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- PDB-5g3t: The structure of the L-tryptophan oxidase VioA from Chromobacteri... -

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Basic information

Entry
Database: PDB / ID: 5g3t
TitleThe structure of the L-tryptophan oxidase VioA from Chromobacterium violaceum
ComponentsL-TRYPTOPHAN OXIDASE VIOA
KeywordsOXIDOREDUCTASE / VIOLACEIN / L-TRYPTOPHAN OXIDASE / FLAVOENZYME
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 / Flavin-dependent L-tryptophan oxidase VioA
Similarity search - Component
Biological speciesCHROMOBACTERIUM VIOLACEUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKrausze, J. / Rabe, J. / Moser, J.
CitationJournal: 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 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other / Category: atom_site / pdbx_database_status
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 / _pdbx_database_status.status_code_sf
Revision 2.1May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: L-TRYPTOPHAN OXIDASE VIOA
B: L-TRYPTOPHAN OXIDASE VIOA
C: L-TRYPTOPHAN OXIDASE VIOA
D: L-TRYPTOPHAN OXIDASE VIOA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,99929
Polymers188,8544
Non-polymers4,14525
Water24,5181361
1
A: L-TRYPTOPHAN OXIDASE VIOA
B: L-TRYPTOPHAN OXIDASE VIOA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,33912
Polymers94,4272
Non-polymers1,91210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: L-TRYPTOPHAN OXIDASE VIOA
D: L-TRYPTOPHAN OXIDASE VIOA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,66017
Polymers94,4272
Non-polymers2,23315
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.090, 89.160, 144.430
Angle α, β, γ (deg.)90.00, 92.66, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99974, 0.01948, -0.01207), (0.0194, 0.99979, 0.00666), (0.0122, 0.00642, -0.9999)177.48364, -2.64028, 183.06073
2given(0.99455, -0.10322, 0.0148), (0.09965, 0.98262, 0.15663), (-0.03073, -0.1543, 0.98755)-18.3603, -63.97067, 34.74739
3given(-0.99197, 0.12504, -0.01888), (0.12029, 0.97904, 0.16435), (0.03904, 0.16076, -0.98622)161.98184, -66.70381, 213.30214
4given(-0.9965, -0.08355, -0.00353), (-0.08209, 0.9854, -0.14917), (0.01595, -0.14835, -0.98881)158.91324, -19.47407, 212.55051
5given(0.9944, 0.10541, 0.00774), (-0.10291, 0.9823, -0.15654), (-0.0241, 0.15487, 0.98764)-15.63145, -17.16276, 37.18066
6given(-0.99975, 0.02109, -0.00746), (0.02104, 0.99975, 0.00739), (0.00761, 0.00723, -0.99994)145.2356, -2.61166, 248.65086

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
L-TRYPTOPHAN OXIDASE VIOA


Mass: 47213.609 Da / Num. of mol.: 4 / 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

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Non-polymers , 6 types, 1386 molecules

