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- PDB-5af7: 3-Sulfinopropionyl-coenzyme A (3SP-CoA) desulfinase from Advenell... -

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Basic information

Entry
Database: PDB / ID: 5af7
Title3-Sulfinopropionyl-coenzyme A (3SP-CoA) desulfinase from Advenella mimigardefordensis DPN7T: crystal structure and function of a desulfinase with an acyl-CoA dehydrogenase fold. Native crystal structure
ComponentsACYL-COA DEHYDROGENASE
KeywordsHYDROLASE / DESULFINASE / ACYL-COA DEHYDROGENASE / 3-SULFINOPROPIONYL-COENZYME A / FLAVIN ADENINE DINUCLEOTIDE
Function / homology
Function and homology information


3-sulfinopropanoyl-CoA desulfinase / acyl-CoA dehydrogenase activity / flavin adenine dinucleotide binding / hydrolase activity
Similarity search - Function
: / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain ...: / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / 3-sulfinopropanoyl-CoA desulfinase
Similarity search - Component
Biological speciesAdvenella mimigardefordensis DPN7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsCianci, M. / Schuermann, M. / Meijers, R. / Schneider, T.R. / Steinbuechel, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: 3-Sulfinopropionyl-Coenzyme a (3Sp-Coa) Desulfinase from Advenella Mimigardefordensis Dpn7(T): Crystal Structure and Function of a Desulfinase with an Acyl-Coa Dehydrogenase Fold.
Authors: Schurmann, M. / Meijers, R. / Schneider, T.R. / Steinbuchel, A. / Cianci, M.
History
DepositionJan 20, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Data collection / Database references
Revision 1.2Mar 7, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_gene_src_scientific_name ..._diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: ACYL-COA DEHYDROGENASE
B: ACYL-COA DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9196
Polymers87,1632
Non-polymers1,7554
Water14,970831
1
A: ACYL-COA DEHYDROGENASE
B: ACYL-COA DEHYDROGENASE
hetero molecules

A: ACYL-COA DEHYDROGENASE
B: ACYL-COA DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,83812
Polymers174,3274
Non-polymers3,5118
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area24810 Å2
ΔGint-127.1 kcal/mol
Surface area51740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.674, 100.652, 118.573
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2073-

HOH

21A-2278-

HOH

31A-2289-

HOH

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Components

#1: Protein ACYL-COA DEHYDROGENASE / 3-SULFINOPROPIONYL-COENZYME A DESULFINASE


Mass: 43581.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Advenella mimigardefordensis DPN7 (bacteria)
Plasmid: PET23A / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: K4L7X3, 3-sulfinopropanoyl-CoA desulfinase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 831 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.4
Details: THE CRYSTALS WERE GROWN IN 24-WELL LINBRO PLATES (HAMPTON RESEARCH) BY VAPOUR DIFFUSION IN A HANGING DROP CONFIGURATION FROM 0.1 M BIS-TRIS PH 6.5 AND 10 % PEG 3350 AT A PROTEIN ...Details: THE CRYSTALS WERE GROWN IN 24-WELL LINBRO PLATES (HAMPTON RESEARCH) BY VAPOUR DIFFUSION IN A HANGING DROP CONFIGURATION FROM 0.1 M BIS-TRIS PH 6.5 AND 10 % PEG 3350 AT A PROTEIN CONCENTRATION OF 10 MG/ML, BY MIXING 2 UL OF THE PROTEIN SOLUTION WITH 2 UL MOTHER LIQUOR.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.968
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 17, 2012
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 1.89→100.65 Å / Num. obs: 69785 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 19.08 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.1
Reflection shellResolution: 1.89→1.93 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UKW

1ukw


Resolution: 1.89→63.79 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 18.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2017 3509 5 %
Rwork0.1625 --
obs0.1645 69748 95.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.3 Å2
Refinement stepCycle: LAST / Resolution: 1.89→63.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5929 0 118 831 6878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076206
X-RAY DIFFRACTIONf_angle_d0.9948408
X-RAY DIFFRACTIONf_dihedral_angle_d13.9792291
X-RAY DIFFRACTIONf_chiral_restr0.038933
X-RAY DIFFRACTIONf_plane_restr0.0041088
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.91590.27361400.23592668X-RAY DIFFRACTION97
1.9159-1.94330.27661490.22062695X-RAY DIFFRACTION98
1.9433-1.97230.25721350.21552661X-RAY DIFFRACTION97
1.9723-2.00310.24951300.20132687X-RAY DIFFRACTION97
2.0031-2.03590.23461330.20242671X-RAY DIFFRACTION97
2.0359-2.07110.25221350.1992655X-RAY DIFFRACTION97
2.0711-2.10870.27351550.19422676X-RAY DIFFRACTION97
2.1087-2.14930.23621460.18312655X-RAY DIFFRACTION97
2.1493-2.19320.22071320.17412675X-RAY DIFFRACTION97
2.1932-2.24080.21121640.17492620X-RAY DIFFRACTION96
2.2408-2.2930.21481330.16952666X-RAY DIFFRACTION97
2.293-2.35030.25491290.16672661X-RAY DIFFRACTION96
2.3503-2.41390.19221640.16092628X-RAY DIFFRACTION96
2.4139-2.48490.18211250.15942675X-RAY DIFFRACTION96
2.4849-2.56510.23151260.16352658X-RAY DIFFRACTION96
2.5651-2.65680.22571450.15712649X-RAY DIFFRACTION96
2.6568-2.76320.17341410.15882628X-RAY DIFFRACTION95
2.7632-2.88890.20081510.15782650X-RAY DIFFRACTION95
2.8889-3.04120.19631590.15922617X-RAY DIFFRACTION95
3.0412-3.23180.1781420.15452625X-RAY DIFFRACTION94
3.2318-3.48130.18961250.15332632X-RAY DIFFRACTION94
3.4813-3.83160.16611430.14652614X-RAY DIFFRACTION93
3.8316-4.38590.18121200.12752643X-RAY DIFFRACTION93
4.3859-5.52530.16431410.13842602X-RAY DIFFRACTION91
5.5253-63.82630.18231460.16122628X-RAY DIFFRACTION88

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