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- PDB-8vyy: The crystal structure of MarE in complex with its native substrat... -

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Basic information

Entry
Database: PDB / ID: 8vyy
TitleThe crystal structure of MarE in complex with its native substrate, beta-methyl-L-tryptophan
ComponentsTryptophan 2,3-dioxygenase
KeywordsOXIDOREDUCTASE / Oxygenase / Monooxygenase / Heme-dependent aromatic oxygenase (HDAO)
Function / homologyTryptophan/Indoleamine 2,3-dioxygenase-like / L-tryptophan catabolic process to kynurenine / dioxygenase activity / heme binding / metal ion binding / (betaS)-beta-methyl-L-tryptophan / PROTOPORPHYRIN IX CONTAINING FE / Tryptophan 2,3-dioxygenase
Function and homology information
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsShin, I. / Liu, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM108988 United States
Welch FoundationAX-2110-20220331 United States
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Structural insights into 2-oxindole-forming monooxygenase MarE: Divergent architecture and substrate positioning versus tryptophan dioxygenases.
Authors: Shin, I. / Nguyen, R.C. / Montoya, S.R. / Liu, A.
History
DepositionFeb 9, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 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: Tryptophan 2,3-dioxygenase
B: Tryptophan 2,3-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8506
Polymers61,1802
Non-polymers1,6694
Water1,65792
1
A: Tryptophan 2,3-dioxygenase
B: Tryptophan 2,3-dioxygenase
hetero molecules

A: Tryptophan 2,3-dioxygenase
B: Tryptophan 2,3-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,70012
Polymers122,3614
Non-polymers3,3398
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-11
Buried area30570 Å2
ΔGint-212 kcal/mol
Surface area31260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)196.119, 196.119, 113.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein Tryptophan 2,3-dioxygenase


Mass: 30590.178 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (bacteria) / Gene: marE / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: X2D878
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-78U / (betaS)-beta-methyl-L-tryptophan


Mass: 218.252 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C12H14N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 4.44 Å3/Da / Density % sol: 72.31 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / Details: Ethylene glycol (25% v/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 40492 / % possible obs: 100 % / Redundancy: 25 % / Biso Wilson estimate: 52.27 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.034 / Rrim(I) all: 0.174 / Χ2: 0.731 / Net I/σ(I): 3.4 / Num. measured all: 1010353
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.45-2.4913.42.34819850.3850.7460.6432.440.799.9
2.49-2.5417.52.13520090.5650.850.5162.1980.699100
2.54-2.59211.85519750.720.9150.411.9010.698100
2.59-2.6423.91.61420020.8150.9480.3351.6490.709100
2.64-2.725.81.29519960.8690.9640.2591.3210.718100
2.7-2.76261.13520390.8920.9710.2261.1570.714100
2.76-2.83240.90719820.9340.9830.1870.9260.72100
2.83-2.927.70.80219810.960.990.1550.8170.724100
2.9-2.9927.80.63620190.9680.9920.1220.6480.735100
2.99-3.0927.60.53120100.9780.9940.1030.5410.748100
3.09-3.227.20.45619980.9820.9960.0890.4650.74899.9
3.2-3.3226.50.32720490.990.9970.0650.3340.765100
3.32-3.4824.50.23119910.9930.9980.0470.2360.789100
3.48-3.6627.40.19520240.9960.9990.0380.1980.811100
3.66-3.8927.50.14120220.9980.9990.0270.1440.855100
3.89-4.1927.10.10520570.99910.020.1070.804100
4.19-4.61250.08420280.99910.0170.0860.774100
4.61-5.2827.70.07920460.99910.0150.080.728100
5.28-6.6525.90.07920890.99910.0160.0810.662100
6.65-5025.10.0362190110.0070.0370.478100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→43.85 Å / SU ML: 0.3159 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.7967
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2095 2000 5.03 %
Rwork0.1766 37790 -
obs0.1783 39790 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.61 Å2
Refinement stepCycle: LAST / Resolution: 2.45→43.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3902 0 118 92 4112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00854187
X-RAY DIFFRACTIONf_angle_d1.14825727
X-RAY DIFFRACTIONf_chiral_restr0.0444597
X-RAY DIFFRACTIONf_plane_restr0.0102745
X-RAY DIFFRACTIONf_dihedral_angle_d9.3746573
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.510.34321340.3332536X-RAY DIFFRACTION93.62
2.51-2.580.33711380.27082623X-RAY DIFFRACTION96.14
2.58-2.660.25251380.2252588X-RAY DIFFRACTION96.7
2.66-2.740.24251410.20332663X-RAY DIFFRACTION97.77
2.74-2.840.22431410.20222664X-RAY DIFFRACTION97.46
2.84-2.950.25371400.19942648X-RAY DIFFRACTION98.1
2.95-3.090.23241430.2112710X-RAY DIFFRACTION98.72
3.09-3.250.24091420.20032685X-RAY DIFFRACTION98.6
3.25-3.450.2321430.17972703X-RAY DIFFRACTION99.27
3.45-3.720.22131450.17172742X-RAY DIFFRACTION99.55
3.72-4.10.21151460.16122753X-RAY DIFFRACTION99.79
4.1-4.690.18141470.13612762X-RAY DIFFRACTION99.62
4.69-5.90.17911480.16492801X-RAY DIFFRACTION99.83
5.9-43.850.16511540.16012912X-RAY DIFFRACTION99.16

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