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- PDB-1i29: CRYSTAL STRUCTURE OF CSDB COMPLEXED WITH L-PROPARGYLGLYCINE -

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Basic information

Entry
Database: PDB / ID: 1i29
TitleCRYSTAL STRUCTURE OF CSDB COMPLEXED WITH L-PROPARGYLGLYCINE
ComponentsCSDB
KeywordsLYASE / External aldimine
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 / cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / sulfur compound 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 / cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / sulfur compound 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
(2S)-2-aminobut-3-ynoic acid / PYRIDOXAL-5'-PHOSPHATE / : / Cysteine desulfurase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.8 Å
AuthorsMihara, H. / Fujii, T. / Kurihara, T. / Hata, Y. / Esaki, N.
Citation
Journal: J.BIOCHEM.(TOKYO) / Year: 2002
Title: Structure of external aldimine of Escherichia coli CsdB, an IscS/NifS homolog: implications for its specificity toward selenocysteine.
Authors: Mihara, H. / Fujii, T. / Kato, S. / Kurihara, T. / Hata, Y. / Esaki, N.
#1: Journal: Biochemistry / Year: 2000
Title: Structure of a NifS Homologue: X-ray Structure Analysis of CsdB, An Escherichia coli Counterpart of Mammalian Selenocysteine Lyase
Authors: Fujii, T. / Maeda, M. / Mihara, H. / Kurihara, T. / Esaki, N. / Hata, Y.
#2: Journal: J.Biol.Chem. / Year: 1999
Title: A NifS-like Gene, CsdB, Encodes an Escherichia coli Counterpart of Mammalian Selenocysteine Lyase: Gene Cloning, Purification, Characterization and Preliminary X-ray Crystallographic Studies
Authors: Mihara, H. / Maeda, M. / Fujii, T. / Kurihara, T. / Hata, Y. / Esaki, N.
History
DepositionFeb 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Mar 2, 2022Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / struct_conn / struct_site
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 9, 2023Group: 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: CSDB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8273
Polymers44,4811
Non-polymers3462
Water00
1
A: CSDB
hetero molecules

A: CSDB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6546
Polymers88,9612
Non-polymers6924
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7720 Å2
ΔGint-39 kcal/mol
Surface area26760 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)128.459, 128.459, 136.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe second part of the biological assembly is generated by the two fold axis: y, x, -z.

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Components

#1: Protein CSDB


Mass: 44480.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CSDB OR SUFS / Plasmid: PUC118 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: GenBank: 12619308, UniProt: P77444*PLUS, selenocysteine lyase
#2: Chemical ChemComp-LPG / (2S)-2-aminobut-3-ynoic acid / 2-AMINO-BUT-3-YNOIC ACID / 2-amino-3-butynoic acid


Type: L-peptide linking / Mass: 99.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO2
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P

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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: 298.15 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: sodium acetate, potassium phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1droppH7.4
20.1 MKPB1reservoir
31.4 Msodium acetate1reservoirpH6.8
410 mMKPB1drop

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Data collection

DiffractionMean temperature: 293.15 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 23, 1998 / Details: GRAPHITE-MONOCHROMATER
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 25650 / Num. obs: 23684 / % possible obs: 82.3 % / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Biso Wilson estimate: 42.782 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 10.6
Reflection shellResolution: 2.8→5.1 Å / Rmerge(I) obs: 0.341 / % possible all: 78.5
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 65095 / Rmerge(I) obs: 0.0963

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Processing

Software
NameClassification
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1C0N

1c0n


Resolution: 2.8→50 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 215785.24 / Data cutoff low absF: 0 / Isotropic thermal model: ISOTROPIC / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1152 4.9 %RANDOM
Rwork0.209 ---
all-23684 --
obs-23684 82.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.91 Å2 / ksol: 0.318 e/Å3
Displacement parametersBiso mean: 40.9 Å2
Baniso -1Baniso -2Baniso -3
1-5.54 Å20 Å20 Å2
2--5.54 Å20 Å2
3----11.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.93 Å0.95 Å
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3096 0 21 0 3117
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.172
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it2.112
X-RAY DIFFRACTIONc_scbond_it1.952
X-RAY DIFFRACTIONc_scangle_it3.292.5
LS refinement shellResolution: 2.8→2.93 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.42 120 5.3 %
Rwork0.42 2784 -
obs-2022 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PARA.PLPTOPO.PLP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 50 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75
LS refinement shell
*PLUS
Rfactor Rfree: 0.425 / Rfactor Rwork: 0.421

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