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- PDB-6ywj: Arabidopsis aspartate transcarbamoylase mutant F161A complex with UMP -

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Basic information

Entry
Database: PDB / ID: 6ywj
TitleArabidopsis aspartate transcarbamoylase mutant F161A complex with 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: 2.4 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 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0576
Polymers74,2252
Non-polymers8334
Water1448
1
A: PYRB
hetero molecules

A: PYRB
hetero molecules

A: PYRB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,5869
Polymers111,3373
Non-polymers1,2496
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 area9990 Å2
ΔGint-41 kcal/mol
Surface area34520 Å2
MethodPISA
2
B: PYRB
hetero molecules

B: PYRB
hetero molecules

B: PYRB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,5869
Polymers111,3373
Non-polymers1,2496
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 area10080 Å2
ΔGint-40 kcal/mol
Surface area34250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.343, 104.343, 127.845
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein PYRB


Mass: 37112.391 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 54.56 %
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) and with 5 mM UMP. Crystallization solution: 18-22 % PEG3350, 0.1 M ...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) and with 5 mM UMP. Crystallization solution: 18-22 % PEG3350, 0.1 M Na2SO4 and 0.1 M bis-tris pH 6.5 Crystals were cryo-protected by soaking in a solution containing the mother liquor supplemented with 20% glycerol and the 5 mM UMP.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.4827
pseudo-merohedral22-K, -H, -L20.5173
ReflectionResolution: 2.4→48.304 Å / Num. obs: 30917 / % possible obs: 100 % / Redundancy: 10 % / CC1/2: 0.992 / Rmerge(I) obs: 0.194 / Net I/σ(I): 8.5
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 1.255 / Mean I/σ(I) obs: 2 / Num. unique obs: 3526 / CC1/2: 0.629

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YPO

6ypo


Resolution: 2.4→48.304 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.608 / SU ML: 0.091 / Cross valid method: FREE R-VALUE / ESU R: 0.051 / ESU R Free: 0.04
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1903 1539 4.982 %
Rwork0.1383 --
all0.141 --
obs-30890 99.977 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.89 Å2
Baniso -1Baniso -2Baniso -3
1-11.617 Å20 Å20 Å2
2--11.617 Å20 Å2
3----23.234 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.304 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4884 0 54 8 4946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0135012
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174821
X-RAY DIFFRACTIONr_angle_refined_deg1.7841.6426753
X-RAY DIFFRACTIONr_angle_other_deg1.2971.58111155
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.955621
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.09621.699259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.26115929
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4351540
X-RAY DIFFRACTIONr_chiral_restr0.0720.2663
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025543
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021049
X-RAY DIFFRACTIONr_nbd_refined0.2030.21013
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2050.24669
X-RAY DIFFRACTIONr_nbtor_refined0.1670.22401
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0910.22329
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2112
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1480.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2470.26
X-RAY DIFFRACTIONr_nbd_other0.2030.283
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1570.29
X-RAY DIFFRACTIONr_mcbond_it4.3534.3862490
X-RAY DIFFRACTIONr_mcbond_other4.3514.3852489
X-RAY DIFFRACTIONr_mcangle_it5.7746.5893109
X-RAY DIFFRACTIONr_mcangle_other5.7746.593110
X-RAY DIFFRACTIONr_scbond_it4.8224.742521
X-RAY DIFFRACTIONr_scbond_other4.8224.7422518
X-RAY DIFFRACTIONr_scangle_it6.8476.9353644
X-RAY DIFFRACTIONr_scangle_other6.8466.9353645
X-RAY DIFFRACTIONr_lrange_it8.34450.995379
X-RAY DIFFRACTIONr_lrange_other8.34350.9895380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.4620.2631260.1592181X-RAY DIFFRACTION99.9134
2.462-2.530.2321040.1852074X-RAY DIFFRACTION100
2.53-2.6030.2551220.1642052X-RAY DIFFRACTION100
2.603-2.6830.2481010.1531983X-RAY DIFFRACTION100
2.683-2.7710.226910.161945X-RAY DIFFRACTION100
2.771-2.8680.2731040.1931851X-RAY DIFFRACTION100
2.868-2.9760.2820.151809X-RAY DIFFRACTION100
2.976-3.0980.212830.1541756X-RAY DIFFRACTION100
3.098-3.2350.2071000.1451671X-RAY DIFFRACTION100
3.235-3.3930.174960.1511562X-RAY DIFFRACTION100
3.393-3.5760.238660.1451541X-RAY DIFFRACTION100
3.576-3.7930.177970.1491385X-RAY DIFFRACTION100
3.793-4.0540.171780.131359X-RAY DIFFRACTION100
4.054-4.3780.155630.1131267X-RAY DIFFRACTION100
4.378-4.7950.135560.0961161X-RAY DIFFRACTION100
4.795-5.3590.134420.1121052X-RAY DIFFRACTION100
5.359-6.1840.213450.129934X-RAY DIFFRACTION100
6.184-7.5650.192350.131802X-RAY DIFFRACTION100
7.565-10.6620.119300.104617X-RAY DIFFRACTION100
10.662-48.3040.21180.186349X-RAY DIFFRACTION98.6559

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