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- PDB-8odq: SufS-SufU complex from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 8odq
TitleSufS-SufU complex from Mycobacterium tuberculosis
Components
  • (Cysteine desulfurase) x 2
  • Nitrogen fixation protein
KeywordsTRANSFERASE / CYSTEINE DESULFURASE SULFUR TRANSFERASE METAL BINDING PROTEIN IRON-SULFUR CLUSTER BIOSYNTHESIS SUF MACHINERY
Function / homology
Function and homology information


cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / iron-sulfur cluster assembly / iron-sulfur cluster binding / pyridoxal phosphate binding / lyase activity / iron ion binding
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 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain ...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 / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / PYRIDOXAL-5'-PHOSPHATE / NifU-like protein / Cysteine desulfurase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsElchennawi, I. / Carpentier, P. / Caux, C. / Ponge, M. / Ollagnier de Choudens, S.
Funding support France, 3items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)labex ARCANE, ANR-11-LABX-0003-01 France
Agence Nationale de la Recherche (ANR)CBH-EUR-GS (ANR-17-EURE-0003) France
Agence Nationale de la Recherche (ANR)Labex GRAL (ANR-10-LABX-49-01) France
CitationJournal: Biomolecules / Year: 2023
Title: Structural and Biochemical Characterization of Mycobacterium tuberculosis Zinc SufU-SufS Complex.
Authors: Elchennawi, I. / Carpentier, P. / Caux, C. / Ponge, M. / Ollagnier de Choudens, S.
History
DepositionMar 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Cysteine desulfurase
D: Cysteine desulfurase
A: Nitrogen fixation protein
C: Nitrogen fixation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,03415
Polymers125,8284
Non-polymers1,20611
Water19,4741081
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14410 Å2
ΔGint-99 kcal/mol
Surface area35730 Å2
Unit cell
Length a, b, c (Å)62.250, 75.553, 75.602
Angle α, β, γ (deg.)92.40, 109.57, 99.71
Int Tables number1
Space group name H-MP1

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Components

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Protein , 3 types, 4 molecules BDAC

#1: Protein Cysteine desulfurase


Mass: 44770.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: csd / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0A045IZN1
#2: Protein Cysteine desulfurase


Mass: 44706.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: csd / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0A045IZN1
#3: Protein Nitrogen fixation protein


Mass: 18175.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: nifU, ERS007661_01045, ERS007663_04335, ERS007665_04180, ERS007679_01173, ERS007681_01466, ERS007688_01535, ERS007703_01815, ERS007720_00538, ERS007722_01936, ERS007739_01318, ERS007741_02197, ...Gene: nifU, ERS007661_01045, ERS007663_04335, ERS007665_04180, ERS007679_01173, ERS007681_01466, ERS007688_01535, ERS007703_01815, ERS007720_00538, ERS007722_01936, ERS007739_01318, ERS007741_02197, ERS024276_01485, ERS027646_03963, ERS027659_01472, ERS027661_04026, SAMEA2683035_01054
Production host: Escherichia coli (E. coli) / References: UniProt: A0A045HJY9

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Non-polymers , 5 types, 1092 molecules

#4: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: NO3
#5: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1081 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.71 Å3/Da / Density % sol: 54.59 % / Description: Elongated crystals of yellowish color
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7 / Details: 0.4 M KNO3, 16% PEG 3350, 0.1M MOPS pH 6.7

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryogenic stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2022 / Details: double SI(111) monochromator
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 147290 / % possible obs: 95.7 % / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Biso Wilson estimate: 29.1 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.104 / Net I/σ(I): 7.47
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 0.96 / Num. unique obs: 22934 / CC1/2: 0.541 / % possible all: 92.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→48.72 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.928 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21373 7209 4.9 %RANDOM
Rwork0.17886 ---
obs0.18056 140036 95.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.033 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å20.95 Å2-0.52 Å2
2--2.28 Å20.77 Å2
3----1.44 Å2
Refinement stepCycle: 1 / Resolution: 1.65→48.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8451 0 69 1081 9601
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0138900
X-RAY DIFFRACTIONr_bond_other_d0.0030.0178278
X-RAY DIFFRACTIONr_angle_refined_deg1.6061.64912103
X-RAY DIFFRACTIONr_angle_other_deg1.4591.5819059
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.69151164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.01820.537503
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.033151384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6751590
X-RAY DIFFRACTIONr_chiral_restr0.0820.21141
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0210233
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021977
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_it2.1022.6734531
X-RAY DIFFRACTIONr_mcbond_other2.1012.6724530
X-RAY DIFFRACTIONr_mcangle_it2.8263.9965650
X-RAY DIFFRACTIONr_mcangle_other2.8263.9975651
X-RAY DIFFRACTIONr_scbond_it2.8763.0084369
X-RAY DIFFRACTIONr_scbond_other2.8743.0054367
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2044.396425
X-RAY DIFFRACTIONr_long_range_B_refined6.20533.99910513
X-RAY DIFFRACTIONr_long_range_B_other5.97133.1910125
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.691 Å
RfactorNum. reflection% reflection
Rfree0.386 487 -
Rwork0.372 9704 -
obs--89.78 %

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