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- PDB-6ypo: Arabidopsis aspartate transcarbamoylase bound to UMP -

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Basic information

Entry
Database: PDB / ID: 6ypo
TitleArabidopsis aspartate transcarbamoylase bound to UMP
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
URIDINE-5'-MONOPHOSPHATE / aspartate carbamoyltransferase / Aspartate carbamoyltransferase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsRamon Maiques, S. / Del Cano Ochoa, F. / Bellin, L. / Mohlmann, T.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesBFU2016-80570-R Spain
Spanish Ministry of Science, Innovation, and UniversitiesRTI2018-098084-B-100 Spain
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 16, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3948
Polymers74,3772
Non-polymers1,0176
Water9,854547
1
A: PYRB
hetero molecules

A: PYRB
hetero molecules

A: PYRB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,09112
Polymers111,5653
Non-polymers1,5259
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-y+2,x-y+2,z1
crystal symmetry operation3_575-x+y,-x+2,z1
Buried area10760 Å2
ΔGint-39 kcal/mol
Surface area33660 Å2
MethodPISA
2
B: PYRB
hetero molecules

B: PYRB
hetero molecules

B: PYRB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,09112
Polymers111,5653
Non-polymers1,5259
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-y+2,x-y+2,z1
crystal symmetry operation3_575-x+y,-x+2,z1
Buried area10850 Å2
ΔGint-36 kcal/mol
Surface area33430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.541, 104.541, 127.790
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-775-

HOH

21B-763-

HOH

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Components

#1: Protein PYRB


Mass: 37188.488 Da / Num. of mol.: 2
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-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 547 / 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: 2.71 Å3/Da / Density % sol: 54.62 %
Crystal growTemperature: 294 K / Method: vapor diffusion
Details: Protein at 5 mg/ml in buffer 20 mM Tris pH 7.0, 0.1 M NaCl, 2 % glycerol and 0.2 mM tris(2-carboxyethyl) phosphine (TCEP). Crystallization reservoir: 22 % PEG 3350, 0.1 M sodium sulfate, 0.1 M bis-tris pH 6.5

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.67→90.54 Å / Num. obs: 91035 / % possible obs: 99.38 % / Redundancy: 10.3 % / Biso Wilson estimate: 28.26 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1046 / Net I/σ(I): 12.74
Reflection shellResolution: 1.67→1.73 Å / Redundancy: 10 % / Rmerge(I) obs: 1.396 / Mean I/σ(I) obs: 1.64 / Num. unique obs: 9119 / CC1/2: 0.601 / % possible all: 99.99

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Processing

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

5g1n


Resolution: 1.67→90.54 Å / Cross valid method: FREE R-VALUE / σ(F): 21.86 / Phase error: 25.6742
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1679 4638 5.09 %
Rwork0.1494 86397 -
obs0.1518 91035 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.15 Å2
Refinement stepCycle: LAST / Resolution: 1.67→90.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4896 0 66 557 5519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055141
X-RAY DIFFRACTIONf_angle_d0.64256946
X-RAY DIFFRACTIONf_chiral_restr0.0438783
X-RAY DIFFRACTIONf_plane_restr0.0044890
X-RAY DIFFRACTIONf_dihedral_angle_d7.22074329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.70.34882270.28614322X-RAY DIFFRACTION94.99
1.7-1.730.27912200.29054348X-RAY DIFFRACTION95.18
1.73-1.760.27872010.27624366X-RAY DIFFRACTION95.6
1.76-1.80.26462770.24884297X-RAY DIFFRACTION93.94
1.8-1.840.26082280.24464330X-RAY DIFFRACTION95
1.84-1.880.21532230.22384344X-RAY DIFFRACTION95.12
1.88-1.930.2272350.21624327X-RAY DIFFRACTION94.85
1.93-1.980.2292270.20714364X-RAY DIFFRACTION95.06
1.98-2.040.22422070.19584346X-RAY DIFFRACTION95.45
2.04-2.10.18232320.18734326X-RAY DIFFRACTION94.91
2.1-2.180.17962540.1774327X-RAY DIFFRACTION94.46
2.18-2.270.18842470.18053771X-RAY DIFFRACTION82.3
2.27-2.370.17972800.17214286X-RAY DIFFRACTION93.87
2.37-2.490.17942380.1714339X-RAY DIFFRACTION94.8
2.49-2.650.18872320.16134334X-RAY DIFFRACTION94.92
2.65-2.850.18152010.14834374X-RAY DIFFRACTION95.61
2.85-3.140.13922160.13524387X-RAY DIFFRACTION95.31
3.14-3.60.15612290.12534360X-RAY DIFFRACTION94.99
3.6-4.530.12272280.09764375X-RAY DIFFRACTION95.05
4.53-30.130.14832350.12134421X-RAY DIFFRACTION94.95

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