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- PDB-6yvb: Arabidopsis aspartate transcarbamoylase complex with carbamoyl ph... -

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Basic information

Entry
Database: PDB / ID: 6yvb
TitleArabidopsis aspartate transcarbamoylase complex with 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 / amino acid binding / chloroplast stroma / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / chloroplast / cytosol
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
ACETATE ION / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER / aspartate carbamoyltransferase / Aspartate carbamoyltransferase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.826 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 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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

Downloads & links

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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)226,22540
Polymers223,1316
Non-polymers3,09434
Water24,0321334
1
A: PYRB
B: PYRB
C: PYRB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,41524
Polymers111,5653
Non-polymers1,84921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11750 Å2
ΔGint-47 kcal/mol
Surface area35630 Å2
MethodPISA
2
D: PYRB
E: PYRB
F: PYRB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,81016
Polymers111,5653
Non-polymers1,24513
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9930 Å2
ΔGint-42 kcal/mol
Surface area35440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.268, 109.481, 212.042
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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-CP / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER


Mass: 141.020 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: CH4NO5P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1334 / 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: 2.83 Å3/Da / Density % sol: 56.52 %
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), with 10 mM carbamoyl phosphate. Crystallization solution: 25% PEG3350, ...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), with 10 mM carbamoyl phosphate. Crystallization solution: 25% PEG3350, 0.2 M Li2SO4 and 0.1 M bis-tris pH 5.5. Cryo-conditions achieved by increasing glycerol concentration up to 20% in presence of carbamoyl phosphate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.826→76.278 Å / Num. obs: 212623 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Net I/σ(I): 17.6
Reflection shellResolution: 1.826→1.93 Å / Rmerge(I) obs: 1.058 / Num. unique obs: 30789 / CC1/2: 0.704

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YS6

6ys6


Resolution: 1.826→76.278 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.192 / SU ML: 0.093 / Cross valid method: FREE R-VALUE / ESU R: 0.113 / ESU R Free: 0.114
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.213 10800 5.082 %
Rwork0.172 --
all0.174 --
obs-212513 99.906 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.606 Å2
Baniso -1Baniso -2Baniso -3
1-1.068 Å20 Å20 Å2
2---0.039 Å20 Å2
3----1.028 Å2
Refinement stepCycle: LAST / Resolution: 1.826→76.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14733 0 196 1334 16263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01315633
X-RAY DIFFRACTIONr_bond_other_d0.0010.01714920
X-RAY DIFFRACTIONr_angle_refined_deg1.6921.64521109
X-RAY DIFFRACTIONr_angle_other_deg1.4071.58134518
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.89651996
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.03121.683814
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.809152863
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.37715126
X-RAY DIFFRACTIONr_chiral_restr0.0830.22040
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217680
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023330
X-RAY DIFFRACTIONr_nbd_refined0.1990.23081
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.214261
X-RAY DIFFRACTIONr_nbtor_refined0.1620.27477
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.27254
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.21163
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.080.29
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2250.218
X-RAY DIFFRACTIONr_nbd_other0.1880.2102
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1650.231
X-RAY DIFFRACTIONr_mcbond_it3.3033.7737820
X-RAY DIFFRACTIONr_mcbond_other3.3033.7737818
X-RAY DIFFRACTIONr_mcangle_it4.2125.6359837
X-RAY DIFFRACTIONr_mcangle_other4.2125.6359838
X-RAY DIFFRACTIONr_scbond_it4.2534.1737813
X-RAY DIFFRACTIONr_scbond_other4.2534.1747814
X-RAY DIFFRACTIONr_scangle_it6.1056.08311263
X-RAY DIFFRACTIONr_scangle_other6.1056.08311264
X-RAY DIFFRACTIONr_lrange_it7.50945.00917585
X-RAY DIFFRACTIONr_lrange_other7.48244.63417321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.826-1.8740.2977790.29714777X-RAY DIFFRACTION99.8652
1.874-1.9250.3077550.2714447X-RAY DIFFRACTION99.9868
1.925-1.9810.2937470.25114055X-RAY DIFFRACTION99.973
1.981-2.0420.2836530.2313653X-RAY DIFFRACTION99.986
2.042-2.1090.2627350.2113213X-RAY DIFFRACTION99.9857
2.109-2.1830.2366810.19512832X-RAY DIFFRACTION99.9926
2.183-2.2650.2396840.18212314X-RAY DIFFRACTION99.9769
2.265-2.3580.236820.17911864X-RAY DIFFRACTION99.9681
2.358-2.4620.2276340.17311399X-RAY DIFFRACTION99.9751
2.462-2.5820.2296150.17310899X-RAY DIFFRACTION99.9826
2.582-2.7220.2155630.16610447X-RAY DIFFRACTION99.9728
2.722-2.8870.2245410.1659861X-RAY DIFFRACTION99.9712
2.887-3.0860.2115030.179245X-RAY DIFFRACTION99.9487
3.086-3.3330.2014760.178682X-RAY DIFFRACTION99.9018
3.333-3.6510.214070.1728014X-RAY DIFFRACTION99.9644
3.651-4.0810.183640.1487282X-RAY DIFFRACTION99.9477
4.081-4.7120.1643970.136403X-RAY DIFFRACTION99.7945
4.712-5.7680.1822800.155497X-RAY DIFFRACTION99.7238
5.768-8.1450.2282170.1824292X-RAY DIFFRACTION99.6684
8.145-76.2780.217870.1662538X-RAY DIFFRACTION99.2814

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