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- PDB-5nnq: Aspartate transcarbamoylase from Chaetomium thermophilum CAD-like... -

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Basic information

Entry
Database: PDB / ID: 5nnq
TitleAspartate transcarbamoylase from Chaetomium thermophilum CAD-like bound to carbamoyl phosphate
ComponentsctATC
KeywordsTRANSFERASE / Carbamoyl phosphate / transcarbamoylase superfamily / CAD / Ura2
Function / homology
Function and homology information


carbamoyl-phosphate synthase complex / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / aspartate carbamoyltransferase activity / L-arginine biosynthetic process / glutamine metabolic process / amino acid binding / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / hydrolase activity / ATP binding / metal ion binding
Similarity search - Function
Carbamoyl-phosphate synthase small subunit, N-terminal domain / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain / Carbamoyl-phosphate synthase large subunit, CPSase domain / Carbamoyl-phosphate synthase, small subunit / Carbamoyl-phosphate synthase, large subunit / Carbamoyl-phosphate synthase small subunit, GATase1 domain / Carbamoyl-phosphate synthase small subunit, N-terminal domain superfamily / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain superfamily / Carbamoyl-phosphate synthase small chain, CPSase domain / Carbamoyl-phosphate synthetase large chain, oligomerisation domain ...Carbamoyl-phosphate synthase small subunit, N-terminal domain / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain / Carbamoyl-phosphate synthase large subunit, CPSase domain / Carbamoyl-phosphate synthase, small subunit / Carbamoyl-phosphate synthase, large subunit / Carbamoyl-phosphate synthase small subunit, GATase1 domain / Carbamoyl-phosphate synthase small subunit, N-terminal domain superfamily / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain superfamily / Carbamoyl-phosphate synthase small chain, CPSase domain / Carbamoyl-phosphate synthetase large chain, oligomerisation domain / Carbamoyl-phosphate synthetase large chain, oligomerisation domain / Carbamoyl-phosphate synthase small chain, CPSase domain / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily / MGS-like domain / MGS-like domain profile. / MGS-like domain / 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 / Glutamine amidotransferase / Glutamine amidotransferase class-I / Glutamine amidotransferase type 1 domain profile. / Carbamoyl-phosphate synthase subdomain signature 1. / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / Class I glutamine amidotransferase-like / Metal-dependent hydrolase / Carbamoyl-phosphate synthase subdomain signature 2. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsMoreno-Morcillo, M. / Grande-Garcia, A. / Ramon-Maiques, S.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2013-48365-P and BFU2016-80570-R Spain
Citation
Journal: Structure / Year: 2017
Title: Structural Insight into the Core of CAD, the Multifunctional Protein Leading De Novo Pyrimidine Biosynthesis.
Authors: Moreno-Morcillo, M. / Grande-Garcia, A. / Ruiz-Ramos, A. / Del Cano-Ochoa, F. / Boskovic, J. / Ramon-Maiques, S.
#1: Journal: To Be Published
Title: Structural insight into the core of CAD, the multifunctional protein leading de novo pyrimidine biosynthesis
Authors: Moreno-Morcillo, M. / Grande-Garcia, A. / Ruiz-Ramos, A. / del Cano-Ochoa, F. / Boskovic, J. / Ramon-Maiques, S.
History
DepositionApr 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 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: ctATC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7443
Polymers35,5601
Non-polymers1842
Water97354
1
A: ctATC
hetero molecules

A: ctATC
hetero molecules

A: ctATC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,2339
Polymers106,6803
Non-polymers5536
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
Buried area7130 Å2
ΔGint-12 kcal/mol
Surface area35650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.638, 138.638, 138.638
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11A-2453-

HOH

21A-2454-

HOH

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Components

#1: Protein ctATC


Mass: 35560.051 Da / Num. of mol.: 1 / Fragment: UNP Residues 1939-2253
Source method: isolated from a genetically manipulated source
Details: Synthetic gene / Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: CTHT_0032600 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: G0S583
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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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: 3.27 Å3/Da / Density % sol: 62.42 % / Description: Diamond shape
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.8 M succinic acid pH 7.0 Soaking with carbamoyl phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.91976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91976 Å / Relative weight: 1
ReflectionResolution: 1.797→49.28 Å / Num. obs: 43537 / % possible obs: 99.67 % / Redundancy: 39.1 % / Biso Wilson estimate: 35.84 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.1738 / Rpim(I) all: 0.02807 / Net I/σ(I): 22.3
Reflection shellResolution: 1.797→1.862 Å / Redundancy: 38.7 % / Rmerge(I) obs: 11.39 / Mean I/σ(I) obs: 0.58 / Num. unique obs: 4235 / CC1/2: 0.209 / Rpim(I) all: 1.829 / % possible all: 96.91

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5G1N

5g1n


Resolution: 2.26→49.016 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2435 1141 5.2 %Random selection
Rwork0.1973 ---
obs0.1997 21926 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.26→49.016 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2457 0 12 54 2523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142529
X-RAY DIFFRACTIONf_angle_d1.2913427
X-RAY DIFFRACTIONf_dihedral_angle_d13.1141556
X-RAY DIFFRACTIONf_chiral_restr0.065396
X-RAY DIFFRACTIONf_plane_restr0.009439
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.36290.34161340.29692546X-RAY DIFFRACTION100
2.3629-2.48750.30061550.26692514X-RAY DIFFRACTION100
2.4875-2.64330.27831460.25292534X-RAY DIFFRACTION100
2.6433-2.84740.32631260.23552581X-RAY DIFFRACTION100
2.8474-3.13390.26561400.22042567X-RAY DIFFRACTION100
3.1339-3.58720.24751340.20832611X-RAY DIFFRACTION100
3.5872-4.5190.21481470.1662625X-RAY DIFFRACTION100
4.519-49.02740.22271590.17472807X-RAY DIFFRACTION100

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