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- PDB-4isy: Crystal structure of IscS from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 4isy
TitleCrystal structure of IscS from Mycobacterium tuberculosis
ComponentsCysteine desulfurase
KeywordsTRANSFERASE / Desulfurase / PLP cofactor
Function / homology
Function and homology information


cysteine desulfurase / cysteine desulfurase activity / iron-sulfur cluster assembly / transaminase activity / iron-sulfur cluster binding / metal ion binding
Similarity search - Function
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 ...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
Iscs-like cysteine desulfurase / IscS-like cysteine desulfurase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsRybniker, J. / Pojer, F. / Cole, S.T.
CitationJournal: Biochem.J. / Year: 2014
Title: The cysteine desulfurase IscS of Mycobacterium tuberculosis is involved in iron-sulfur cluster biogenesis and oxidative stress defence.
Authors: Rybniker, J. / Pojer, F. / Marienhagen, J. / Kolly, G.S. / Chen, J.M. / van Gumpel, E. / Hartmann, P. / Cole, S.T.
History
DepositionJan 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references
Revision 1.2Sep 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 / 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 / _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
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cysteine desulfurase
B: Cysteine desulfurase
C: Cysteine desulfurase
D: Cysteine desulfurase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,82013
Polymers169,9874
Non-polymers8339
Water4,882271
1
C: Cysteine desulfurase
hetero molecules

A: Cysteine desulfurase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6429
Polymers84,9942
Non-polymers6497
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area7270 Å2
ΔGint-36 kcal/mol
Surface area27000 Å2
MethodPISA
2
B: Cysteine desulfurase
D: Cysteine desulfurase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1784
Polymers84,9942
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-26 kcal/mol
Surface area26400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.814, 78.131, 92.774
Angle α, β, γ (deg.)94.54, 104.71, 98.57
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.999808, -0.007037, 0.018304), (-0.006555, -0.999634, -0.026243), (0.018482, 0.026118, -0.999488)32.94883, -8.62634, 82.56178

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Components

#1: Protein
Cysteine desulfurase /


Mass: 42496.773 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: iscS, MT3109, Rv3025c / Plasmid: pQE-80L / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O53272, UniProt: P9WQ71*PLUS, cysteine desulfurase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.72 Å3/Da / Density % sol: 54.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 ammonium sulfate, 0.1M bis-Tris pH 5.5, 5% glycerol and 10% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2011
RadiationMonochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. all: 104706 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Net I/σ(I): 11.15
Reflection shellResolution: 2.59→2.75 Å / Mean I/σ(I) obs: 3.61 / % possible all: 90.1

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LVM

3lvm


Resolution: 2.59→45.22 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.854 / SU B: 10.919 / SU ML: 0.227 / Cross valid method: THROUGHOUT / ESU R: 0.722 / ESU R Free: 0.308 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24533 2759 5.1 %RANDOM
Rwork0.18596 ---
obs0.18904 51516 97.94 %-
all-51516 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.162 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.59→45.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11208 0 53 271 11532
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01911424
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8331.96315500
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.95851506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.86722.966472
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.094151748
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.34815112
X-RAY DIFFRACTIONr_chiral_restr0.1180.21813
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218608
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.59→2.657 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 171 -
Rwork0.348 3536 -
obs--90.99 %

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