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- PDB-5ynz: Crystal structure of the dihydroorotase domain (K1556A) of human CAD -

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Basic information

Entry
Database: PDB / ID: 5ynz
TitleCrystal structure of the dihydroorotase domain (K1556A) of human CAD
ComponentsCAD protein
KeywordsHYDROLASE / dihydroorotase / Human CAD / ZN
Function / homology
Function and homology information


aspartate binding / response to cortisol / carbamoyl-phosphate synthase (glutamine-hydrolysing) / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / dihydroorotase / citrulline biosynthetic process / aspartate carbamoyltransferase / glutaminase ...aspartate binding / response to cortisol / carbamoyl-phosphate synthase (glutamine-hydrolysing) / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / dihydroorotase / citrulline biosynthetic process / aspartate carbamoyltransferase / glutaminase / aspartate carbamoyltransferase activity / dihydroorotase activity / Pyrimidine biosynthesis / UDP biosynthetic process / glutaminase activity / UTP biosynthetic process / response to caffeine / response to testosterone / response to starvation / glutamine metabolic process / response to amine / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / animal organ regeneration / cellular response to epidermal growth factor stimulus / lactation / xenobiotic metabolic process / liver development / cell projection / female pregnancy / peptidyl-threonine phosphorylation / response to insulin / terminal bouton / nuclear matrix / heart development / protein autophosphorylation / protein kinase activity / neuronal cell body / enzyme binding / protein-containing complex / extracellular exosome / zinc ion binding / ATP binding / membrane / identical protein binding / nucleus / cytosol / cytoplasm
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 / Dihydroorotase signature 1. / Dihydroorotase signature 2. / Dihydroorotase, conserved site / 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 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / 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
Multifunctional protein CAD
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.774 Å
AuthorsHuang, Y.H. / Chen, K.L. / Cheng, J.H. / Huang, C.Y.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Crystal structures of monometallic dihydropyrimidinase and the human dihydroorotase domain K1556A mutant reveal no lysine carbamylation within the active site
Authors: Cheng, J.H. / Huang, Y.H. / Lin, J.J. / Huang, C.Y.
History
DepositionOct 26, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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

Downloads & links

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Assembly

Deposited unit
A: CAD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7262
Polymers42,6611
Non-polymers651
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-35 kcal/mol
Surface area14220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.841, 108.630, 99.219
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-2009-

HOH

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Components

#1: Protein CAD protein /


Mass: 42660.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Fragment: RESIDUES 1456-1846 / Source: (gene. exp.) Homo sapiens (human) / Gene: CAD / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: P27708, carbamoyl-phosphate synthase (glutamine-hydrolysing), aspartate carbamoyltransferase, dihydroorotase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.81 Å3/Da / Density % sol: 56.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2M sodium chloride, 100mM MES sodium salt pH6.5, 200mM sodium acetate

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.975 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.77→30 Å / Num. obs: 12440 / % possible obs: 99.9 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 23.68
Reflection shellResolution: 2.77→2.87 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 2.74 / Num. unique obs: 1201 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C6B

4c6b


Resolution: 2.774→29.805 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.66
RfactorNum. reflection% reflectionSelection details
Rfree0.2889 600 4.83 %RANDOM
Rwork0.226 ---
obs0.229 12420 99.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.774→29.805 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2788 0 1 14 2803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112863
X-RAY DIFFRACTIONf_angle_d1.1883907
X-RAY DIFFRACTIONf_dihedral_angle_d4.021718
X-RAY DIFFRACTIONf_chiral_restr0.054439
X-RAY DIFFRACTIONf_plane_restr0.008514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7742-3.05310.40851550.30962878X-RAY DIFFRACTION99
3.0531-3.49430.41451560.28342906X-RAY DIFFRACTION100
3.4943-4.40020.26361500.21892944X-RAY DIFFRACTION100
4.4002-29.80710.22091390.18983092X-RAY DIFFRACTION100

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