#2: Chemical
ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1361 / 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: 2.32 Å3/Da / Density % sol: 47.12 % / Description: NONE
Crystal growTemperature: 277 K / pH: 8.5
Details: 0.08 M TRIS PH 8.5, 24 %(W/V) PEG 4000, 0.16 M MGCL2, 20 %(V/V) GLYCEROL AT 277 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033184
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2013 / Details: FOCUSSING MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL SI(111) AND SI(113) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033184 Å / Relative weight: 1
ReflectionResolution: 1.8→19.98 Å / Num. obs: 157109 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 22.91 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.91
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 6.94 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 2 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 1.8→19.992 Å / SU ML: 0.17 / σ(F): 1.35 / Phase error: 21.26 / Stereochemistry target values: ML
Details: THE HYDROGEN ATOMS IN THE STRUCTURE ARE RIDING HYDROGENS AND THEIR POSITIONS WERE NOT REFINED
RfactorNum. reflection% reflection
Rfree0.1922 7851 5 %
Rwork0.1568 --
obs0.1585 157061 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.46 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12747 0 259 1361 14367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813460
X-RAY DIFFRACTIONf_angle_d0.93518284
X-RAY DIFFRACTIONf_dihedral_angle_d14.4587896
X-RAY DIFFRACTIONf_chiral_restr0.0531925
X-RAY DIFFRACTIONf_plane_restr0.0062345
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82050.25072570.24064878X-RAY DIFFRACTION97
1.8205-1.84190.28652600.23094944X-RAY DIFFRACTION97
1.8419-1.86430.2742550.21464849X-RAY DIFFRACTION97
1.8643-1.88790.23872580.20914901X-RAY DIFFRACTION97
1.8879-1.91270.22782590.1974921X-RAY DIFFRACTION98
1.9127-1.93890.23012610.19454954X-RAY DIFFRACTION98
1.9389-1.96660.22662560.18444867X-RAY DIFFRACTION98
1.9666-1.99590.25842600.17774940X-RAY DIFFRACTION98
1.9959-2.02710.23992600.17844934X-RAY DIFFRACTION98
2.0271-2.06030.22532600.17024938X-RAY DIFFRACTION98
2.0603-2.09570.19792580.16374909X-RAY DIFFRACTION98
2.0957-2.13380.19782620.16134965X-RAY DIFFRACTION98
2.1338-2.17480.21632610.15574967X-RAY DIFFRACTION98
2.1748-2.21910.18772610.15364955X-RAY DIFFRACTION99
2.2191-2.26730.19612600.15374950X-RAY DIFFRACTION99
2.2673-2.320.19422610.14894961X-RAY DIFFRACTION99
2.32-2.37790.22192630.15334988X-RAY DIFFRACTION99
2.3779-2.44210.17542640.14385024X-RAY DIFFRACTION99
2.4421-2.51380.17662610.14654947X-RAY DIFFRACTION99
2.5138-2.59480.20012610.15144969X-RAY DIFFRACTION99
2.5948-2.68740.21262650.15755026X-RAY DIFFRACTION99
2.6874-2.79470.21232630.15844989X-RAY DIFFRACTION99
2.7947-2.92150.20462630.15314997X-RAY DIFFRACTION99
2.9215-3.0750.17942650.15115052X-RAY DIFFRACTION99
3.075-3.26690.16422650.15165021X-RAY DIFFRACTION99
3.2669-3.51790.18482650.15185044X-RAY DIFFRACTION99
3.5179-3.86960.16272660.14435053X-RAY DIFFRACTION99
3.8696-4.42420.15162660.13055050X-RAY DIFFRACTION100
4.4242-5.55420.1822680.1385085X-RAY DIFFRACTION99
5.5542-19.99320.19142670.17615132X-RAY DIFFRACTION99
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)
10.7050.0271-0.0470.3944-0.040.4782-0.0088-0.18290.13920.04050.03130.0141-0.1003-0.048-0.03190.10880.0201-0.00680.1405-0.030.114176.00381.660875.2835
20.3724-0.11960.11850.1352-0.12290.41650.08130.1997-0.2416-0.16120.04340.06020.05370.09080.0560.16970.0147-0.03310.1116-0.02420.213894.613-12.220947.3947
30.1328-0.22180.11680.26360.0650.4501-0.0053-0.0783-0.14620.12170.0240.094-0.0315-0.01960.00010.11950.00940.00950.09930.01150.163393.0874-8.490356.851
40.7336-0.03280.2460.2967-0.06050.6453-0.0037-0.2041-0.01360.02880.04240.0574-0.0077-0.16660.00090.10750.01460.00790.1639-0.0060.096473.9882-6.285982.8058
50.9240.0528-0.17830.3429-0.02130.3677-0.0391-0.1520.1112-0.05730.0299-0.1060.01770.1555-0.02380.1313-0.0178-0.00940.1384-0.02440.142197.2648-0.111171.6195
60.631-0.0441-0.3470.4136-0.48250.39840.0091-0.1489-0.0278-0.04930.0406-0.02420.0689-0.02580.08330.1216-0.0163-0.00320.1048-0.00630.098580.0894-7.882172.8408
70.80840.1204-0.31260.3592-0.15750.86760.04060.0485-0.013-0.0113-0.01430.01250.01050.1140.00020.11010.0196-0.01320.14270.00830.118194.982-2.5473116.9227
