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- PDB-6pnz: The structure of the Aspartate Transcarbamoylase trimer from Stap... -

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Basic information

Entry
Database: PDB / ID: 6pnz
TitleThe structure of the Aspartate Transcarbamoylase trimer from Staphylococcus aureus complexed with PALA at 2.27 Resolution.
ComponentsAspartate carbamoyltransferase
KeywordsTRANSFERASE / Transferase-Inhibitor complex / Trimer / Pyrimidines
Function / homology
Function and homology information


aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / amino acid metabolic process / amino acid binding / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process
Similarity search - Function
Aspartate/ornithine carbamoyltransferase / 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 / Rossmann fold ...Aspartate/ornithine carbamoyltransferase / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-(PHOSPHONACETYL)-L-ASPARTIC ACID / Aspartate carbamoyltransferase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsEdwards, B.F.P. / Evans, D.R. / Patel, C.
Funding support United States, 1items
OrganizationGrant numberCountry
American Heart Association17PRE33660545 United States
CitationJournal: To Be Published
Title: The structure of the Aspartate Transcarbamoylase trimer from Staphylococcus aureus complexed with PALA at 2.27 Resolution.
Authors: Edwards, B.F.P. / Evans, D.R. / Patel, C.
History
DepositionJul 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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: Aspartate carbamoyltransferase
B: Aspartate carbamoyltransferase
C: Aspartate carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,6596
Polymers99,8933
Non-polymers7653
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8260 Å2
ΔGint-48 kcal/mol
Surface area31060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.998000, 111.998000, 151.358000
Angle α, β, γ (deg.)90.000000, 90.000000, 120.000000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Aspartate carbamoyltransferase / / Aspartate transcarbamylase / ATCase


Mass: 33297.727 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain COL) (bacteria)
Strain: COL / Gene: pyrB, SACOL1212 / Plasmid: pMCSG19C / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Hi-control E. coli BL21(DE3) / References: UniProt: Q5HGN2, aspartate carbamoyltransferase
#2: Chemical ChemComp-PAL / N-(PHOSPHONACETYL)-L-ASPARTIC ACID


Mass: 255.119 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H10NO8P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.74 Å3/Da / Density % sol: 55.16 % / Description: small cube
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1uL Protein Solution: ATC Staac (8 mg/ml) with 200uM PALA 50mM Tris 7.5, 200mM NaCl, 1mM dithiothreitol (DTT) + 1uL Well Solution: 2M ammonium sulfate., 5% PEG 400, 0.1M 2-(N-morpholino) ...Details: 1uL Protein Solution: ATC Staac (8 mg/ml) with 200uM PALA 50mM Tris 7.5, 200mM NaCl, 1mM dithiothreitol (DTT) + 1uL Well Solution: 2M ammonium sulfate., 5% PEG 400, 0.1M 2-(N-morpholino) ethane sulfonic acid (MES) pH6.5
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 22, 2017 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.27→96.99 Å / Num. obs: 49596 / % possible obs: 96.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 44.9 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.023 / Rrim(I) all: 0.064 / Net I/av σ(I): 21.9 / Net I/σ(I): 21.9
Reflection shellResolution: 2.27→2.39 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.652 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 7392 / CC1/2: 0.853 / Rpim(I) all: 0.252 / Rsym value: 0.701 / % possible all: 100

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Processing

Software
NameClassification
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R7D

3r7d


Resolution: 2.27→96.99 Å / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.267 / ESU R Free: 0.19
Details: Solved, built, and refined with Phenix (Phaser, Autobuild, Refine). "Polished" with PDB_REDO (Refmac).
RfactorNum. reflection% reflectionSelection details
Rfree0.20779 2402 4.8 %RANDOM
Rwork0.18111 ---
obs0.18243 47164 96.82 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 32.552 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20.1 Å20 Å2
2--0.2 Å2-0 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 2.27→96.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7011 0 48 179 7238
LS refinement shellResolution: 2.272→2.331 Å
RfactorNum. reflection% reflection
Rfree0.296 189 5.3 %
Rwork0.231 3559 -
obs--99.92 %

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