Plasmodium falciparum with bound inhibitor indole
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 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
Similarity search - Domain/homology
INDOLE / aspartate carbamoyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.946 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 6, 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)121,4797
Polymers121,0523
Non-polymers4264
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-52 kcal/mol
Surface area39040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.714, 103.822, 87.067
Angle α, β, γ (deg.)90.000, 117.922, 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-IND / INDOLE / Indole


Mass: 117.148 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H7N / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 31 / 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: 57 %
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: 2.946→44.8 Å / Num. obs: 28662 / % possible obs: 99 % / Redundancy: 3.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.086 / Rrim(I) all: 0.123 / Net I/σ(I): 9
Reflection shellResolution: 2.95→3.12 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.409 / Num. unique obs: 4263 / CC1/2: 0.857 / Rpim(I) all: 0.39 / Rrim(I) all: 0.566

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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: 2.946→43.54 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.915 / SU B: 44.653 / SU ML: 0.353 / Cross valid method: FREE R-VALUE / ESU R Free: 0.393
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2385 1331 4.647 %
Rwork0.1911 27314 -
all0.193 --
obs-28645 98.888 %
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: 69.716 Å2
Baniso -1Baniso -2Baniso -3
1--4.222 Å20 Å20.636 Å2
2--7.994 Å2-0 Å2
3----2.847 Å2
Refinement stepCycle: LAST / Resolution: 2.946→43.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8172 0 28 31 8231
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0138356
X-RAY DIFFRACTIONr_bond_other_d0.0010.0157978
X-RAY DIFFRACTIONr_angle_refined_deg1.7151.6411287
X-RAY DIFFRACTIONr_angle_other_deg1.241.58618419
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.61651002
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.90124.009424
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.805151549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9291531
X-RAY DIFFRACTIONr_chiral_restr0.0750.21129
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029322
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021900
X-RAY DIFFRACTIONr_nbd_refined0.2190.21786
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.27766
X-RAY DIFFRACTIONr_nbtor_refined0.1730.24041
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.24059
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2157
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0230.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3980.247
X-RAY DIFFRACTIONr_nbd_other0.4260.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2460.24
X-RAY DIFFRACTIONr_mcbond_it2.4764.5334026
X-RAY DIFFRACTIONr_mcbond_other2.4774.5334025
X-RAY DIFFRACTIONr_mcangle_it4.066.7975022
X-RAY DIFFRACTIONr_mcangle_other4.0596.7975023
X-RAY DIFFRACTIONr_scbond_it2.3034.744330
X-RAY DIFFRACTIONr_scbond_other2.2914.7344323
X-RAY DIFFRACTIONr_scangle_it3.9467.0276265
X-RAY DIFFRACTIONr_scangle_other3.9357.0186254
X-RAY DIFFRACTIONr_lrange_it7.43452.3039122
X-RAY DIFFRACTIONr_lrange_other7.43252.2839120
X-RAY DIFFRACTIONr_ncsr_local_group_10.0970.0510707
X-RAY DIFFRACTIONr_ncsr_local_group_20.0970.0510722
X-RAY DIFFRACTIONr_ncsr_local_group_30.1080.0510824
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.09680.05008
12BX-RAY DIFFRACTIONLocal ncs0.09680.05008
23AX-RAY DIFFRACTIONLocal ncs0.096510.05008
24CX-RAY DIFFRACTIONLocal ncs0.096510.05008
35BX-RAY DIFFRACTIONLocal ncs0.107780.05008
36CX-RAY DIFFRACTIONLocal ncs0.107780.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.946-3.0220.342980.3331946X-RAY DIFFRACTION96.4606
3.022-3.1050.326960.3121987X-RAY DIFFRACTION99.7128
3.105-3.1950.297780.2841924X-RAY DIFFRACTION99.4536
3.195-3.2930.254690.241878X-RAY DIFFRACTION99.795
3.293-3.4010.2591050.221779X-RAY DIFFRACTION99.7353
3.401-3.5210.2821030.2091732X-RAY DIFFRACTION99.7283
3.521-3.6530.228920.2081700X-RAY DIFFRACTION99.7218
3.653-3.8020.275960.191611X-RAY DIFFRACTION99.3597
3.802-3.9710.221660.1751561X-RAY DIFFRACTION99.1469
3.971-4.1650.247690.1521485X-RAY DIFFRACTION98.9179
4.165-4.3890.196610.1441416X-RAY DIFFRACTION98.3356
4.389-4.6550.174570.1351322X-RAY DIFFRACTION98.3595
4.655-4.9760.199500.1411267X-RAY DIFFRACTION98.2103
4.976-5.3740.261870.1881137X-RAY DIFFRACTION99.2701
5.374-5.8850.217420.1791103X-RAY DIFFRACTION99.3062
5.885-6.5770.253420.169982X-RAY DIFFRACTION99.3211
6.577-7.5890.184320.157885X-RAY DIFFRACTION98.7083
7.589-9.2830.147240.157723X-RAY DIFFRACTION95.6466
9.283-13.0750.216450.195551X-RAY DIFFRACTION97.7049
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)
13.9065-1.2544-0.1911.0975-0.12381.8965-0.01130.1623-0.14320.04070.0697-0.04440.1520.1739-0.05850.1974-0.02380.06310.1957-0.01180.154250.5511-0.118813.4523
22.36680.0132-1.04871.007-1.38472.90050.01180.09-0.16160.0714-0.03120.15670.1616-0.01670.01940.2845-0.03110.03140.0106-0.02410.168721.1086-4.710845.4241
31.93020.15560.84580.7636-0.13963.6432-0.02150.3764-0.0041-0.20120.10070.26980.0188-0.22-0.07920.1359-0.02770.0170.31340.06860.32718.6558.91296.2053
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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