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- PDB-6yy1: Arabidopsis aspartate transcarbamoylase in apo state -

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Basic information

Entry
Database: PDB / ID: 6yy1
TitleArabidopsis aspartate transcarbamoylase in apo state
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/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
aspartate carbamoyltransferase / Aspartate carbamoyltransferase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.06 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
DepositionMay 4, 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

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Assembly

Deposited unit
A: PYRB
B: PYRB
C: PYRB
D: PYRB
E: PYRB
F: PYRB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,3158
Polymers223,1316
Non-polymers1842
Water99155
1
A: PYRB
B: PYRB
E: PYRB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,7505
Polymers111,5653
Non-polymers1842
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-17 kcal/mol
Surface area36410 Å2
MethodPISA
2
C: PYRB
D: PYRB
F: PYRB


Theoretical massNumber of molelcules
Total (without water)111,5653
Polymers111,5653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-16 kcal/mol
Surface area36220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.690, 109.570, 208.580
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.: 6
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.82 Å3/Da / Density % sol: 56.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: Protein at 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). Crystallization solution was 18-22% PEG 3350 and 150-200 mM potassium ...Details: Protein at 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). Crystallization solution was 18-22% PEG 3350 and 150-200 mM potassium acetate. Crystals were cryo-protected by soaking in a solution containing the mother liquor supplemented with 20% glycerol

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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: 3.06→92.85 Å / Num. obs: 45073 / % possible obs: 99.29 % / Redundancy: 5.2 % / Biso Wilson estimate: 66.92 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.14 / Net I/σ(I): 11.16
Reflection shellResolution: 3.06→3.18 Å / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2.33 / Num. unique obs: 4435 / CC1/2: 0.686 / % possible all: 99.57

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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: 3.06→92.85 Å / SU ML: 0.3908 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.1086
RfactorNum. reflection% reflection
Rfree0.245 2241 4.97 %
Rwork0.1902 --
obs0.1929 45066 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 56.51 Å2
Refinement stepCycle: LAST / Resolution: 3.06→92.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14455 0 12 55 14522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011514700
X-RAY DIFFRACTIONf_angle_d1.010719807
X-RAY DIFFRACTIONf_chiral_restr0.05952258
X-RAY DIFFRACTIONf_plane_restr0.00542545
X-RAY DIFFRACTIONf_dihedral_angle_d8.162710758
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.06-3.130.34361300.27992654X-RAY DIFFRACTION99.61
3.13-3.20.35671520.27982614X-RAY DIFFRACTION99.68
3.2-3.280.32981390.26052641X-RAY DIFFRACTION99.46
3.28-3.370.30861390.23532646X-RAY DIFFRACTION99.46
3.37-3.470.29951400.22342658X-RAY DIFFRACTION99.5
3.47-3.580.28031140.21292677X-RAY DIFFRACTION99.61
3.58-3.710.24691660.19022621X-RAY DIFFRACTION99.89
3.71-3.860.21891360.19122695X-RAY DIFFRACTION99.68
3.86-4.040.20151370.16832659X-RAY DIFFRACTION99.79
4.04-4.250.21821410.16992673X-RAY DIFFRACTION99.75
4.25-4.520.2171340.15192699X-RAY DIFFRACTION99.65
4.52-4.870.2491650.16132652X-RAY DIFFRACTION99.4
4.87-5.350.20321360.16582690X-RAY DIFFRACTION99.16
5.35-6.130.25541570.19862694X-RAY DIFFRACTION98.89
6.13-7.720.2321250.19582730X-RAY DIFFRACTION98.79
7.72-92.850.22261300.18052822X-RAY DIFFRACTION96.69

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