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- PDB-5b89: Crystal structure of a Cysteine Desulfurase from Thermococcus onn... -

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Basic information

Entry
Database: PDB / ID: 5b89
TitleCrystal structure of a Cysteine Desulfurase from Thermococcus onnurineus NA1 in complex with alanine at 1.5 Angstrom resolution
ComponentsCysteine desulfurase
KeywordsTRANSFERASE / Cysteine desulfurase / L-cysteine sulfur-transferase
Function / homology
Function and homology information


cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / pyridoxal phosphate binding
Similarity search - Function
Cysteine desulfurase, SufS / 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, SufS / 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
ALANINE / PYRIDOXAL-5'-PHOSPHATE / cysteine desulfurase
Similarity search - Component
Biological speciesThermococcus onnurineus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHo, T.-H. / Kang, L.-W.
CitationJournal: Archaea / Year: 2017
Title: Catalytic Intermediate Crystal Structures of Cysteine Desulfurase from the ArchaeonThermococcus onnurineus NA1.
Authors: Ho, T.-H. / Huynh, K.-H. / Nguyen, D.Q. / Park, H. / Jung, K. / Sur, B. / Ahn, Y.-J. / Cha, S.-S. / Kang, L.-W.
History
DepositionJun 13, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 8, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 15, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,2358
Polymers93,4082
Non-polymers8276
Water9,818545
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8480 Å2
ΔGint-38 kcal/mol
Surface area26710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.939, 78.718, 171.908
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cysteine desulfurase


Mass: 46704.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus onnurineus (strain NA1) (archaea)
Strain: NA1 / Gene: TON_0289 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B6YT87, cysteine desulfurase

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Non-polymers , 5 types, 551 molecules

#2: Chemical ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO2
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 545 / 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: 2.28 Å3/Da / Density % sol: 46.04 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.03M NaNO3, 0.03M Na2HPO4 , 0.03M (NH4)2SO4, 20% (v/v) ethylene glycol, 15% (w/v) PEG 8000, 0.1M Imidazol/MES pH 6.5
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 11, 2014
RadiationMonochromator: DCM Si (111) Crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 128618 / % possible obs: 94.1 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 62.9
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 12.4 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 6.5 / % possible all: 91.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B7S

5b7s


Resolution: 1.5→49.16 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.148 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19424 6444 5 %RANDOM
Rwork0.1667 ---
obs0.16806 122068 94.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.348 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→49.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6256 0 52 545 6853
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0196442
X-RAY DIFFRACTIONr_bond_other_d0.0030.026246
X-RAY DIFFRACTIONr_angle_refined_deg2.4581.9718697
X-RAY DIFFRACTIONr_angle_other_deg1.178314400
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0245800
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.12924.07285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.757151119
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.181536
X-RAY DIFFRACTIONr_chiral_restr0.160.2964
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0217184
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021414
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_it1.8361.6943212
X-RAY DIFFRACTIONr_mcbond_other1.8321.6943211
X-RAY DIFFRACTIONr_mcangle_it2.4342.5394008
X-RAY DIFFRACTIONr_mcangle_other2.4352.5394009
X-RAY DIFFRACTIONr_scbond_it3.5912.1263230
X-RAY DIFFRACTIONr_scbond_other3.5892.1263230
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2683.0184690
X-RAY DIFFRACTIONr_long_range_B_refined6.48215.2617644
X-RAY DIFFRACTIONr_long_range_B_other6.38315.0287535
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.502→1.541 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 469 -
Rwork0.216 8568 -
obs--90.55 %

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