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- PDB-1c0n: CSDB PROTEIN, NIFS HOMOLOGUE -

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Basic information

Entry
Database: PDB / ID: 1c0n
TitleCSDB PROTEIN, NIFS HOMOLOGUE
ComponentsPROTEIN (CSDB PROTEIN)
KeywordsLYASE / ALPHA/BETA FOLD
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
ACETIC ACID / PYRIDOXAL-5'-PHOSPHATE / Cysteine desulfurase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsFujii, T. / Maeda, M. / Mihara, H. / Kurihara, T. / Esaki, N. / Hata, Y.
Citation
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.
#1: 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
DepositionJul 17, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2000Provider: 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 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: PROTEIN (CSDB PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3843
Polymers44,0771
Non-polymers3072
Water00
1
A: PROTEIN (CSDB PROTEIN)
hetero molecules

A: PROTEIN (CSDB PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,7686
Polymers88,1542
Non-polymers6144
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7320 Å2
ΔGint-36 kcal/mol
Surface area26250 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)128.1, 128.1, 137.0
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PROTEIN (CSDB PROTEIN)


Mass: 44077.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PCSDB / Production host: Escherichia coli (E. coli) / References: UniProt: P77444
#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: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
Has protein modificationN

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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 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: sodium acetate, pottasium phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal
*PLUS
Density % sol: 62 %
Crystal grow
*PLUS
Temperature: 25 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlenzyme1drop
2100 mMpotassium phosphate1reservoir
31.4 Msodium acetate1reservoir
40.01 mMPLP1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 17, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→93.6 Å / Num. all: 27061 / Num. obs: 27061 / % possible obs: 94.2 % / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Biso Wilson estimate: 44.1 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 9.62
Reflection shellResolution: 2.8→3 Å / Rmerge(I) obs: 0.216 / Num. unique all: 4641 / % possible all: 88.5
Reflection
*PLUS
Num. obs: 23770 / Num. measured all: 73138
Reflection shell
*PLUS
% possible obs: 88.5 %

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Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.851refinement
RefinementResolution: 2.8→8 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection
Rfree0.239 1090
Rwork0.187 -
all0.19 22429
obs0.19 22429
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3083 0 19 0 3102
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.003
X-RAY DIFFRACTIONx_angle_deg0.821
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
LS refinement shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.92 Å / Rfactor Rfree: 0.345 / Rfactor Rwork: 0.29 / Num. reflection obs: 2000

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