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- PDB-4r5f: X-ray structure of the D199K mutant of the cysteine desulfurase I... -

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Basic information

Entry
Database: PDB / ID: 4r5f
TitleX-ray structure of the D199K mutant of the cysteine desulfurase IscS from A. fulgidus
ComponentsCysteine desulfurase IscS 2
KeywordsMETAL BINDING PROTEIN
Function / homology
Function and homology information


cysteine desulfurase / cysteine desulfurase activity / [2Fe-2S] cluster assembly / 2 iron, 2 sulfur cluster binding / pyridoxal phosphate binding / metal ion binding / cytoplasm
Similarity search - Function
Cysteine desulfurase IscS / Cysteine desulfurase / 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 ...Cysteine desulfurase IscS / Cysteine desulfurase / 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
ACETATE ION / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Cysteine desulfurase IscS 2
Similarity search - Component
Biological speciesArchaeoglobus fulgidus DSM 4304 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPagnier, A. / Nicolet, Y. / Fontecilla-Camps, J.C.
CitationJournal: Biochim.Biophys.Acta / Year: 2015
Title: IscS from Archaeoglobus fulgidus has no desulfurase activity but may provide a cysteine ligand for [Fe2S2] cluster assembly.
Authors: Pagnier, A. / Nicolet, Y. / Fontecilla-Camps, J.C.
History
DepositionAug 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 1.2Apr 29, 2015Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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: Cysteine desulfurase IscS 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,07415
Polymers41,9031
Non-polymers2,17114
Water6,774376
1
A: Cysteine desulfurase IscS 2
hetero molecules

A: Cysteine desulfurase IscS 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,14730
Polymers83,8052
Non-polymers4,34228
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area11370 Å2
ΔGint-50 kcal/mol
Surface area26680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.620, 102.890, 108.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cysteine desulfurase IscS 2


Mass: 41902.676 Da / Num. of mol.: 1 / Mutation: D199K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea)
Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126
Gene: iscS2, AF_0564 / Plasmid: pAra-13 / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: O29689, cysteine desulfurase

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Non-polymers , 6 types, 390 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13N2O5P
#5: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.35 Å3/Da / Density % sol: 47.74 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M calcium acetate, 0.1 sodium cacodylate pH 6.5, 15% (v/v) PEG 300, 2% (v/v) PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 13, 2013
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→46 Å / Num. all: 31629 / Num. obs: 30914 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→2 Å / % possible all: 94.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
REFMACrefinement
ADSCQuantumdata collection
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HVK

4hvk


Resolution: 1.9→25.657 Å / SU ML: 0.22 / σ(F): 1.35 / Phase error: 24.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2008 1542 4.99 %5% random
Rwork0.1506 ---
obs0.1531 30885 97.7 %-
all-31629 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→25.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2794 0 90 376 3260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113224
X-RAY DIFFRACTIONf_angle_d1.2534378
X-RAY DIFFRACTIONf_dihedral_angle_d13.9921241
X-RAY DIFFRACTIONf_chiral_restr0.051494
X-RAY DIFFRACTIONf_plane_restr0.006579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.898-1.95910.35531280.30652422X-RAY DIFFRACTION90
1.9591-2.02910.25211390.22732655X-RAY DIFFRACTION99
2.0291-2.11030.2841410.20262692X-RAY DIFFRACTION99
2.1103-2.20630.20681420.1792683X-RAY DIFFRACTION99
2.2063-2.32250.24821390.16162685X-RAY DIFFRACTION99
2.3225-2.46790.22861420.16142689X-RAY DIFFRACTION100
2.4679-2.65830.23741420.16142700X-RAY DIFFRACTION99
2.6583-2.92540.21391430.15512714X-RAY DIFFRACTION99
2.9254-3.3480.21661410.14592684X-RAY DIFFRACTION98
3.348-4.21510.16081410.11362689X-RAY DIFFRACTION97
4.2151-25.65920.15381440.12562730X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 25.556 Å / Origin y: 16.3574 Å / Origin z: 13.2656 Å
111213212223313233
T0.1929 Å20.0177 Å20.0168 Å2-0.2406 Å2-0.0071 Å2--0.1667 Å2
L1.6585 °20.1498 °20.5446 °2-0.6096 °2-0.114 °2--1.3857 °2
S-0.0147 Å °0.1525 Å °0.112 Å °-0.052 Å °0.0026 Å °0.1033 Å °-0.0423 Å °-0.156 Å °0.0096 Å °
Refinement TLS groupSelection details: all

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