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- PDB-1otj: Crystal structure of APO (iron-free) TauD -

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Basic information

Entry
Database: PDB / ID: 1otj
TitleCrystal structure of APO (iron-free) TauD
ComponentsAlpha-Ketoglutarate-Dependent Taurine Dioxygenase
KeywordsOXIDOREDUCTASE / Jelly roll motif / alpha ketoglutarate-dependent dioxygenase / taurine
Function / homology
Function and homology information


taurine catabolic process / taurine dioxygenase complex / taurine dioxygenase / taurine dioxygenase activity / sulfur compound metabolic process / L-ascorbic acid binding / ferrous iron binding / protein homotetramerization / identical protein 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
2-AMINOETHANESULFONIC ACID / Alpha-ketoglutarate-dependent taurine dioxygenase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Direct methods, MAD / Resolution: 1.9 Å
AuthorsO'Brien, J.R. / Schuller, D.J. / Yang, V.S. / Dillard, B.D. / Lanzilotta, W.N.
CitationJournal: Biochemistry / Year: 2003
Title: Substrate-induced conformational changes in Escherichia coli taurine/alpha-ketoglutarate dioxygenase and insight into the oligomeric structure
Authors: O'Brien, J.R. / Schuller, D.J. / Yang, V.S. / Dillard, B.D. / Lanzilotta, W.N.
History
DepositionMar 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Alpha-Ketoglutarate-Dependent Taurine Dioxygenase
B: Alpha-Ketoglutarate-Dependent Taurine Dioxygenase
C: Alpha-Ketoglutarate-Dependent Taurine Dioxygenase
D: Alpha-Ketoglutarate-Dependent Taurine Dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,29610
Polymers129,8144
Non-polymers4826
Water12,791710
1
A: Alpha-Ketoglutarate-Dependent Taurine Dioxygenase
D: Alpha-Ketoglutarate-Dependent Taurine Dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1035
Polymers64,9072
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-33 kcal/mol
Surface area25050 Å2
MethodPISA
2
B: Alpha-Ketoglutarate-Dependent Taurine Dioxygenase
C: Alpha-Ketoglutarate-Dependent Taurine Dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1935
Polymers64,9072
Non-polymers2863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.848, 117.845, 118.262
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTwo biological dimers are found in the crystallographic tetramer. They are monomers A & E, and B & D.

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Components

#1: Protein
Alpha-Ketoglutarate-Dependent Taurine Dioxygenase / 2-aminoethanesulfonate dioxygenase / Sulfate starvation-induced protein 3 / SSI3


Mass: 32453.467 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P37610, taurine dioxygenase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-TAU / 2-AMINOETHANESULFONIC ACID


Mass: 125.147 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H7NO3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 710 / 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: 2.4 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 295 K / Method: batch / pH: 8
Details: PEG 4000, Isopropanol, Sodium citrate, pH 8.0, Batch, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mMTris11pH8.0
2100 mMEDTA11pH8.0
395 %nitrogen11
45 %hydrogen gas11

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 21, 2002 / Details: Osmic Blue confocal mirrors
RadiationMonochromator: Confocal Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 105897 / Num. obs: 99459 / % possible obs: 94 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.049 / Net I/σ(I): 15.4
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3.1 / Num. unique all: 600 / Rsym value: 0.34 / % possible all: 93.5
Reflection
*PLUS
Highest resolution: 1.9 Å / % possible obs: 96.9 % / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
Highest resolution: 1.9 Å / % possible obs: 78.9 % / Rmerge(I) obs: 0.334

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: Direct methods, MAD / Resolution: 1.9→50 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 6438 -RANDOM
Rwork0.212 ---
obs0.221 99459 93.9 %-
all-105897 --
Displacement parametersBiso mean: 34.3 Å2
Baniso -1Baniso -2Baniso -3
1-8.35 Å2-2.1 Å2-6.25 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9171 0 24 710 9905
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it1.0061.5
X-RAY DIFFRACTIONo_mcangle_it1.6042
X-RAY DIFFRACTIONo_scbond_it1.4412
X-RAY DIFFRACTIONo_scangle_it2.1792.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ligand.param
Refinement
*PLUS
Num. reflection Rfree: 5034 / Rfactor Rfree: 0.254
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.005
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.34

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