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- PDB-5g3u: The structure of the L-tryptophan oxidase VioA from Chromobacteri... -

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Basic information

Entry
Database: PDB / ID: 5g3u
TitleThe structure of the L-tryptophan oxidase VioA from Chromobacterium violaceum in complex with its inhibitor 2-(1H-indol-3-ylmethyl)prop-2- enoic acid
ComponentsL-TRYPTOPHAN OXIDASE VIOA
KeywordsOXIDOREDUCTASE / VIOLACEIN / L-TRYPTOPHAN OXIDASE / FLAVOENZYME / TRYPTOPHAN DERIVATIVE / INHIBITOR / 2-(1H-INDOL-3-YLMETHYL)PROP-2-ENOIC ACID / PROPENOIC ACID
Function / homology
Function and homology information


7-chloro-L-tryptophan oxidase / antibiotic biosynthetic process / oxidoreductase activity / metal ion binding
Similarity search - Function
Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / 2-[(1H-indol-3-yl)methyl]prop-2-enoic acid / Flavin-dependent L-tryptophan oxidase VioA
Similarity search - Component
Biological speciesCHROMOBACTERIUM VIOLACEUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.377 Å
AuthorsKrausze, J. / Rabe, J. / Moser, J.
Citation
Journal: J.Biol.Chem. / Year: 2016
Title: Biosynthesis of Violacein, Structure and Function of l-Tryptophan Oxidase VioA from Chromobacterium violaceum.
Authors: Fuller, J.J. / Ropke, R. / Krausze, J. / Rennhack, K.E. / Daniel, N.P. / Blankenfeldt, W. / Schulz, S. / Jahn, D. / Moser, J.
#1: Journal: J.Biol.Chem. / Year: 2016
Title: Biosynthesis of Violacein: Structure and Function of L-Tryptophan Oxidase Vioa Chromobacterium Violaceum
Authors: Fuller, J. / Roepke, R. / Krausze, J. / Rennhack, K.E. / Daniel, N.P. / Blankenfeldt, W. / Schulz, S. / Jahn, D. / Moser, J.
History
DepositionMay 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Oct 5, 2016Group: Database references
Revision 2.0May 8, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Experimental preparation / Other
Category: atom_site / citation ...atom_site / citation / citation_author / database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_biol / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.pdbx_auth_atom_name / _atom_site.pdbx_formal_charge / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-TRYPTOPHAN OXIDASE VIOA
B: L-TRYPTOPHAN OXIDASE VIOA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5617
Polymers94,4912
Non-polymers2,0705
Water5,350297
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.270, 81.460, 167.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.35038, -0.46053, -0.81556), (-0.91712, -0.00801, 0.39853), (-0.19006, 0.88761, -0.41956)
Vector: 64.05034, 23.74118, 108.9662)

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Components

#1: Protein L-TRYPTOPHAN OXIDASE VIOA


Mass: 47245.676 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHROMOBACTERIUM VIOLACEUM (bacteria) / Strain: 12472 / Plasmid: PGEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): LAMBDA / References: UniProt: Q9S3V1, 7-chloro-L-tryptophan oxidase
#2: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#3: Chemical ChemComp-ITW / 2-[(1H-indol-3-yl)methyl]prop-2-enoic acid


Mass: 201.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H11NO2
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details2-(1H-INDOL-3-YLMETHYL)PROP-2-ENOIC ACID (ITW): TRYPTOPHAN DERIVATIVE

