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- PDB-4n6e: Crystal structure of Amycolatopsis orientalis BexX/CysO complex -

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Basic information

Entry
Database: PDB / ID: 4n6e
TitleCrystal structure of Amycolatopsis orientalis BexX/CysO complex
Components
  • Putative thiosugar synthase
  • ThiS/MoaD family protein
KeywordsLyase/BIOSYNTHETIC PROTEIN / Alpha beta barrel / protein-protein complex / BexX / thiosugar synthase / CysO / sulfur carrier protein / Lyase-BIOSYNTHETIC PROTEIN complex
Function / homology
Function and homology information


thiazole synthase / thiazole synthase activity / thiamine diphosphate biosynthetic process / metal ion binding
Similarity search - Function
Thiazole synthase / MoaD, archaeal-type / Thiazole synthase ThiG / : / Thiazole biosynthesis protein ThiG / Sulfur carrier ThiS/MoaD-like / ThiS family / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / Beta-grasp domain / Beta-grasp domain superfamily ...Thiazole synthase / MoaD, archaeal-type / Thiazole synthase ThiG / : / Thiazole biosynthesis protein ThiG / Sulfur carrier ThiS/MoaD-like / ThiS family / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / Beta-grasp domain / Beta-grasp domain superfamily / Ubiquitin-like (UB roll) / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Roll / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
thiazole synthase / MoaD family protein
Similarity search - Component
Biological speciesAmycolatopsis orientalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsZhang, X. / Zhang, Y. / Kinsland, C. / Sasaki, E. / Sun, H.G. / Lu, M.J. / Liu, T. / Ou, A. / Li, J. / Chen, Y. ...Zhang, X. / Zhang, Y. / Kinsland, C. / Sasaki, E. / Sun, H.G. / Lu, M.J. / Liu, T. / Ou, A. / Li, J. / Chen, Y. / Liu, H. / Ealick, S.E.
CitationJournal: Nature / Year: 2014
Title: Co-opting sulphur-carrier proteins from primary metabolic pathways for 2-thiosugar biosynthesis.
Authors: Sasaki, E. / Zhang, X. / Sun, H.G. / Lu, M.Y. / Liu, T.L. / Ou, A. / Li, J.Y. / Chen, Y.H. / Ealick, S.E. / Liu, H.W.
History
DepositionOct 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Database references
Revision 1.2Jul 9, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Putative thiosugar synthase
B: ThiS/MoaD family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8923
Polymers36,7962
Non-polymers961
Water99155
1
A: Putative thiosugar synthase
B: ThiS/MoaD family protein
hetero molecules

A: Putative thiosugar synthase
B: ThiS/MoaD family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7846
Polymers73,5924
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_635y+3/2,x-3/2,-z+1/21
Buried area7520 Å2
ΔGint-90 kcal/mol
Surface area26760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.362, 106.362, 181.674
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Putative thiosugar synthase


Mass: 27126.107 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis orientalis (bacteria) / Strain: subsp. vinearia / Gene: bexX / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D7RFL7
#2: Protein ThiS/MoaD family protein


Mass: 9669.981 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis orientalis (bacteria) / Strain: HCCB10007 / Gene: AORI_6493 / Plasmid: pTYB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: R4T9W5*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 55 / 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: 3.49 Å3/Da / Density % sol: 64.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 28% PEG4000, 0.1 M Tris, pH 8.0, 0.2 M Lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 16381 / % possible obs: 99.6 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.145 / Χ2: 0.941 / Net I/σ(I): 5.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.6-2.645.20.4757990.945199.8
2.64-2.695.50.4518080.9721100
2.69-2.746.20.4218100.9261100
2.74-2.86.30.3768090.9351100
2.8-2.866.20.3378020.9261100
2.86-2.936.20.3377960.9081100
2.93-36.20.318010.9861100
3-3.086.10.2728210.917199.5
3.08-3.1760.2538100.955199.8
3.17-3.285.90.2427960.883198.9
3.28-3.395.80.2148120.926199.6
3.39-3.535.30.198150.921199.9
3.53-3.696.30.1738290.937199.9
3.69-3.886.20.1618120.9771100
3.88-4.136.10.1378240.9331100
4.13-4.4560.1178280.932199.8
4.45-4.895.70.1088240.946198.6
4.89-5.65.50.0958401.003199.4
5.6-7.0560.0848460.925199.4
7.05-505.40.0618990.967197.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→46.06 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.914 / Occupancy max: 1 / Occupancy min: 1 / SU B: 8.246 / SU ML: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.394 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2403 1650 10.1 %RANDOM
Rwork0.1956 ---
obs0.2001 16381 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 113.14 Å2 / Biso mean: 46.8253 Å2 / Biso min: 20.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å2-0 Å2
2--0.11 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.6→46.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2483 0 5 55 2543
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192518
X-RAY DIFFRACTIONr_bond_other_d0.0010.022495
X-RAY DIFFRACTIONr_angle_refined_deg1.2311.9913419
X-RAY DIFFRACTIONr_angle_other_deg0.74635725
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6595331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.47523.529102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.41415426
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6151525
X-RAY DIFFRACTIONr_chiral_restr0.0640.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212844
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02513
X-RAY DIFFRACTIONr_mcbond_it2.3194.481330
X-RAY DIFFRACTIONr_mcbond_other2.3154.4791329
X-RAY DIFFRACTIONr_mcangle_it3.7216.711659
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 113 -
Rwork0.243 1070 -
all-1183 -
obs--98.5 %

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