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- PDB-6zek: Crystal structure of mouse CSAD -

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Basic information

Entry
Database: PDB / ID: 6zek
TitleCrystal structure of mouse CSAD
ComponentsCysteine sulfinic acid decarboxylase
KeywordsLYASE / amino acid decarboxylase / pyridoxal phosphate / cysteine sulphinic acid
Function / homology
Function and homology information


L-cysteine catabolic process to hypotaurine / sulfinoalanine decarboxylase / sulfinoalanine decarboxylase activity / L-cysteine catabolic process to taurine / aspartate 1-decarboxylase / aspartate 1-decarboxylase activity / taurine metabolic process / taurine biosynthetic process / carboxy-lyase activity / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Pyridoxal-phosphate binding site / DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site. / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
: / Cysteine sulfinic acid decarboxylase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMahootchi, E. / Raasakka, A. / Haavik, J. / Kursula, P.
CitationJournal: J.Struct.Biol. / Year: 2021
Title: Structure and substrate specificity determinants of the taurine biosynthetic enzyme cysteine sulphinic acid decarboxylase.
Authors: Mahootchi, E. / Raasakka, A. / Luan, W. / Muruganandam, G. / Loris, R. / Haavik, J. / Kursula, P.
History
DepositionJun 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: Cysteine sulfinic acid decarboxylase
B: Cysteine sulfinic acid decarboxylase
C: Cysteine sulfinic acid decarboxylase
D: Cysteine sulfinic acid decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,85726
Polymers234,6964
Non-polymers1,16122
Water11,403633
1
A: Cysteine sulfinic acid decarboxylase
C: Cysteine sulfinic acid decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,95913
Polymers117,3482
Non-polymers61111
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14800 Å2
ΔGint-198 kcal/mol
Surface area31890 Å2
MethodPISA
2
B: Cysteine sulfinic acid decarboxylase
D: Cysteine sulfinic acid decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,89813
Polymers117,3482
Non-polymers55011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14030 Å2
ΔGint-186 kcal/mol
Surface area31870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.940, 113.260, 113.370
Angle α, β, γ (deg.)90.000, 95.808, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Cysteine sulfinic acid decarboxylase / Aspartate 1-decarboxylase / Cysteine-sulfinate decarboxylase / Sulfinoalanine decarboxylase


Mass: 58674.059 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Csad / Production host: Escherichia coli (E. coli)
References: UniProt: Q9DBE0, sulfinoalanine decarboxylase, aspartate 1-decarboxylase

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Non-polymers , 5 types, 655 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 633 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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 % sol: 38.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.15 M KBr, 30% PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 96877 / % possible obs: 90.7 % / Redundancy: 2.7 % / Biso Wilson estimate: 32.3 Å2 / CC1/2: 0.993 / Rrim(I) all: 0.151 / Rsym value: 0.125 / Net I/σ(I): 7.7
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 6937 / CC1/2: 0.389 / Rrim(I) all: 1.411 / Rsym value: 1.165 / % possible all: 88.5

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2jis

2jis


Resolution: 2.1→46.89 Å / SU ML: 0.2833 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.1435
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2352 1999 2.06 %
Rwork0.1794 94825 -
obs0.1806 96824 90.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.08 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15000 0 46 633 15679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007215339
X-RAY DIFFRACTIONf_angle_d0.863720741
X-RAY DIFFRACTIONf_chiral_restr0.04522288
X-RAY DIFFRACTIONf_plane_restr0.00542676
X-RAY DIFFRACTIONf_dihedral_angle_d18.16455707
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.35221380.31456534X-RAY DIFFRACTION88.36
2.15-2.210.3191430.28416769X-RAY DIFFRACTION90.54
2.21-2.280.35771460.26126902X-RAY DIFFRACTION92.75
2.28-2.350.31551460.23316969X-RAY DIFFRACTION93.38
2.35-2.430.30991460.22056917X-RAY DIFFRACTION92.89
2.43-2.530.25281440.19886848X-RAY DIFFRACTION92.16
2.53-2.650.24361410.18446709X-RAY DIFFRACTION90.14
2.65-2.790.23431480.17636927X-RAY DIFFRACTION92.73
2.79-2.960.24011440.16716869X-RAY DIFFRACTION92.2
2.96-3.190.25491440.16986805X-RAY DIFFRACTION91.29
3.19-3.510.21631410.16226728X-RAY DIFFRACTION89.71
3.51-4.020.19721410.14586665X-RAY DIFFRACTION88.77
4.02-5.060.17841400.14186645X-RAY DIFFRACTION88.77
5.06-46.890.22131370.17886538X-RAY DIFFRACTION85.68

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