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- PDB-5nnl: Inactive dihydroorotase-like domain of Chaetomium thermophilum CA... -

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Basic information

Entry
Database: PDB / ID: 5nnl
TitleInactive dihydroorotase-like domain of Chaetomium thermophilum CAD-like multifunctional protein
ComponentsInactive dihydroorotase-like domain
KeywordsOXIDOREDUCTASE / TIM-barrel / de novo pyrimidine biosynthesis / CAD / URA2
Function / homology
Function and homology information


carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / aspartate carbamoyltransferase activity / amino acid binding / glutamine metabolic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / 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 / MGS-like domain profile. / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily / MGS-like domain / MGS-like domain / Aspartate carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / Glutamine amidotransferase class-I / Glutamine amidotransferase / 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 / Carbamoyl-phosphate synthase subdomain signature 1. / Glutamine amidotransferase type 1 domain profile. / 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 hydrolases / Metal-dependent hydrolase / Carbamoyl-phosphate synthase subdomain signature 2. / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsRamon-Maiques, S. / Moreno-Morcillo, M. / Grande-Garcia, A.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2013-48365-P Spain
Spanish Ministry of Economy and CompetitivenessBFU2016-80570-R Spain
CitationJournal: 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.
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: Inactive dihydroorotase-like domain
B: Inactive dihydroorotase-like domain


Theoretical massNumber of molelcules
Total (without water)74,7562
Polymers74,7562
Non-polymers00
Water3,585199
1
A: Inactive dihydroorotase-like domain


  • defined by author&software
  • Evidence: assay for oligomerization, Dimer validated by size-exclusion chromatography coupled to multi-angle light scattering. Dimerization surface identified by usage of site-specific mutants. ...Evidence: assay for oligomerization, Dimer validated by size-exclusion chromatography coupled to multi-angle light scattering. Dimerization surface identified by usage of site-specific mutants. Mutaion L1660C converts the dimer into monomers.
  • 37.4 kDa, 1 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)37,3781
Polymers37,3781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Inactive dihydroorotase-like domain


Theoretical massNumber of molelcules
Total (without water)37,3781
Polymers37,3781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.771, 109.177, 58.314
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1994-

HOH

21A-2012-

HOH

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Components

#1: Protein Inactive dihydroorotase-like domain


Mass: 37377.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0032600 / Plasmid: pOPIN-F / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: G0S583
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.18 Å3/Da / Density meas: 2.18 Mg/m3 / Density % sol: 44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: A construct spanning the DHO-like and ATC domains of C. thermophilum CAD-like protein was used for crystallization at 5 mg/ml. Crystals appear after 2-3 weeks in conditions with 20% PEG ...Details: A construct spanning the DHO-like and ATC domains of C. thermophilum CAD-like protein was used for crystallization at 5 mg/ml. Crystals appear after 2-3 weeks in conditions with 20% PEG 20,000 and 0.1 M citric acid pH 4.5. The crystals only contained the DHO-like domain of the construct that was cleaved off during crystallization.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.93927 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93927 Å / Relative weight: 1
ReflectionResolution: 2.13→48 Å / Num. obs: 36234 / % possible obs: 98.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 33.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.047 / Net I/σ(I): 11.3
Reflection shellResolution: 2.13→2.25 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.984 / Mean I/σ(I) obs: 2 / Num. unique obs: 5197 / CC1/2: 0.702 / Rpim(I) all: 0.411 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C6M

4c6m


Resolution: 2.13→45.814 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.49
RfactorNum. reflection% reflection
Rfree0.232 1736 4.8 %
Rwork0.1989 --
obs0.2004 36184 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.13→45.814 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5197 0 0 199 5396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035354
X-RAY DIFFRACTIONf_angle_d0.6067304
X-RAY DIFFRACTIONf_dihedral_angle_d14.1853258
X-RAY DIFFRACTIONf_chiral_restr0.068872
X-RAY DIFFRACTIONf_plane_restr0.004941
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.19270.32521550.28362814X-RAY DIFFRACTION98
2.1927-2.26350.32771720.26962757X-RAY DIFFRACTION98
2.2635-2.34440.27021400.24882845X-RAY DIFFRACTION98
2.3444-2.43820.28271310.2332841X-RAY DIFFRACTION98
2.4382-2.54920.23181570.22532824X-RAY DIFFRACTION99
2.5492-2.68360.24881440.21332836X-RAY DIFFRACTION99
2.6836-2.85170.26141290.22132910X-RAY DIFFRACTION99
2.8517-3.07180.26391370.22122875X-RAY DIFFRACTION99
3.0718-3.38080.22891410.19822892X-RAY DIFFRACTION99
3.3808-3.86980.21361250.18422944X-RAY DIFFRACTION99
3.8698-4.87470.19681630.16212894X-RAY DIFFRACTION98
4.8747-45.82420.2031420.18013016X-RAY DIFFRACTION97

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