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- PDB-8sbg: Crystal structure of B. theta tryptophanase in holo form -

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Basic information

Entry
Database: PDB / ID: 8sbg
TitleCrystal structure of B. theta tryptophanase in holo form
ComponentsTryptophanase
KeywordsLYASE / PLP-dependent enzyme / tryptophanase / tryptophan-indole lyase
Function / homologyPYRIDOXAL-5'-PHOSPHATE
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsGraboski, A.L. / Redinbo, M.R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM135218 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM137286 United States
CitationJournal: Cell Chem Biol / Year: 2023
Title: Mechanism-based inhibition of gut microbial tryptophanases reduces serum indoxyl sulfate.
Authors: Graboski, A.L. / Kowalewski, M.E. / Simpson, J.B. / Cao, X. / Ha, M. / Zhang, J. / Walton, W.G. / Flaherty, D.P. / Redinbo, M.R.
History
DepositionApr 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tryptophanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8342
Polymers54,5871
Non-polymers2471
Water3,387188
1
A: Tryptophanase
hetero molecules

A: Tryptophanase
hetero molecules

A: Tryptophanase
hetero molecules

A: Tryptophanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,3358
Polymers218,3474
Non-polymers9894
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445-x-1,-y-1,z1
crystal symmetry operation7_555y,x,-z+1/31
crystal symmetry operation10_445-y-1,-x-1,-z+1/31
Buried area20320 Å2
ΔGint-98 kcal/mol
Surface area56990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.836, 100.836, 228.406
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Space group name HallP642(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z
#9: y,x,-z+1/3
#10: -y,-x,-z+1/3
#11: -x+y,y,-z
#12: x,x-y,-z+2/3

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Components

#1: Protein Tryptophanase


Mass: 54586.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Plasmid: pLIC-His / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
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: 3.21 Å3/Da / Density % sol: 61.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.0065 M tris hydrochloride pH 8.5, 5.2% w/v PEG3350, 35% w/w glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.94→29.11 Å / Num. obs: 51350 / % possible obs: 99 % / Redundancy: 2 % / Biso Wilson estimate: 40.37 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.025 / Net I/σ(I): 14.66
Reflection shellResolution: 1.94→2.04 Å / Rmerge(I) obs: 0.783 / Mean I/σ(I) obs: 0.75 / Num. unique obs: 4796 / CC1/2: 0.476 / CC star: 0.803 / % possible all: 90.83

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→29.11 Å / SU ML: 0.2743 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.9793
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2466 1990 3.89 %
Rwork0.2205 49104 -
obs0.2215 51094 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.3 Å2
Refinement stepCycle: LAST / Resolution: 1.94→29.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3593 0 15 188 3796
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813685
X-RAY DIFFRACTIONf_angle_d0.96524988
X-RAY DIFFRACTIONf_chiral_restr0.0627543
X-RAY DIFFRACTIONf_plane_restr0.0069648
X-RAY DIFFRACTIONf_dihedral_angle_d18.74851351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.990.38491180.38662883X-RAY DIFFRACTION82.9
1.99-2.040.40731400.35043452X-RAY DIFFRACTION99.86
2.04-2.10.33551420.31693516X-RAY DIFFRACTION99.92
2.1-2.170.33921390.28523451X-RAY DIFFRACTION99.92
2.17-2.250.30061430.27023499X-RAY DIFFRACTION99.78
2.25-2.340.29141410.253495X-RAY DIFFRACTION99.95
2.34-2.440.28761420.25543504X-RAY DIFFRACTION99.97
2.44-2.570.27591430.24413521X-RAY DIFFRACTION99.95
2.57-2.730.30381430.23963537X-RAY DIFFRACTION100
2.73-2.940.27831430.23953537X-RAY DIFFRACTION100
2.94-3.240.29181450.22423576X-RAY DIFFRACTION100
3.24-3.710.21451460.20323593X-RAY DIFFRACTION99.97
3.71-4.670.21411480.17813653X-RAY DIFFRACTION100
4.67-29.110.19111570.23887X-RAY DIFFRACTION100

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