80.1750.19350.15890.3128-0.1230.334-0.0066-0.0277-0.255-0.11690.0083-0.07330.07960.06960.0030.14340.01040.00950.10530.00480.186683.6436-8.9233127.2505
90.77830.0903-0.38920.3960.00911.18570.01430.13350.0647-0.0086-0.00650.05280.0528-0.0543-0.00150.13720.0271-0.00930.13350.02240.093889.3368-3.1209107.5884
100.23460.0336-0.2440.10560.01860.9839-0.00410.0235-0.00660.00670.04790.01070.12650.1070.09520.17160.05920.00520.15430.00190.110696.4176-8.5566111.086
110.37540.2497-0.11870.19230.17890.38530.0627-0.06810.04830.0470.02440.0344-0.0839-0.14930.00950.12780.00580.00910.1690.01850.134556.5715-45.1185111.834
121.2999-0.5113-0.33840.26590.21830.43930.00770.1007-0.0901-0.02070.04010.04080.0431-0.02570.01220.1371-0.0003-0.00870.1034-0.00640.140272.6289-51.440788.0685
130.70560.0901-0.01960.1647-0.12931.26230.0323-0.1104-0.0439-0.01680.03950.01140.1293-0.17640.04680.1029-0.0095-0.01160.05180.00470.095360.0405-51.7332113.5922
140.9084-0.1222-0.16160.6824-0.18760.91860.0384-0.0640.1361-0.03490.0122-0.1939-0.09960.11790.02390.1262-0.01690.00220.077-0.02180.164484.652-36.542199.8282
150.34080.3132-0.32040.1719-0.1630.7939-0.00160.0096-0.0823-0.04640.0663-0.00080.1312-0.12520.01720.1588-0.0245-0.02560.11420.02170.140158.8947-55.6737106.2833
160.1437-0.11690.06080.4101-0.04910.13190.00550.03040.06040.089-0.09140.1703-0.0205-0.1522-0.0860.1232-0.00380.02980.2173-0.0630.200695.5618-6.2528155.8653
170.4898-0.1091-0.44160.04220.15290.24610.09440.01170.15770.04020.0489-0.019-0.1635-0.00250.01610.146-0.01340.00550.14-0.03110.1541113.17114.6203145.8575
181.17740.0533-0.18190.2535-0.18040.23790.00360.3688-0.0557-0.11590.0141-0.0156-0.0074-0.13630.01820.14010.0011-0.00680.2156-0.02680.1728118.1537-5.0715126.7252
190.33270.22320.08770.23330.27720.18420.011-0.0017-0.2706-0.0609-0.00310.04630.0563-0.1630.00020.1683-0.01280.00120.1889-0.00370.1772123.1082-10.286129.7259
200.62640.27840.1590.5341-0.05240.42550.0130.03720.0570.0308-0.03040.0807-0.0709-0.059-0.00050.09160.02460.00220.1-0.03380.1217105.1183-0.7219148.6886
210.1137-0.14060.15320.4346-0.04620.18360.0073-0.11-0.06830.1678-0.11540.09130.1626-0.072-0.03210.1671-0.04160.02830.1802-0.03290.1689104.5748-13.1245162.903
220.5017-0.252-0.10070.15310.05220.21090.03090.0607-0.22290.1556-0.0337-0.1770.00810.0714-0.02790.14390.0080.00140.1018-0.02630.141115.9232-13.2597148.3735
230.56480.493-0.27780.6817-0.25580.50780.0515-0.12540.1008-0.0082-0.0883-0.0487-0.04050.0565-0.00150.13-0.0156-0.00280.1446-0.00260.1638131.84527.9052139.4795
240.47070.0424-0.71620.3254-0.17830.8598-0.05110.1584-0.1353-0.04070.0060.03420.0891-0.10460.00070.1193-0.0178-0.00570.128-0.03720.1444106.6156-11.6454146.1746
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 130 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 131 THROUGH 170 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 171 THROUGH 248 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 249 THROUGH 341 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 342 THROUGH 418 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 3 THROUGH 130 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 131 THROUGH 170 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 171 THROUGH 341 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 342 THROUGH 418 )
11X-RAY DIFFRACTION11CHAIN 'C' AND (RESID 1 THROUGH 70 )
12X-RAY DIFFRACTION12CHAIN 'C' AND (RESID 71 THROUGH 169 )
13X-RAY DIFFRACTION13CHAIN 'C' AND (RESID 170 THROUGH 273 )
14X-RAY DIFFRACTION14CHAIN 'C' AND (RESID 274 THROUGH 352 )
15X-RAY DIFFRACTION15CHAIN 'C' AND (RESID 353 THROUGH 418 )
16X-RAY DIFFRACTION16CHAIN 'D' AND (RESID 3 THROUGH 38 )
17X-RAY DIFFRACTION17CHAIN 'D' AND (RESID 39 THROUGH 70 )
18X-RAY DIFFRACTION18CHAIN 'D' AND (RESID 71 THROUGH 130 )
19X-RAY DIFFRACTION19CHAIN 'D' AND (RESID 131 THROUGH 169 )
20X-RAY DIFFRACTION20CHAIN 'D' AND (RESID 170 THROUGH 214 )
21X-RAY DIFFRACTION21CHAIN 'D' AND (RESID 215 THROUGH 248 )
22X-RAY DIFFRACTION22CHAIN 'D' AND (RESID 249 THROUGH 273 )
23X-RAY DIFFRACTION23CHAIN 'D' AND (RESID 274 THROUGH 352 )
24X-RAY DIFFRACTION24CHAIN 'D' AND (RESID 353 THROUGH 418 )

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  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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