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- PDB-6fba: Crystal Structure of truncated aspartate transcarbamoylase from P... -

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Basic information

Entry
Database: PDB / ID: 6fba
TitleCrystal Structure of truncated aspartate transcarbamoylase from Plasmodium falciparum with bound inhibitor 2,3-naphthalenediol
Components(Aspartate transcarbamoylaseAspartate carbamoyltransferase) x 2
KeywordsTRANSFERASE / Falciparum Malaria Pyrimidine biosynthesis Trimer Hit 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/ornithine carbamoyltransferase / 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 / Rossmann fold ...Aspartate/ornithine carbamoyltransferase / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
naphthalene-2,3-diol / MALONATE ION / DI(HYDROXYETHYL)ETHER / aspartate carbamoyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLunev, S. / Bosch, S.S. / Batista, F.A. / Wang, C. / Wrenger, C. / Groves, M.R.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Identification of a non-competitive inhibitor of Plasmodium falciparum aspartate transcarbamoylase.
Authors: Lunev, S. / Bosch, S.S. / Batista, F.A. / Wang, C. / Li, J. / Linzke, M. / Kruithof, P. / Chamoun, G. / Domling, A.S.S. / Wrenger, C. / Groves, M.R.
History
DepositionDec 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aspartate transcarbamoylase
B: Aspartate transcarbamoylase
C: Aspartate transcarbamoylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,70119
Polymers121,0683
Non-polymers1,63316
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9580 Å2
ΔGint-48 kcal/mol
Surface area36720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.757, 86.757, 138.151
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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Protein , 2 types, 3 molecules ABC

#1: Protein Aspartate transcarbamoylase / Aspartate carbamoyltransferase


Mass: 40350.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: ATCase / Production host: Escherichia coli (E. coli) / References: UniProt: O15804, aspartate carbamoyltransferase
#2: Protein Aspartate transcarbamoylase / Aspartate carbamoyltransferase


Mass: 40366.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CYS 212 was modelled as CSO
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: ATCase / Production host: Escherichia coli (E. coli) / References: UniProt: O15804, aspartate carbamoyltransferase

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Non-polymers , 8 types, 158 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-D48 / naphthalene-2,3-diol


Mass: 160.169 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H8O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

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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: 2.48 Å3/Da / Density % sol: 50.49 % / Description: Trimer
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Bis-tris propane pH 7.5 200 mM Na-sulphate 15 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→75.14 Å / Num. all: 228939 / Num. obs: 74373 / % possible obs: 98.7 % / Observed criterion σ(I): 1.45 / Redundancy: 3.16 % / CC1/2: 0.998 / Rrim(I) all: 0.081 / Net I/σ(I): 11.46
Reflection shellResolution: 2.05→2.17 Å / Redundancy: 3.185 % / Mean I/σ(I) obs: 1.45 / Num. unique obs: 11695 / CC1/2: 0.506 / Rrim(I) all: 0.988 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
Aimlessdata scaling
XDSdata reduction
DIMPLEmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ILQ

5ilq


Resolution: 2→75.13 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 11.505 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.151 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22526 3991 5.1 %RANDOM
Rwork0.18417 ---
obs0.18621 74373 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.799 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20.26 Å20 Å2
2--0.52 Å20 Å2
3----1.69 Å2
Refinement stepCycle: 1 / Resolution: 2→75.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7826 0 106 142 8074
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0198074
X-RAY DIFFRACTIONr_bond_other_d0.0030.027518
X-RAY DIFFRACTIONr_angle_refined_deg2.3071.96910888
X-RAY DIFFRACTIONr_angle_other_deg1.2172.99717507
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6325963
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22825.171381
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.357151494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.491533
X-RAY DIFFRACTIONr_chiral_restr0.140.21241
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.028781
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021580
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9322.4933864
X-RAY DIFFRACTIONr_mcbond_other1.932.4923863
X-RAY DIFFRACTIONr_mcangle_it2.9963.7264823
X-RAY DIFFRACTIONr_mcangle_other2.9963.7284824
X-RAY DIFFRACTIONr_scbond_it2.6182.8124210
X-RAY DIFFRACTIONr_scbond_other2.6082.8124210
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9014.0876066
X-RAY DIFFRACTIONr_long_range_B_refined6.39648.10834645
X-RAY DIFFRACTIONr_long_range_B_other6.39548.10834645
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 264 -
Rwork0.336 5486 -
obs--99.31 %
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)
12.44170.0906-0.05173.481.24211.66940.01290.07870.11650.0725-0.06890.29930.0277-0.23350.0560.0449-0.02740.01740.0910.01340.188461.909844.0301-135.9273
23.3510.34540.28462.4098-0.08090.98970.0125-0.2655-0.46330.3978-0.03330.08940.2435-0.2510.02080.1447-0.080.04990.1875-0.05940.236456.465621.9972-134.1156
32.9947-0.61081.3482.4280.91132.3038-0.076-0.03950.20120.00110.04330.007-0.0749-0.03910.03270.035-0.00120.05710.0076-0.0210.186480.66963.8459-127.633
41.61580.173-0.72572.34931.01111.37140.0218-0.2306-0.21450.3354-0.16270.15560.1174-0.20180.14080.10230.0114-0.02770.1580.00240.269562.548976.8604-119.0308
53.43310.49620.35091.0258-0.00510.48940.06080.0518-0.1735-0.0154-0.0598-0.04820.16760.0663-0.0010.11050.02450.01020.0155-0.010.094193.184638.7128-132.9926
60.971-0.13460.09191.36520.45093.0787-0.0704-0.27460.11130.2068-0.0195-0.08840.02570.1440.08990.0390.01110.00680.0933-0.00980.1708107.972142.0906-118.7713
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A47 - 193
2X-RAY DIFFRACTION2A194 - 373
3X-RAY DIFFRACTION3B47 - 181
4X-RAY DIFFRACTION4B182 - 373
5X-RAY DIFFRACTION5C47 - 213
6X-RAY DIFFRACTION6C214 - 373

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