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- PDB-2jis: Human cysteine sulfinic acid decarboxylase (CSAD) in complex with PLP. -

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Basic information

Entry
Database: PDB / ID: 2jis
TitleHuman cysteine sulfinic acid decarboxylase (CSAD) in complex with PLP.
ComponentsCYSTEINE SULFINIC ACID DECARBOXYLASE
KeywordsLYASE / PYRIDOXAL PHOSPHATE / ALTERNATIVE SPLICING / PYRIDOXAL PHOSPHATE (PLP) / STRUCTURAL GENOMICS CONSORTIUM (SGC) / VITAMIN B6 / DECARBOXYLASE
Function / homology
Function and homology information


L-cysteine catabolic process to hypotaurine / sulfinoalanine decarboxylase / sulfinoalanine decarboxylase activity / L-cysteine catabolic process to taurine / Degradation of cysteine and homocysteine / aspartate 1-decarboxylase / aspartate 1-decarboxylase activity / taurine biosynthetic process / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Aspartate Aminotransferase, domain 1 - #170 / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / PYRIDOXAL-5'-PHOSPHATE / Cysteine sulfinic acid decarboxylase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsCollins, R. / Moche, M. / Arrowsmith, C. / Berglund, H. / Busam, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. / Graslund, S. ...Collins, R. / Moche, M. / Arrowsmith, C. / Berglund, H. / Busam, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Lehtio, L. / Nordlund, P. / Nyman, T. / Ogg, D. / Persson, C. / Sagemark, J. / Stenmark, P. / Sundstrom, M. / Thorsell, A.G. / Tresaugues, L. / van den Berg, S. / Weigelt, J. / Welin, M. / Holmberg-Schiavone, L. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The Crystal Structure of Human Cysteine Sulfinic Acid Decarboxylase (Csad)
Authors: Collins, R. / Moche, M. / Arrowsmith, C. / Berglund, H. / Busam, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Johansson, I. ...Authors: Collins, R. / Moche, M. / Arrowsmith, C. / Berglund, H. / Busam, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Lehtio, L. / Nordlund, P. / Nyman, T. / Ogg, D. / Persson, C. / Sagemark, J. / Stenmark, P. / Sundstrom, M. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Holmberg-Schiavone, L.
History
DepositionJun 30, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,9166
Polymers115,2982
Non-polymers6184
Water17,096949
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14470 Å2
ΔGint-116.1 kcal/mol
Surface area39350 Å2
MethodPQS
Unit cell
Length a, b, c (Å)65.318, 100.636, 163.104
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9646, 0.257, 0.05824), (0.2573, -0.9663, 0.002899), (0.0575, 0.01232, -0.9983)
Vector: -28.01, 193.2, 90.94)

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Components

#1: Protein CYSTEINE SULFINIC ACID DECARBOXYLASE / SULFINOALANINE DECARBOXYLASE / CYSTEINE-SULFINATE DECARBOXYLASE


Mass: 57648.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CONSTRUCT CONTAINS AN N-TERMINAL HEXAHISTIDINE TAIL
Source: (gene. exp.) HOMO SAPIENS (human) / Description: MAMMALIAN GENE COLLECTION (MGC) / Plasmid: PNIC-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y600, sulfinoalanine decarboxylase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 949 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsOUR CONSTRUCT CONTAINS AN N-TERMINAL HEXAHISTIDINE SEQUENCE AND A LINKER REGION. THE CONFLICT ...OUR CONSTRUCT CONTAINS AN N-TERMINAL HEXAHISTIDINE SEQUENCE AND A LINKER REGION. THE CONFLICT ANNOTATED BELOW HAS BEEN ANNOTATED IN THE UNIPROT ENTRY AS COMING FROM EMBL ENTRY AAD32545.

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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: 2.19 Å3/Da / Density % sol: 43.38 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.972
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 30, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. obs: 139849 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 14.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 21.8
Reflection shellResolution: 1.6→1.8 Å / Redundancy: 14.9 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 9.14 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.6→39.87 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.156 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.179 5594 4 %RANDOM
Rwork0.153 ---
obs0.154 134254 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20 Å20 Å2
2--0.1 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 1.6→39.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7571 0 38 949 8558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0227957
X-RAY DIFFRACTIONr_bond_other_d0.0010.025493
X-RAY DIFFRACTIONr_angle_refined_deg1.241.9710791
X-RAY DIFFRACTIONr_angle_other_deg0.928313340
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.51951006
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.77323.479365
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.394151388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0141566
X-RAY DIFFRACTIONr_chiral_restr0.1060.21182
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028942
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021652
X-RAY DIFFRACTIONr_nbd_refined0.2250.21721
X-RAY DIFFRACTIONr_nbd_other0.1960.26034
X-RAY DIFFRACTIONr_nbtor_refined0.1790.23890
X-RAY DIFFRACTIONr_nbtor_other0.0830.24021
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2707
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2240.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.242
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.31526359
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.53237879
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4443549
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.42552903
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.208 403
Rwork0.157 9681

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