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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: 2.5 Å3/Da / Density % sol: 50.89 % / Description: NONE
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M HEPES PH 7.0, 10 %(W/V) PEG 6000, 0.1 M LICL, 0.00375 M 2-(1H-INDOL-3-YLMETHYL)PROP-2-ENOIC ACID AT 290 K, THEN SUPPLEMENTED WITH 20 %(V/V) GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 30, 2014 / Details: MIRRORS
RadiationMonochromator: SI111-DCM WITH SAGITAL BENDER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 2.38→45.98 Å / Num. obs: 38865 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 25.96 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 11
Reflection shellResolution: 2.38→2.44 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.377→45.983 Å / SU ML: 0.26 / σ(F): 1.37 / Phase error: 20.28 / Stereochemistry target values: ML
Details: THE HYDROGEN ATOMS IN THE STRUCTURE ARE RIDING HYDROGENS AND THEIR POSITIONS WERE NOT REFINE
RfactorNum. reflection% reflection
Rfree0.2133 1944 5 %
Rwork0.177 --
obs0.1789 38860 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.21 Å2
Refinement stepCycle: LAST / Resolution: 2.377→45.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6398 0 142 297 6837
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026714
X-RAY DIFFRACTIONf_angle_d0.5739107
X-RAY DIFFRACTIONf_dihedral_angle_d13.2313903
X-RAY DIFFRACTIONf_chiral_restr0.04950
X-RAY DIFFRACTIONf_plane_restr0.0021172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.377-2.43640.25061360.22392581X-RAY DIFFRACTION100
2.4364-2.50230.2971360.21992587X-RAY DIFFRACTION100
2.5023-2.57590.27061380.21692614X-RAY DIFFRACTION100
2.5759-2.6590.26941370.20692605X-RAY DIFFRACTION100
2.659-2.75410.22811370.20542610X-RAY DIFFRACTION100
2.7541-2.86430.26591380.19952610X-RAY DIFFRACTION100
2.8643-2.99470.23221370.1972608X-RAY DIFFRACTION100
2.9947-3.15250.24381390.19052644X-RAY DIFFRACTION100
3.1525-3.350.21711370.17922605X-RAY DIFFRACTION100
3.35-3.60850.20761380.17482620X-RAY DIFFRACTION100
3.6085-3.97150.19451400.14712649X-RAY DIFFRACTION100
3.9715-4.54570.19921400.13442667X-RAY DIFFRACTION100
4.5457-5.72540.15291420.14852699X-RAY DIFFRACTION100
5.7254-45.99140.17961490.18692817X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.24240.1161-0.16141.86940.78271.0421-0.07630.03440.05610.03680.00120.3330.1051-0.16260.0810.1333-0.0303-0.00310.22650.03970.21828.0008-16.6551-38.8015
21.64420.15480.29651.11420.0881.0734-0.06330.1628-0.0093-0.10660.0272-0.0864-0.0730.05470.04380.15880.00960.0420.1870.02860.213321.046110.7487-38.7466
30.24140.13780.19391.269-0.31960.6858-0.1120.1078-0.0788-0.08230.11440.15090.1966-0.08890.01620.13-0.03380.01480.2173-0.00970.192616.6498-24.6804-40.4184
40.98070.1419-0.24291.8710.09390.81050.1366-0.16440.14390.4767-0.03770.2035-0.1879-0.0466-0.04750.24740.00780.07370.19340.01840.190215.1187-2.7844-21.8173
50.9029-0.0351-0.32251.74120.66271.1521-0.04470.21510.0813-0.18760.0740.0039-0.06960.1001-0.01420.15280.00390.01430.27250.04130.223719.1013-14.9-45.5589
60.29740.10910.03272.64590.73510.8465-0.0197-0.0640.00890.4801-0.0414-0.02560.0722-0.00990.06640.30260.0095-0.00550.26140.01530.181226.7424-47.1627-8.9739
70.67730.33130.26322.18640.18740.7992-0.0213-0.08050.00440.2219-0.0582-0.01630.02780.04440.07910.22090.03860.0180.22210.01840.180524.6317-38.824-14.5851
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 3 THROUGH 96 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 97 THROUGH 170 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 171 THROUGH 248 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 249 THROUGH 352 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 353 THROUGH 418 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 3 THROUGH 170 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 171 THROUGH 418 )

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