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- PDB-1jf9: Crystal Structure of selenocysteine lyase -

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Basic information

Entry
Database: PDB / ID: 1jf9
TitleCrystal Structure of selenocysteine lyase
ComponentsSELENOCYSTEINE LYASE
KeywordsLYASE / NIFS / SELENOCYSTEINE / CYSTEINE / PURSULFIDE / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


selenium compound metabolic process / Hydrolases; Acting on carbon-sulfur bonds; Acting on carbon-sulfur bonds / cysteine sulfinate desulfinase activity / selenocysteine lyase / selenocysteine lyase activity / sulfur compound metabolic process / cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / iron-sulfur cluster assembly ...selenium compound metabolic process / Hydrolases; Acting on carbon-sulfur bonds; Acting on carbon-sulfur bonds / cysteine sulfinate desulfinase activity / selenocysteine lyase / selenocysteine lyase activity / sulfur compound metabolic process / cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / iron-sulfur cluster assembly / pyridoxal phosphate binding / hydrolase activity / protein homodimerization activity / cytoplasm
Similarity search - Function
Cysteine desulfurase, SufS / 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 ...Cysteine desulfurase, SufS / 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 / Cysteine desulfurase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsLima, C.D. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Analysis of the E. coli NifS CsdB Protein at 2.0A Reveals the Structural Basis for Perselenide and Persulfide Intermediate Formation
Authors: Lima, C.D.
History
DepositionJun 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 21, 2015Group: Refinement description
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_conn ...audit_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag ..._audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: SELENOCYSTEINE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8722
Polymers44,6251
Non-polymers2471
Water10,431579
1
A: SELENOCYSTEINE LYASE
hetero molecules

A: SELENOCYSTEINE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,7444
Polymers89,2492
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7650 Å2
ΔGint-40 kcal/mol
Surface area26890 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)126.375, 126.375, 133.578
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein SELENOCYSTEINE LYASE / NifS/CdsB / SELENOCYSTEINE REDUCTASE / SELENOCYSTEINE BETA-LYASE / SCL


Mass: 44624.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: NIFS/CSDB / Plasmid: PET28B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P77444, selenocysteine lyase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 579 / 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

Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 4M NACL, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 mg/mlprotein1drop
210 mMTris-HCl1droppH8.
350 mM1dropNaCl
41 mMdithiothreitol1drop
54-4.5 M1reservoirNaCl
6100 mMMES1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 1, 2000
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 119406 / Num. obs: 119406 / % possible obs: 85.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 25.268 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 11.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.267 / % possible all: 60.1
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Num. obs: 67725 / % possible obs: 91.7 % / Num. measured all: 358903
Reflection shell
*PLUS
% possible obs: 75.5 % / Mean I/σ(I) obs: 2.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
REFMACrefinement
RefinementResolution: 2→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2067 3409 5.3 %random
Rwork0.1783 ---
all-63941 --
obs-63941 --
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3119 0 15 579 3713
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / σ(I): 0 / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.179 / Rfactor Rfree: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.7

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