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- PDB-7a0a: Crystal structure of mouse CSAD in apo form -

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Basic information

Entry
Database: PDB / ID: 7a0a
TitleCrystal structure of mouse CSAD in apo form
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: 2.8 Å
AuthorsMahootchi, E. / Raasakka, A. / Haavik, J. / Kursula, P.
CitationJournal: To be published
Title: The structure of cysteine sulphinic acid decarboxylase reveals structural determinants for substrate specificity of pyridoxal phosphate-dependent decarboxylases
Authors: Mahootchi, E. / Raasakka, A. / Luan, W. / Muruganandam, G. / Loris, R. / Haavik, J. / Kursula, P.
History
DepositionAug 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)233,9498
Polymers233,7844
Non-polymers1654
Water36020
1
A: Cysteine sulfinic acid decarboxylase
C: Cysteine sulfinic acid decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,0345
Polymers116,8922
Non-polymers1423
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cysteine sulfinic acid decarboxylase
D: Cysteine sulfinic acid decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,9153
Polymers116,8922
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.060, 114.880, 113.760
Angle α, β, γ (deg.)90.000, 95.804, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 14 through 332 or resid 341 through 458 or resid 462 through 493))
d_2ens_1(chain "B" and resid 14 through 493)
d_3ens_1(chain "C" and (resid 14 through 332 or resid 341 through 458 or resid 462 through 493))
d_4ens_1(chain "D" and (resid 14 through 339 or resid 341 through 458 or resid 462 through 493))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1PROGLNA2 - 320
d_12ens_1LYSHISA324 - 441
d_13ens_1ALALEUA443 - 474
d_21ens_1PROLEUB2 - 470
d_31ens_1PROGLNC3 - 321
d_32ens_1LYSHISC326 - 443
d_33ens_1ALALEUC447 - 478
d_41ens_1PROGLND1 - 319
d_42ens_1LYSHISD321 - 438
d_43ens_1ALALEUD442 - 473

NCS oper:
IDCodeMatrixVector
1given(0.999999746686, 0.000311838594446, 0.000639831923397), (0.000316686929799, -0.999971134328, -0.00759145704519), (0.000637446144924, 0.00759165774858, -0.999970979776)36.5209338461, -35.8959785965, -158.090038974
2given(-0.999977690582, 0.00286974862216, 0.00603182240469), (0.00543648055226, -0.175021848332, 0.98454954029), (0.00388111039278, 0.984560367448, 0.175002342364)-114.296484719, 37.5599199656, -31.0320829918
3given(-0.999965669812, 0.000838102888014, 0.00824359030015), (-0.00800075201448, 0.161168765377, -0.986894430542), (-0.00215572834335, -0.986926505192, -0.16115652697)-77.7195570287, -73.6157344215, -126.454956755

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Components

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


Mass: 58445.941 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
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
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: 39.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 200 mM sodium sulphate, 100 mM bis-tris propane, 20% PEG3350, pH 6.5

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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: 2.8→50 Å / Num. obs: 45520 / % possible obs: 98.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 57.31 Å2 / CC1/2: 0.949 / Rrim(I) all: 0.504 / Rsym value: 0.426 / Net I/σ(I): 3.4
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 0.4 / Num. unique obs: 3321 / CC1/2: 0.184 / Rrim(I) all: 3.809 / Rsym value: 3.231 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.18rc7_3834refinement
XDSdata processing
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2jis

2jis


Resolution: 2.8→47.02 Å / SU ML: 0.539 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.5106
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2917 1973 4.39 %
Rwork0.2427 42959 -
obs0.2449 44932 97.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.64 Å2
Refinement stepCycle: LAST / Resolution: 2.8→47.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14912 0 8 20 14940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003315218
X-RAY DIFFRACTIONf_angle_d0.612320573
X-RAY DIFFRACTIONf_chiral_restr0.042282
X-RAY DIFFRACTIONf_plane_restr0.00462665
X-RAY DIFFRACTIONf_dihedral_angle_d16.55445666
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.611354109458
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.585497539378
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS1.02410141282
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.45831270.41672759X-RAY DIFFRACTION88.53
2.87-2.950.41621400.38622986X-RAY DIFFRACTION94.84
2.95-3.030.33991360.35323035X-RAY DIFFRACTION96.65
3.03-3.130.3691400.3373046X-RAY DIFFRACTION97.7
3.13-3.240.42041410.33533085X-RAY DIFFRACTION98.29
3.24-3.370.35941410.2963095X-RAY DIFFRACTION98.09
3.37-3.530.33351420.2733075X-RAY DIFFRACTION98.38
3.53-3.710.28621430.24973102X-RAY DIFFRACTION98.6
3.71-3.950.29091440.22993109X-RAY DIFFRACTION98.94
3.95-4.250.27191420.20893121X-RAY DIFFRACTION98.55
4.25-4.680.25491420.18923090X-RAY DIFFRACTION98.51
4.68-5.350.2411430.20353123X-RAY DIFFRACTION98.76
5.35-6.740.32451460.22443156X-RAY DIFFRACTION98.89
6.74-47.020.19441460.17853177X-RAY DIFFRACTION98.9

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