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- PDB-1os7: Crystal structure of TauD with iron, alpha-ketoglutarate and Taur... -

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Basic information

Entry
Database: PDB / ID: 1os7
TitleCrystal structure of TauD with iron, alpha-ketoglutarate and Taurine bound at pH 7.5
ComponentsAlpha-ketoglutarate-dependent taurine dioxygenase
KeywordsOXIDOREDUCTASE / Iron Di-oxygenase / Taurine / TauD / Alpha-Ketoglutarate
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-OXOGLUTARIC ACID / : / 2-AMINOETHANESULFONIC ACID / Alpha-ketoglutarate-dependent taurine dioxygenase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Direct methods, Molecular replacement / Resolution: 2.5 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 18, 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: Non-polymer description / 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_conn / struct_site
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_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: 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)130,99715
Polymers129,8144
Non-polymers1,18311
Water6,359353
1
A: Alpha-ketoglutarate-dependent taurine dioxygenase
D: Alpha-ketoglutarate-dependent taurine dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4367
Polymers64,9072
Non-polymers5295
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-ketoglutarate-dependent taurine dioxygenase
C: Alpha-ketoglutarate-dependent taurine dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5618
Polymers64,9072
Non-polymers6546
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.594, 118.855, 118.832
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTwo copies of the proposed biological dimer are found in the crystallographic tetramer. This corresponds to monomers A & D and B & C respectively.

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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-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-TAU / 2-AMINOETHANESULFONIC ACID / Taurine


Mass: 125.147 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H7NO3S
#4: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H6O5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2.44 Å3/Da / Density % sol: 49.18 %
Crystal growTemperature: 297 K / Method: batch / pH: 7.5
Details: PEG 400, 20% PEG 4000, 20% Isopropanol, 0.1 M TRIS, pH 7.5, BATCH, temperature 297K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 8 / 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: Apr 1, 2002 / Details: mirrors
RadiationMonochromator: Osmic Blue Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→38 Å / Num. all: 46090 / Num. obs: 45814 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.073
Reflection
*PLUS
Highest resolution: 2.5 Å / % possible obs: 99.9 % / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.59 Å / % possible obs: 98.4 % / Rmerge(I) obs: 0.431

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: Direct methods, Molecular replacement
Resolution: 2.5→38 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.278 2318 -RANDOM
Rwork0.224 ---
obs0.225 45814 99.4 %-
all-46090 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.46 Å20 Å20 Å2
2---0.634 Å20 Å2
3---10.094 Å2
Refinement stepCycle: LAST / Resolution: 2.5→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9100 0 65 353 9518
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_mcbond_it1.2731.5
X-RAY DIFFRACTIONc_scbond_it1.7672
X-RAY DIFFRACTIONc_mcangle_it2.1082
X-RAY DIFFRACTIONc_scangle_it2.62.5
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
Lowest resolution: 36.5 Å / Num. reflection obs: 46047 / Num. reflection Rfree: 2321 / Rfactor Rwork: 0.225
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.35

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