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- PDB-9ca3: Crystal structure of MarE C280S in complex with cyanide bound hem... -

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Basic information

Entry
Database: PDB / ID: 9ca3
TitleCrystal structure of MarE C280S in complex with cyanide bound heme and its native substrate, beta-methyl-L-tryptophan
ComponentsTryptophan 2,3-dioxygenase
KeywordsOXIDOREDUCTASE / heme-dependent aromatic oxygenase / HDAO / heme / cyanide / beta-methyl-L-tryptophan
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 / CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Tryptophan 2,3-dioxygenase
Function and homology information
Biological speciesStreptomyces sp. B9173 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsShin, I. / Liu, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM108988 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
DepositionJun 16, 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

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Assembly

Deposited unit
A: Tryptophan 2,3-dioxygenase
B: Tryptophan 2,3-dioxygenase
C: Tryptophan 2,3-dioxygenase
D: Tryptophan 2,3-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,53016
Polymers128,0874
Non-polymers3,44312
Water9,368520
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33680 Å2
ΔGint-205 kcal/mol
Surface area32040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.030, 112.961, 83.338
Angle α, β, γ (deg.)90.000, 111.250, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Tryptophan 2,3-dioxygenase


Mass: 32021.684 Da / Num. of mol.: 4 / Mutation: C280S
Source method: isolated from a genetically manipulated source
Details: N-terminal histag was removed by TEV protease. Full-length. C280S mutant.
Source: (gene. exp.) Streptomyces sp. B9173 (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.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CN / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-78U / (betaS)-beta-methyl-L-tryptophan


Mass: 218.252 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H14N2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 520 / 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: 2.43 Å3/Da / Density % sol: 49.44 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 8% Tacsimate pH 6.0, 20% PEG 3350

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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: Apr 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 94295 / % possible obs: 96.6 % / Redundancy: 6.5 % / Biso Wilson estimate: 31.95 Å2 / CC1/2: 0.977 / CC star: 0.994 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.066 / Rrim(I) all: 0.173 / Χ2: 0.988 / Net I/σ(I): 4.1 / Num. measured all: 612990
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.89-1.925.81.08941630.670.8960.4621.1860.66185.2
1.92-1.965.91.02342960.6990.9070.4321.1130.66988.5
1.96-25.90.91744000.7490.9260.3870.9980.69790.8
2-2.045.90.82245790.7830.9370.3460.8940.7194
2.04-2.085.90.747260.8470.9580.2960.7620.7397.2
2.08-2.1360.63247670.8490.9580.270.6890.75897.8
2.13-2.185.80.54446370.8840.9690.2390.5960.80895.3
2.18-2.246.60.46347910.9230.980.190.5010.80498.6
2.24-2.316.90.40148170.940.9840.1610.4330.87498.7
2.31-2.386.90.35347860.9490.9870.1420.3810.93398.6
2.38-2.476.80.30448270.960.990.1230.3290.97498.8
2.47-2.576.80.27448240.9670.9910.1110.2971.0399.1
2.57-2.686.70.22948370.9710.9930.0940.2481.05499.3
2.68-2.826.30.20547290.9710.9930.0890.2241.1696.5
2.82-370.1848150.980.9950.0720.1941.22699.3
3-3.237.10.15748930.9820.9950.0630.1691.22799.4
3.23-3.5670.13448360.9850.9960.0540.1441.27899.3
3.56-4.076.60.12547790.9850.9960.0520.1361.28497.7
4.07-5.1370.11248930.990.9980.0450.121.15498.9
5.13-506.80.12449000.9880.9970.0510.1341.29498.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data scaling
DENZOdata reduction
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→43.24 Å / SU ML: 0.2558 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.9525
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2409 1991 2.12 %
Rwork0.1933 92061 -
obs0.1942 94052 95.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.17 Å2
Refinement stepCycle: LAST / Resolution: 1.89→43.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8221 0 244 520 8985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00948697
X-RAY DIFFRACTIONf_angle_d1.105811874
X-RAY DIFFRACTIONf_chiral_restr0.05351243
X-RAY DIFFRACTIONf_plane_restr0.00931547
X-RAY DIFFRACTIONf_dihedral_angle_d9.55181186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.940.45721090.36565343X-RAY DIFFRACTION77.55
1.94-1.990.33721460.3336104X-RAY DIFFRACTION89.44
1.99-2.050.30191360.30116429X-RAY DIFFRACTION93.99
2.05-2.110.31271450.27636631X-RAY DIFFRACTION97.23
2.11-2.190.331330.24496571X-RAY DIFFRACTION95.77
2.19-2.280.30891460.22186726X-RAY DIFFRACTION98.19
2.28-2.380.25451450.20926747X-RAY DIFFRACTION98.34
2.38-2.50.25941460.19336761X-RAY DIFFRACTION98.69
2.5-2.660.23151480.19086802X-RAY DIFFRACTION99.23
2.66-2.870.23051480.18486662X-RAY DIFFRACTION97.13
2.87-3.150.24171480.1886799X-RAY DIFFRACTION99.33
3.15-3.610.21571450.17996859X-RAY DIFFRACTION99.35
3.61-4.550.2091480.15846744X-RAY DIFFRACTION97.81
4.55-43.240.21231480.17076883X-RAY DIFFRACTION98.57

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