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- PDB-5vn6: Crystal structure of Taurine dioxygenase from Burkholderia ambifaria -

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Basic information

Entry
Database: PDB / ID: 5vn6
TitleCrystal structure of Taurine dioxygenase from Burkholderia ambifaria
ComponentsTaurine dioxygenase
KeywordsOXIDOREDUCTASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


taurine dioxygenase / taurine dioxygenase activity / metal ion binding / cytoplasm
Similarity search - Function
: / Clavaminate synthase-like / Double-stranded beta-helix / TauD/TfdA-like domain / Taurine catabolism dioxygenase TauD, TfdA family / Taurine dioxygenase TauD-like superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBurkholderia ambifaria (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of Taurine dioxygenase from Burkholderia ambifaria
Authors: Abendroth, J. / Dranow, D.M. / Lorimer, D.D. / Edwards, T.E.
History
DepositionApr 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Taurine dioxygenase
B: Taurine dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8134
Polymers65,7642
Non-polymers492
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-27 kcal/mol
Surface area23630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.180, 84.890, 95.680
Angle α, β, γ (deg.)90.000, 110.530, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 or (resid 2 and (name...
21(chain B and (resid 1 through 84 or (resid 92...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETMETMET(chain A and (resid 1 or (resid 2 and (name...AA19
12ARGARGARGARG(chain A and (resid 1 or (resid 2 and (name...AA210
13METMETPHEPHE(chain A and (resid 1 or (resid 2 and (name...AA1 - 2829 - 290
14METMETPHEPHE(chain A and (resid 1 or (resid 2 and (name...AA1 - 2829 - 290
15METMETPHEPHE(chain A and (resid 1 or (resid 2 and (name...AA1 - 2829 - 290
16METMETPHEPHE(chain A and (resid 1 or (resid 2 and (name...AA1 - 2829 - 290
21METMETLYSLYS(chain B and (resid 1 through 84 or (resid 92...BB1 - 849 - 92
22ARGARGARGARG(chain B and (resid 1 through 84 or (resid 92...BB92100
23METMETPHEPHE(chain B and (resid 1 through 84 or (resid 92...BB1 - 2829 - 290
24METMETPHEPHE(chain B and (resid 1 through 84 or (resid 92...BB1 - 2829 - 290
25METMETPHEPHE(chain B and (resid 1 through 84 or (resid 92...BB1 - 2829 - 290
26METMETPHEPHE(chain B and (resid 1 through 84 or (resid 92...BB1 - 2829 - 290

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Components

#1: Protein Taurine dioxygenase


Mass: 32882.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia ambifaria (strain MC40-6) (bacteria)
Strain: MC40-6 / Gene: BamMC406_1605 / Plasmid: BuamA.00024.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B1YQF4, taurine dioxygenase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.35 Å3/Da / Density % sol: 47.71 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.65
Details: RigakuReagents JCSG+ screen, D6: 18% PEG 8000, 100mM Tris base/HCl pH 7.65, 200mM MgCl2: BuamA.00024.a.B1.PS02503 at 20.9mg/ml : cryo: 20% EG: tray 267365D6, puck PRV7-6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 3, 2016
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.1→40.465 Å / Num. obs: 35488 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.21 % / Biso Wilson estimate: 36.43 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.055 / Χ2: 0.985 / Net I/σ(I): 19.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.154.2520.5692.8225980.8360.65299.9
2.15-2.214.2450.473.3225450.9120.53899.8
2.21-2.284.2340.3394.5824620.9370.38899.6
2.28-2.354.2480.2965.1424440.9430.33999.7
2.35-2.424.2650.2376.3323300.9610.271100
2.42-2.514.2710.1678.6522470.9820.191100
2.51-2.64.2730.1579.1121820.9830.1899.8
2.6-2.714.2720.1211.7220840.9890.13899.4
2.71-2.834.2550.09214.9620330.9920.10599.9
2.83-2.974.240.06919.2319130.9950.07999.6
2.97-3.134.2420.05523.5218450.9970.06399.7
3.13-3.324.2170.04329.9217400.9980.049100
3.32-3.554.1840.03435.1616460.9990.03999.8
3.55-3.834.120.03140.2515120.9980.03699.9
3.83-4.24.0660.02745.1614060.9980.03199.4
4.2-4.74.0980.02449.212650.9990.02899.8
4.7-5.424.1150.02350.211290.9990.02799.4
5.42-6.644.1090.02348.679590.9990.026100
6.64-9.394.0660.02152.147410.9990.02599.5
9.39-40.4653.60.01952.514070.9990.02295.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIXmodel building
ARPmodel building
Cootmodel building
PHENIX(dev_2747)refinement
PDB_EXTRACT3.22data extraction
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3pvj

3pvj


Resolution: 2.1→40.465 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.52
RfactorNum. reflection% reflection
Rfree0.2047 1978 5.58 %
Rwork0.1647 --
obs0.167 35477 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 131.92 Å2 / Biso mean: 51.1444 Å2 / Biso min: 21.18 Å2
Refinement stepCycle: final / Resolution: 2.1→40.465 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4188 0 2 290 4480
Biso mean--47.88 46.44 -
Num. residues----541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074310
X-RAY DIFFRACTIONf_angle_d0.8885885
X-RAY DIFFRACTIONf_chiral_restr0.056638
X-RAY DIFFRACTIONf_plane_restr0.007781
X-RAY DIFFRACTIONf_dihedral_angle_d14.4112537
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2423X-RAY DIFFRACTION5.925TORSIONAL
12B2423X-RAY DIFFRACTION5.925TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.15260.27681230.221223732496100
2.1526-2.21070.27061260.211524012527100
2.2107-2.27580.22541460.183723692515100
2.2758-2.34920.24241300.188124222552100
2.3492-2.43320.25931390.173123902529100
2.4332-2.53060.23641350.17823682503100
2.5306-2.64580.23981470.190423812528100
2.6458-2.78520.25261530.188623802533100
2.7852-2.95970.24281400.179623862526100
2.9597-3.18810.22231520.179323822534100
3.1881-3.50880.21291440.169423922536100
3.5088-4.01610.19361490.146424022551100
4.0161-5.05830.1491620.129123982560100
5.0583-40.4730.1791320.16182455258799
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)
13.6831-0.41841.49791.5176-0.93993.4839-0.08950.6707-0.1684-0.4145-0.11570.35670.1304-0.18960.16950.4419-0.1144-0.05740.4609-0.12640.318412.7568-2.61916.6203
21.3848-0.0720.05020.39610.44533.7102-0.19830.19840.048-0.1498-0.02870.1416-0.1494-0.52350.20230.2808-0.0698-0.04740.2756-0.03060.361213.07051.658727.4321
31.34280.2977-0.76240.2470.25661.4442-0.19580.4721-0.0531-0.32240.1811-0.4214-0.26431.21530.16150.56-0.4080.0311.1020.08810.492648.040410.184614.8067
41.45650.42880.12450.5660.0182.8308-0.28980.2231-0.0504-0.11630.1019-0.1479-0.23750.92050.13610.3245-0.1302-0.01030.4680.05540.39739.98298.021133.2681
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 78 )A1 - 78
2X-RAY DIFFRACTION2chain 'A' and (resid 79 through 282 )A79 - 282
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 95 )B1 - 95
4X-RAY DIFFRACTION4chain 'B' and (resid 96 through 282 )B96 - 282

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