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- PDB-4wvz: Crystal structure of artificial crosslinked thiol dioxygenase G95... -

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Basic information

Entry
Database: PDB / ID: 4wvz
TitleCrystal structure of artificial crosslinked thiol dioxygenase G95C variant from Pseudomonas aeruginosa
Components3-mercaptopropionate dioxygenase
KeywordsOXIDOREDUCTASE / thiol dioxygenase / cysteine dioxygenase / 3-MPA dioxygenase / 3-mercaptopropionic acid / non-heme mono-iron / Cupin / beta barrel / crosslink
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
: / Thiol dioxygenase / 3-mercaptopropionate dioxygenase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.09 Å
AuthorsFellner, M. / Tchesnokov, E.P. / Jameson, G.N.L. / Wilbanks, S.M.
CitationJournal: Biochemistry / Year: 2016
Title: Substrate and pH-Dependent Kinetic Profile of 3-Mercaptopropionate Dioxygenase from Pseudomonas aeruginosa.
Authors: Fellner, M. / Aloi, S. / Tchesnokov, E.P. / Wilbanks, S.M. / Jameson, G.N.
History
DepositionNov 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Dec 30, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: audit_author / citation ...audit_author / citation / diffrn_source / entity / entity_name_com / entity_src_gen / pdbx_struct_oper_list / struct_conn / struct_conn_type / struct_keywords / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _audit_author.name / _citation.journal_id_CSD ..._audit_author.name / _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.3Sep 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)95,5188
Polymers95,2954
Non-polymers2234
Water10,088560
1
A: 3-mercaptopropionate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8802
Polymers23,8241
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3-mercaptopropionate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8802
Polymers23,8241
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 3-mercaptopropionate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8802
Polymers23,8241
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 3-mercaptopropionate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8802
Polymers23,8241
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.543, 66.543, 376.852
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
3-mercaptopropionate dioxygenase / Thiol dioxygenase


Mass: 23823.666 Da / Num. of mol.: 4 / Mutation: G95C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: PA2602 / Plasmid: pPR-IBA1/PA2602/P.aeruginosa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: Q9I0N5, UniProt: A0A140UH61*PLUS, 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


Mass: 18.015 Da / Num. of mol.: 560 / 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: 2.19 Å3/Da / Density % sol: 43.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 2.5microl Protein at 18 mg/ml (in 10mM phosphate pH 7.5) was mixed with 1microl of the mother liquor containing 140mM sodiumacetate, PEG 4000 8%, pH 5.3, the reservoir contained 500microl. ...Details: 2.5microl Protein at 18 mg/ml (in 10mM phosphate pH 7.5) was mixed with 1microl of the mother liquor containing 140mM sodiumacetate, PEG 4000 8%, pH 5.3, the reservoir contained 500microl. Cryoprotected with 25% ethylenglycol before freezing.

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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 315r / Detector: CCD / Date: Oct 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.09→47.05 Å / Num. obs: 51753 / % possible obs: 99.6 % / Redundancy: 7 % / Biso Wilson estimate: 30.2 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.018 / Net I/σ(I): 28.1 / Num. measured all: 359980
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.09-2.153.70.2824.21422138500.9150.15796.9
9.11-47.056.20.01666486178110.00798.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.89 Å47.05 Å
Translation7.89 Å47.05 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless0.3.8data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TLF

4tlf


Resolution: 2.09→39.914 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2185 2548 4.95 %
Rwork0.1753 88465 -
obs0.1775 51609 97.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.47 Å2 / Biso mean: 35.5237 Å2 / Biso min: 14.46 Å2
Refinement stepCycle: final / Resolution: 2.09→39.914 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6326 0 4 560 6890
Biso mean--52 41.94 -
Num. residues----794
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066630
X-RAY DIFFRACTIONf_angle_d1.0029035
X-RAY DIFFRACTIONf_chiral_restr0.039938
X-RAY DIFFRACTIONf_plane_restr0.0051217
X-RAY DIFFRACTIONf_dihedral_angle_d13.8122462
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 (%)
2.09-2.11380.33751450.25492482262784
2.1138-2.13860.28591370.24222719285687
2.1386-2.16470.26321370.23512620275788
2.1647-2.19210.27231650.232760292591
2.1921-2.2210.28831480.23722866301493
2.221-2.25140.39151450.3562582272788
2.2514-2.28360.41061540.27092831298592
2.2836-2.31760.29031900.21072886307698
2.3176-2.35380.25351580.188330563214100
2.3538-2.39240.26761410.195630333174100
2.3924-2.43370.26131570.192629923149100
2.4337-2.47790.28241540.201930993253100
2.4779-2.52560.24881650.198329793144100
2.5256-2.57710.24371510.182230403191100
2.5771-2.63320.21511480.18330493197100
2.6332-2.69440.22641570.188230493206100
2.6944-2.76180.28621410.175130593200100
2.7618-2.83640.28451490.175829763125100
2.8364-2.91980.24951320.180731273259100
2.9198-3.01410.27971540.189530173171100
3.0141-3.12170.23011340.181530323166100
3.1217-3.24670.23041440.173330613205100
3.2467-3.39440.20721830.171229983181100
3.3944-3.57320.16421530.163330163169100
3.5732-3.79690.19711830.16482976315999
3.7969-4.08980.18381380.141130973235100
4.0898-4.50090.1721730.137329973170100
4.5009-5.1510.15271670.131530213188100
5.151-6.48520.1891650.161730153180100
6.4852-39.92090.15961360.15993030316699

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