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- PDB-1elq: CRYSTAL STRUCTURE OF THE CYSTINE C-S LYASE C-DES -

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Basic information

Entry
Database: PDB / ID: 1elq
TitleCRYSTAL STRUCTURE OF THE CYSTINE C-S LYASE C-DES
ComponentsL-CYSTEINE/L-CYSTINE C-S LYASE
KeywordsLYASE / FeS cluster biosynthesis / NifS / pyridoxal 5'-phosphate / thiocysteine
Function / homology
Function and homology information


Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain ...Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / PYRIDOXAL-5'-PHOSPHATE / L-cysteine/cystine lyase C-DES
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsClausen, T. / Kaiser, J.T. / Steegborn, C. / Huber, R. / Kessler, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Crystal structure of the cystine C-S lyase from Synechocystis: stabilization of cysteine persulfide for FeS cluster biosynthesis.
Authors: Clausen, T. / Kaiser, J.T. / Steegborn, C. / Huber, R. / Kessler, D.
History
DepositionMar 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-CYSTEINE/L-CYSTINE C-S LYASE
B: L-CYSTEINE/L-CYSTINE C-S LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,2666
Polymers85,6932
Non-polymers5724
Water12,719706
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-37 kcal/mol
Surface area25960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.4, 65.4, 170.1
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer constructed from chain A a non-crystallographic symmetry partner related by a two-fold axis.

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Components

#1: Protein L-CYSTEINE/L-CYSTINE C-S LYASE


Mass: 42846.578 Da / Num. of mol.: 2
Fragment: 11 RESIDUES OF THE WT-N-TERMINUS REPLACED BY OCTAPEPTIDE
Mutation: MADPVNLIPDR TO MTMITPSL
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL MODIFIED C-DES RETAINS FULL CATALYTIC ACTIVITY
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6714 / Production host: Bacteria (eubacteria) / References: UniProt: Q9ZHG9
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 706 / 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: 2.02 Å3/Da / Density % sol: 39.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG8000, ammonium sulphate, phosphate, citrate, barium chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal
*PLUS
Density % sol: 33 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlC-DES1drop
210 mMMOPS/NaOH1drop
30.010 mMPLP1drop
427 %(v/v)PEG80001reservoir
50.1 Mammonium sulfate1reservoir
60.1 Mcitrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.89
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 7, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. all: 170235 / Num. obs: 61410 / % possible obs: 93.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Biso Wilson estimate: 33.7 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 19.1
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.306 / % possible all: 89.7
Reflection
*PLUS
Num. measured all: 170235 / Rmerge(I) obs: 0.047
Reflection shell
*PLUS
% possible obs: 89.7 % / Mean I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassification
SHARPphasing
CNSrefinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 1.8→25 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: maximum likelihood target using amplitudes
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2765 -RANDOM
Rwork0.198 ---
all0.201 170235 --
obs0.201 61410 93.8 %-
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5841 0 32 706 6579
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.6
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 25 Å / σ(F): 0 / Rfactor obs: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27.4 Å2

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