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- PDB-6ys6: Arabidopsis aspartate transcarbamoylase complex with PALA -

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Basic information

Entry
Database: PDB / ID: 6ys6
TitleArabidopsis aspartate transcarbamoylase complex with PALA
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
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: 1.55 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 21, 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)112,84615
Polymers111,5653
Non-polymers1,28012
Water15,151841
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, SEC-MALS analysis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9790 Å2
ΔGint-71 kcal/mol
Surface area34650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.740, 94.930, 132.080
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

#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
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 841 / 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: 2.56 Å3/Da / Density % sol: 51.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion
Details: protein: 5 mg/ml in buffer 20 mM Tris pH 7.0, 0.1 M NaCl, 2% glycerol, 0.2 mM tris(2-carboxyethyl) phosphine (TCEP) with 2 mM PALA Crystallization solution: 25% PEG3350, 0.2 M Li2SO4 and 0.1 M bis-tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.55→72.5 Å / Num. obs: 155447 / % possible obs: 97.4 % / Redundancy: 4.8 % / Biso Wilson estimate: 18.98 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Net I/σ(I): 15.07
Reflection shellResolution: 1.55→1.6 Å / Num. unique obs: 15241 / CC1/2: 0.752

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5G1N

5g1n


Resolution: 1.55→72.5 Å / SU ML: 0.1294 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.4651
RfactorNum. reflection% reflection
Rfree0.1578 7671 4.94 %
Rwork0.1252 --
obs0.1269 155437 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 25.08 Å2
Refinement stepCycle: LAST / Resolution: 1.55→72.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7280 0 79 841 8200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00817875
X-RAY DIFFRACTIONf_angle_d1.026310673
X-RAY DIFFRACTIONf_chiral_restr0.05591198
X-RAY DIFFRACTIONf_plane_restr0.00571392
X-RAY DIFFRACTIONf_dihedral_angle_d5.8496518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.560.23842650.17464825X-RAY DIFFRACTION96.66
1.56-1.580.22592770.16994831X-RAY DIFFRACTION96.5
1.58-1.60.21992510.15334792X-RAY DIFFRACTION96.94
1.6-1.620.20332630.14234846X-RAY DIFFRACTION97
1.62-1.640.20752510.14234907X-RAY DIFFRACTION96.81
1.64-1.660.20582640.14074827X-RAY DIFFRACTION96.88
1.66-1.690.20882430.13514886X-RAY DIFFRACTION97.6
1.69-1.710.19972490.13024878X-RAY DIFFRACTION97.27
1.71-1.740.18832690.1284873X-RAY DIFFRACTION97.26
1.74-1.770.16912450.12764871X-RAY DIFFRACTION97.45
1.77-1.80.20252210.12734926X-RAY DIFFRACTION97.57
1.8-1.830.15952480.1234942X-RAY DIFFRACTION97.7
1.83-1.870.16632370.12024910X-RAY DIFFRACTION97.78
1.87-1.910.16652500.11494931X-RAY DIFFRACTION97.64
1.91-1.950.15872610.10984871X-RAY DIFFRACTION97.18
1.95-1.990.15952280.10444922X-RAY DIFFRACTION97.72
1.99-2.040.14532180.1024881X-RAY DIFFRACTION95.77
2.04-2.10.1592580.10424830X-RAY DIFFRACTION96
2.1-2.160.14562580.10264961X-RAY DIFFRACTION98.05
2.16-2.230.13622810.09884948X-RAY DIFFRACTION98.51
2.23-2.310.13612490.09984946X-RAY DIFFRACTION98.24
2.31-2.40.13252600.10344993X-RAY DIFFRACTION98.19
2.4-2.510.13962690.10684930X-RAY DIFFRACTION97.85
2.51-2.640.14452830.11324964X-RAY DIFFRACTION98
2.64-2.810.15832670.11984973X-RAY DIFFRACTION97.96
2.81-3.020.13962470.1244978X-RAY DIFFRACTION97.88
3.02-3.330.15862440.13385013X-RAY DIFFRACTION97.57
3.33-3.810.14162670.13154974X-RAY DIFFRACTION96.75
3.81-4.80.1312790.11765036X-RAY DIFFRACTION97.2
4.8-72.50.20912690.17865301X-RAY DIFFRACTION98.13

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