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- PDB-6ysp: Arabidopsis aspartate transcarbamoylase complex with PALA and car... -

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Basic information

Entry
Database: PDB / ID: 6ysp
TitleArabidopsis aspartate transcarbamoylase complex with PALA and carbamoyl phosphate
ComponentsPYRB
KeywordsPLANT PROTEIN / Transferase / chloroplast / pyrimidine de novo biosynthesis
Function / homology
Function and homology information


aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / cellular response to phosphate starvation / amino acid metabolic process / chloroplast stroma / amino acid binding / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / chloroplast
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
PHOSPHORIC ACID MONO(FORMAMIDE)ESTER / N-(PHOSPHONACETYL)-L-ASPARTIC ACID / aspartate carbamoyltransferase / Aspartate carbamoyltransferase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsRamon Maiques, S. / Del Cano Ochoa, F. / Bellin, L. / Mohlmann, T.
Funding support Spain, Germany, 4items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesBFU2016-80570-R Spain
Spanish Ministry of Science, Innovation, and UniversitiesRTI2018-098084-B-100 Spain
German Research Foundation (DFG)Mo 1032/4-1) Germany
German Research Foundation (DFG)IRTG 1830 Germany
CitationJournal: Nat Commun / Year: 2021
Title: Mechanisms of feedback inhibition and sequential firing of active sites in plant aspartate transcarbamoylase.
Authors: Bellin, L. / Del Cano-Ochoa, F. / Velazquez-Campoy, A. / Mohlmann, T. / Ramon-Maiques, S.
History
DepositionApr 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PYRB
B: PYRB
C: PYRB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,84714
Polymers111,5653
Non-polymers1,28211
Water12,340685
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, SEC-MALS analysis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10120 Å2
ΔGint-68 kcal/mol
Surface area33120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.484, 94.570, 131.839
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein PYRB


Mass: 37188.488 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AXX17_At3g21670 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A178VJE3, UniProt: P49077*PLUS

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Non-polymers , 5 types, 696 molecules

#2: Chemical ChemComp-CP / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER


Mass: 141.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH4NO5P / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PAL / N-(PHOSPHONACETYL)-L-ASPARTIC ACID


Mass: 255.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10NO8P / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 685 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 294 K / Method: vapor diffusion
Details: Protein at 5 mg/ml in 20 mM Tris pH 7.0, 0.1 M NaCl, 2% glycerol, 0.2 mM tris(2-carboxyethyl) phosphine (TCEP) and 2 mM PALA Crystallization condition: 25% PEG3350, 0.2 M Li2SO4 and 0.1 M ...Details: Protein at 5 mg/ml in 20 mM Tris pH 7.0, 0.1 M NaCl, 2% glycerol, 0.2 mM tris(2-carboxyethyl) phosphine (TCEP) and 2 mM PALA Crystallization condition: 25% PEG3350, 0.2 M Li2SO4 and 0.1 M bis-tris pH 5.5. Crystals soaked in mother liquor plus 2 mM PALA and 10 mM carbamoyl phosphate with increasing glycerol concentration (up to 20%) prior to freezing

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97924 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.38→76.84 Å / Num. obs: 221343 / % possible obs: 99.97 % / Redundancy: 6.7 % / Biso Wilson estimate: 17.49 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.71
Reflection shellResolution: 1.38→1.43 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.154 / Mean I/σ(I) obs: 1.35 / Num. unique obs: 21917 / CC1/2: 0.512 / % possible all: 99.98

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YPO

6ypo


Resolution: 1.38→76.84 Å / SU ML: 0.1551 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.3317
RfactorNum. reflection% reflection
Rfree0.1676 11050 4.99 %
Rwork0.1449 --
obs0.146 221287 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 23.79 Å2
Refinement stepCycle: LAST / Resolution: 1.38→76.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7270 0 78 685 8033
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00867709
X-RAY DIFFRACTIONf_angle_d1.094710435
X-RAY DIFFRACTIONf_chiral_restr0.07661172
X-RAY DIFFRACTIONf_plane_restr0.0061357
X-RAY DIFFRACTIONf_dihedral_angle_d8.21054606
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.40.32673520.28687007X-RAY DIFFRACTION99.99
1.4-1.410.28173800.2646905X-RAY DIFFRACTION99.99
1.41-1.430.2823660.24666906X-RAY DIFFRACTION99.97
1.43-1.450.27353930.24156964X-RAY DIFFRACTION99.96
1.45-1.470.23143490.21986932X-RAY DIFFRACTION99.97
1.47-1.490.22513750.18686932X-RAY DIFFRACTION99.95
1.49-1.510.22043430.17036981X-RAY DIFFRACTION99.96
1.51-1.530.19183560.156978X-RAY DIFFRACTION99.97
1.53-1.550.17113460.14276941X-RAY DIFFRACTION99.96
1.55-1.580.18053710.14046959X-RAY DIFFRACTION99.99
1.58-1.610.16683550.13216990X-RAY DIFFRACTION99.99
1.61-1.640.17043700.13276963X-RAY DIFFRACTION100
1.64-1.670.17173980.13636916X-RAY DIFFRACTION99.99
1.67-1.70.16413690.13076964X-RAY DIFFRACTION100
1.7-1.740.14373600.12396982X-RAY DIFFRACTION100
1.74-1.780.16233560.12517004X-RAY DIFFRACTION99.99
1.78-1.820.16443470.12147002X-RAY DIFFRACTION100
1.82-1.870.16373560.12746989X-RAY DIFFRACTION99.96
1.87-1.930.16133690.12547013X-RAY DIFFRACTION100
1.93-1.990.14743560.12596981X-RAY DIFFRACTION99.96
1.99-2.060.1593930.12667003X-RAY DIFFRACTION99.99
2.06-2.140.16623920.12576974X-RAY DIFFRACTION100
2.14-2.240.14453450.12227058X-RAY DIFFRACTION99.99
2.24-2.360.15833810.12886999X-RAY DIFFRACTION99.95
2.36-2.510.16453840.13537044X-RAY DIFFRACTION99.97
2.51-2.70.16573690.13767080X-RAY DIFFRACTION99.97
2.7-2.970.15393630.14837079X-RAY DIFFRACTION99.92
2.97-3.40.17693730.15327115X-RAY DIFFRACTION99.99
3.4-4.290.15413880.13917168X-RAY DIFFRACTION99.96
4.29-76.840.16533950.16527408X-RAY DIFFRACTION99.78

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