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- PDB-4tlf: Crystal structure of Thiol dioxygenase from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 4tlf
TitleCrystal structure of Thiol dioxygenase from Pseudomonas aeruginosa
Components3-mercaptopropionate dioxygenase
KeywordsOXIDOREDUCTASE / thiol dioxygenase / cysteine dioxygenase / 3-MPA dioxygenase / non-heme mono-iron / Cupin
Function / homology
Function and homology information


3-mercaptopropionate dioxygenase / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / ferrous iron binding / iron ion binding
Similarity search - Function
ATP synthase delta/epsilon subunit, C-terminal domain / Cysteine dioxygenase type I / Cysteine dioxygenase type I / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Jelly Rolls / Up-down Bundle / Sandwich ...ATP synthase delta/epsilon subunit, C-terminal domain / Cysteine dioxygenase type I / Cysteine dioxygenase type I / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Jelly Rolls / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / 3-mercaptopropionate dioxygenase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.137 Å
AuthorsFellner, M. / Tchesnokov, E.P. / Jameson, G.N.L. / Wilbanks, S.M.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: The Cysteine Dioxygenase Homologue from Pseudomonas aeruginosa Is a 3-Mercaptopropionate Dioxygenase.
Authors: Tchesnokov, E.P. / Fellner, M. / Siakkou, E. / Kleffmann, T. / Martin, L.W. / Aloi, S. / Lamont, I.L. / Wilbanks, S.M. / Jameson, G.N.
History
DepositionMay 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
Revision 1.2Oct 14, 2015Group: Database references
Revision 1.3Dec 30, 2020Group: Data collection / Derived calculations / Structure summary
Category: audit_author / diffrn_source ...audit_author / diffrn_source / entity / entity_name_com / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_keywords
Item: _audit_author.name / _diffrn_source.pdbx_synchrotron_site ..._audit_author.name / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _entity.pdbx_ec / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _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_keywords.text
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-mercaptopropionate dioxygenase
B: 3-mercaptopropionate dioxygenase
C: 3-mercaptopropionate dioxygenase
D: 3-mercaptopropionate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,3348
Polymers95,1104
Non-polymers2234
Water10,863603
1
A: 3-mercaptopropionate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8332
Polymers23,7781
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3-mercaptopropionate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8332
Polymers23,7781
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 3-mercaptopropionate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8332
Polymers23,7781
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 3-mercaptopropionate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8332
Polymers23,7781
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.942, 66.942, 377.354
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid A
21chain B and segid B
31chain C and segid C

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AA0
211chain B and segid BB0
311chain C and segid CC0
DetailsThe biological unit is a monomer. Chain A show the best electron density maps.

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Components

#1: Protein
3-mercaptopropionate dioxygenase / Thiol dioxygenase


Mass: 23777.576 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA2602, NC002516.2 / Plasmid: pPR-IBA1/PA2602/P.aeruginosa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: Q9I0N5, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 603 / 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: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.7 / Details: 200mM sodium acetate, 8% PEG 4000

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Mar 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.137→377.354 Å / Num. obs: 49221 / % possible obs: 99.8 % / Redundancy: 13.5 % / Biso Wilson estimate: 23.83 Å2 / Rpim(I) all: 0.034 / Rrim(I) all: 0.122 / Rsym value: 0.114 / Net I/av σ(I): 5.095 / Net I/σ(I): 16.5 / Num. measured all: 665020
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.14-2.2513.30.3711.99207869400.1150.3717.798.7
2.25-2.3914.20.2712.79482966850.0770.2719.6100
2.39-2.5514.30.2013.78980962590.0570.20111.4100
2.55-2.7613.80.1674.48083858670.0490.16713.8100
2.76-3.0214.10.126.17682654560.0340.1217.6100
3.02-3.3813.80.09976839449670.0280.09922.3100
3.38-3.912.40.0976.95486744070.030.09725.1100
3.9-4.7812.70.0867.74854938130.0250.08627.8100
4.78-6.7612.40.0787.83741330190.0240.07825.4100
6.76-47.16911.80.0619.32141718080.0190.06124.799.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.7 Å47.17 Å
Translation7.7 Å47.17 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
PDB_EXTRACT3.14data extraction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3USS

3uss


Resolution: 2.137→44.302 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2507 2478 5.06 %
Rwork0.198 85851 -
obs0.2007 49221 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.71 Å2 / Biso mean: 26.1322 Å2 / Biso min: 6.46 Å2
Refinement stepCycle: final / Resolution: 2.137→44.302 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6219 0 4 603 6826
Biso mean--26.01 31.31 -
Num. residues----781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096388
X-RAY DIFFRACTIONf_angle_d1.1688687
X-RAY DIFFRACTIONf_chiral_restr0.053907
X-RAY DIFFRACTIONf_plane_restr0.0071167
X-RAY DIFFRACTIONf_dihedral_angle_d12.6412373
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2752X-RAY DIFFRACTION6.754TORSIONAL
12B2752X-RAY DIFFRACTION6.754TORSIONAL
13C2752X-RAY DIFFRACTION6.754TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1369-2.16120.33881270.27012725285294
2.1612-2.18660.34321840.238627652949100
2.1866-2.21330.27221240.247529323056100
2.2133-2.24130.37791560.28612861301799
2.2413-2.27080.38911480.30922801294999
2.2708-2.30190.24461530.221629563109100
2.3019-2.33480.27951680.211227532921100
2.3348-2.36970.33111680.221529043072100
2.3697-2.40670.30521810.22728313012100
2.4067-2.44610.27851840.204128223006100
2.4461-2.48830.27021460.20129523098100
2.4883-2.53360.3061610.204127912952100
2.5336-2.58230.30091770.208829113088100
2.5823-2.6350.25241380.2128512989100
2.635-2.69230.25291480.203528482996100
2.6923-2.75490.24011710.192128553026100
2.7549-2.82380.28311120.195129293041100
2.8238-2.90010.2681210.187229273048100
2.9001-2.98540.23941620.18628342996100
2.9854-3.08180.23011120.191728953007100
3.0818-3.19190.21061680.190329023070100
3.1919-3.31960.24331270.191328682995100
3.3196-3.47070.21511280.187828943022100
3.4707-3.65360.25161800.192628533033100
3.6536-3.88240.21271870.192128263013100
3.8824-4.18190.25141760.189228763052100
4.1819-4.60240.20541710.167328162987100
4.6024-5.26740.21331200.16429313051100
5.2674-6.63280.20281280.194728823010100
6.6328-44.31150.21991530.182860301399

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