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- PDB-4c6j: Crystal structure of the dihydroorotase domain of human CAD bound... -

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Basic information

Entry
Database: PDB / ID: 4c6j
TitleCrystal structure of the dihydroorotase domain of human CAD bound to substrate at pH 7.5
ComponentsCAD PROTEIN
KeywordsHYDROLASE / DE NOVO PYRIMIDINE BIOSYNTHESIS / AMIDOHYDROLASE SUPERFAMILY / METALLOENZYME / ZINC BINDING / HISTIDINATE ANION
Function / homology
Function and homology information


Pyrimidine biosynthesis / aspartate binding / response to cortisol / carbamoyl-phosphate synthase (glutamine-hydrolysing) / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / dihydroorotase activity / dihydroorotase / citrulline biosynthetic process / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity ...Pyrimidine biosynthesis / aspartate binding / response to cortisol / carbamoyl-phosphate synthase (glutamine-hydrolysing) / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / dihydroorotase activity / dihydroorotase / citrulline biosynthetic process / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / pyrimidine nucleoside biosynthetic process / UTP biosynthetic process / response to amine / glutamine metabolic process / response to testosterone / drug metabolic process / nitrogen compound metabolic process / response to insulin / 'de novo' UMP biosynthetic process / response to starvation / 'de novo' pyrimidine nucleobase biosynthetic process / response to caffeine / cell projection / cellular response to epidermal growth factor stimulus / lactation / animal organ regeneration / liver development / terminal bouton / nuclear matrix / cellular response to drug / female pregnancy / heart development / peptidyl-threonine phosphorylation / protein kinase activity / protein autophosphorylation / neuronal cell body / enzyme binding / protein-containing complex / zinc ion binding / extracellular exosome / membrane / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Aspartate carbamoyltransferase / Methylglyoxal synthase-like domain / Carbamoyl-phosphate synthase small subunit, N-terminal domain superfamily / Carbamoyl-phosphate synthase small subunit, GATase1 domain / Metal-dependent hydrolase / Class I glutamine amidotransferase-like / Glutamine amidotransferase / Pre-ATP-grasp domain superfamily / ATP-grasp fold, subdomain 1 / ATP-grasp fold ...Aspartate carbamoyltransferase / Methylglyoxal synthase-like domain / Carbamoyl-phosphate synthase small subunit, N-terminal domain superfamily / Carbamoyl-phosphate synthase small subunit, GATase1 domain / Metal-dependent hydrolase / Class I glutamine amidotransferase-like / Glutamine amidotransferase / Pre-ATP-grasp domain superfamily / ATP-grasp fold, subdomain 1 / ATP-grasp fold / Metal-dependent hydrolase, composite domain superfamily / Aspartate/ornithine carbamoyltransferase superfamily / Amidohydrolase-related / Carbamoyl-phosphate synthase, large subunit / Carbamoyl-phosphate synthase, small subunit / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase / Carbamoyl-phosphate synthase large subunit, CPSase domain / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain / Dihydroorotase, conserved site / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain superfamily / Methylglyoxal synthase-like domain superfamily / Dihydroorotase signature 1. / MGS-like domain profile. / Glutamine amidotransferase type 1 domain profile. / ATP-grasp fold profile. / Carbamoyl-phosphate synthase subdomain signature 2. / Glutamine amidotransferase class-I / Dihydroorotase signature 2. / Carbamoyl-phosphate synthase subdomain signature 1. / Aspartate and ornithine carbamoyltransferases signature. / Carbamoyl-phosphate synthetase large chain, oligomerisation domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain / MGS-like domain / Amidohydrolase family / Carbamoyl-phosphate synthase small chain, CPSase domain / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Carbamoyl-phosphate synthase small subunit, N-terminal domain / Metal-dependent hydrolases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
CAD protein
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.299 Å
AuthorsRamon-Maiques, S. / Lallous, N. / Grande-Garcia, A.
CitationJournal: Structure / Year: 2014
Title: Structure, Functional Characterization and Evolution of the Dihydroorotase Domain of Human Cad.
Authors: Grande-Garcia, A. / Lallous, N. / Diaz-Tejada, C. / Ramon-Maiques, S.
Validation Report
SummaryFull reportAbout validation report
History
DepositionSep 18, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CAD PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5859
Polymers42,9161
Non-polymers6698
Water7,638424
1
A: CAD PROTEIN
hetero molecules

A: CAD PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,16918
Polymers85,8322
Non-polymers1,33716
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4990 Å2
ΔGint-263.5 kcal/mol
Surface area25950 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)82.175, 158.908, 61.388
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2031-

HOH

21A-2075-

HOH

31A-2261-

HOH

41A-2350-

HOH

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Components

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Protein/peptide , 1 types, 1 molecules A

#1: Protein/peptide CAD PROTEIN / DIHYDROOROTASE


Mass: 42916.020 Da / Num. of mol.: 1 / Fragment: RESIDUES 1456-1846
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: POPIN-M / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: P27708, dihydroorotase

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Non-polymers , 5 types, 432 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Zinc
#3: Chemical ChemComp-DOR / (4S)-2,6-DIOXOHEXAHYDROPYRIMIDINE-4-CARBOXYLIC ACID / DIHYDROOROTIC ACID


Mass: 158.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6N2O4
#4: Chemical ChemComp-NCD / N-CARBAMOYL-L-ASPARTATE


Mass: 176.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8N2O5
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2 / Formic acid
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / Source method: isolated from a natural source / Formula: H2O / Water

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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: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growpH: 7.5 / Details: pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.31→48.58 Å / Num. obs: 98784 / % possible obs: 99.7 % / Observed criterion σ(I): 1 / Redundancy: 4.4 % / Biso Wilson estimate: 13.05 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 9
Reflection shellResolution: 1.31→1.38 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.9 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4C6C
Resolution: 1.299→48.578 Å / SU ML: 0.09 / σ(F): 1.99 / Phase error: 12.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1409 9515 5 %
Rwork0.1219 --
Obs0.1228 98784 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.299→48.578 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2795 0 35 424 3254
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealNumber
f_bond_d0.0123143
f_angle_d1.3184336
f_dihedral_angle_d14.31195
f_chiral_restr0.082487
f_plane_restr0.007571
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.2985-1.31330.23162810.2313541390
1.3133-1.32870.22643130.20946065100
1.3287-1.34490.22573200.20336049100
1.3449-1.3620.19643100.18546064100
1.362-1.37990.19533220.18146051100
1.3799-1.39880.20273150.16726037100
1.3988-1.41880.18633190.1586095100
1.4188-1.440.16773180.14986015100
1.44-1.46250.16313200.14276059100
1.4625-1.48640.14923170.1334605199
1.4864-1.51210.14723170.1195604099
1.5121-1.53960.14743170.11186031100
1.5396-1.56920.13613180.10596056100
1.5692-1.60120.1473170.10326051100
1.6012-1.6360.12713210.09986048100
1.636-1.67410.12493220.09536062100
1.6741-1.7160.12463200.09396085100
1.716-1.76240.12783190.09646044100
1.7624-1.81420.11533220.09956063100
1.8142-1.87280.12193230.09496086100
1.8728-1.93970.11863170.09796037100
1.9397-2.01740.11353180.09876036100
2.0174-2.10920.12433160.09716083100
2.1092-2.22040.11383230.09696090100
2.2204-2.35950.14713240.10676058100
2.3595-2.54170.12813230.1124600799
2.5417-2.79740.15173090.124603899
2.7974-3.20220.14553160.13636064100
3.2022-4.03410.13063190.1194601499
4.0341-48.61190.1513190.1444604799

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