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- PDB-9ddd: SufS-SufU complex from Mycobacterium Tuberculosis -

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Basic information

Entry
Database: PDB / ID: 9ddd
TitleSufS-SufU complex from Mycobacterium Tuberculosis
Components
  • Possible nitrogen fixation related protein
  • Probable cysteine desulfurase
KeywordsBIOSYNTHETIC PROTEIN / Fe-S cluster biogenesis Cysteine desulfurase Zn binding
Function / homology
Function and homology information


cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / iron-sulfur cluster assembly / ferrous iron binding / 2 iron, 2 sulfur cluster binding / pyridoxal phosphate binding / intracellular iron ion homeostasis / plasma membrane / cytoplasm
Similarity search - Function
NIF system FeS cluster assembly, NifU, N-terminal / NifU-like N terminal 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 / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
ALANINE / Possible nitrogen fixation related protein / Probable cysteine desulfurase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsStuteley, S.M. / Bashiri, G.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Health Research Council (HRC) New Zealand
CitationJournal: Biorxiv / Year: 2025
Title: Feedback regulation of iron-sulfur cluster biogenesis.
Authors: Stuteley, S.M. / Chen, J. / Wang, J. / Dawes, S. / Baker, E.N. / Squire, C.J. / Pandelia, M.E. / Bashiri, G.
History
DepositionAug 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable cysteine desulfurase
B: Probable cysteine desulfurase
C: Possible nitrogen fixation related protein
D: Possible nitrogen fixation related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,5248
Polymers125,2154
Non-polymers3094
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.799, 73.616, 76.349
Angle α, β, γ (deg.)91.03, 100.22, 110.02
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Probable cysteine desulfurase


Mass: 44909.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: csd, Rv1464, MTV007.11
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: P9WQ69, cysteine desulfurase
#2: Protein Possible nitrogen fixation related protein


Mass: 17697.777 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv1465 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): LOBSTR / References: UniProt: O53156
#3: Chemical ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.55 Å3/Da / Density % sol: 51.79 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus 0.1M Carboxylic acids Morpheus Buffer System 1 PH6.5 Morpheus Precipitant mix 1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→48.68 Å / Num. obs: 88203 / % possible obs: 98 % / Redundancy: 7.3 % / CC1/2: 0.998 / Net I/σ(I): 10.8
Reflection shellResolution: 2→2.04 Å / Redundancy: 7 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4246 / CC1/2: 0.808 / % possible all: 91.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0349refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→48.68 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.543 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20272 4434 5 %RANDOM
Rwork0.17939 ---
obs0.18058 83738 97.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.755 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2→48.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8296 0 14 336 8646
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0128500
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167700
X-RAY DIFFRACTIONr_angle_refined_deg1.0091.63311559
X-RAY DIFFRACTIONr_angle_other_deg0.3561.54917822
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.92951098
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.7811074
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.633101274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0470.21319
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210003
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021711
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_it1.6053.3854398
X-RAY DIFFRACTIONr_mcbond_other1.6033.3854398
X-RAY DIFFRACTIONr_mcangle_it2.4995.0635485
X-RAY DIFFRACTIONr_mcangle_other2.4995.0635486
X-RAY DIFFRACTIONr_scbond_it1.9743.6794102
X-RAY DIFFRACTIONr_scbond_other1.9743.6794103
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1915.4166072
X-RAY DIFFRACTIONr_long_range_B_refined4.4640.8829139
X-RAY DIFFRACTIONr_long_range_B_other4.40540.7949075
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.004→2.056 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 290 -
Rwork0.254 5929 -
obs--93.32 %

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