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- PDB-5ahs: 3-Sulfinopropionyl-Coenzyme A (3SP-CoA) desulfinase from Advenell... -

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Basic information

Entry
Database: PDB / ID: 5ahs
Title3-Sulfinopropionyl-Coenzyme A (3SP-CoA) desulfinase from Advenella mimgardefordensis DPN7T: holo crystal structure with the substrate analog succinyl-CoA
ComponentsACYL-COA DEHYDROGENASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


3-sulfinopropanoyl-CoA desulfinase / oxidoreductase activity, acting on the CH-CH group of donors / flavin adenine dinucleotide binding / hydrolase activity
Similarity search - Function
Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal
Similarity search - Domain/homology
COENZYME A / FLAVIN-ADENINE DINUCLEOTIDE / SUCCINIC ACID / 3-sulfinopropanoyl-CoA desulfinase
Similarity search - Component
Biological speciesADVENELLA MIMIGARDEFORDENSIS DPN7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
DepositionFeb 6, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Category: diffrn_detector / diffrn_source
Item: _diffrn_detector.type / _diffrn_source.pdbx_synchrotron_site
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
C: ACYL-COA DEHYDROGENASE
D: ACYL-COA DEHYDROGENASE
E: ACYL-COA DEHYDROGENASE
F: ACYL-COA DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)270,25619
Polymers261,4906
Non-polymers8,76513
Water26,3381462
1
A: ACYL-COA DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1353
Polymers43,5821
Non-polymers1,5532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ACYL-COA DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1353
Polymers43,5821
Non-polymers1,5532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: ACYL-COA DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5814
Polymers43,5821
Non-polymers1,0003
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: ACYL-COA DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1353
Polymers43,5821
Non-polymers1,5532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: ACYL-COA DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1353
Polymers43,5821
Non-polymers1,5532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
F: ACYL-COA DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1353
Polymers43,5821
Non-polymers1,5532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)100.066, 233.493, 121.285
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 6 molecules ABCDEF

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


Mass: 43581.746 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ADVENELLA MIMIGARDEFORDENSIS DPN7 (bacteria)
Plasmid: PET23A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: K4L7X3, 3-sulfinopropanoyl-CoA desulfinase

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Non-polymers , 5 types, 1475 molecules

#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1462 / 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: 2.7 Å3/Da / Density % sol: 55.8 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.4
Details: CRYSTALS USED FOR X-RAY DIFFRACTION STUDIES 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 5- 20 % ...Details: CRYSTALS USED FOR X-RAY DIFFRACTION STUDIES 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 5- 20 % 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: Jun 13, 2013 / Details: KB MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 2.3→121.29 Å / Num. obs: 126487 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.5
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 5 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.9_1692)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5AF7

5af7


Resolution: 2.3→116.746 Å / SU ML: 0.31 / σ(F): 1.91 / Phase error: 27.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2442 12133 5 %
Rwork0.1995 --
obs0.2017 126282 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→116.746 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17832 0 571 1462 19865
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00218770
X-RAY DIFFRACTIONf_angle_d0.61725440
X-RAY DIFFRACTIONf_dihedral_angle_d13.3186903
X-RAY DIFFRACTIONf_chiral_restr0.0252804
X-RAY DIFFRACTIONf_plane_restr0.0023250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32610.34793990.31317713X-RAY DIFFRACTION99
2.3261-2.35350.33384370.29957577X-RAY DIFFRACTION99
2.3535-2.38220.32444290.28157753X-RAY DIFFRACTION99
2.3822-2.41240.29014030.28457570X-RAY DIFFRACTION99
2.4124-2.44410.36183840.28257626X-RAY DIFFRACTION98
2.4441-2.47760.30964370.27537437X-RAY DIFFRACTION97
2.4776-2.5130.31033570.25727618X-RAY DIFFRACTION98
2.513-2.55050.34564370.26437626X-RAY DIFFRACTION100
2.5505-2.59040.30063910.25227706X-RAY DIFFRACTION100
2.5904-2.63280.33264180.24977765X-RAY DIFFRACTION100
2.6328-2.67820.28594120.24317657X-RAY DIFFRACTION100
2.6782-2.7270.30994050.24047595X-RAY DIFFRACTION99
2.727-2.77940.31963660.22517795X-RAY DIFFRACTION100
2.7794-2.83610.28673910.21827658X-RAY DIFFRACTION99
2.8361-2.89780.28444230.21357632X-RAY DIFFRACTION99
2.8978-2.96520.26324300.21417608X-RAY DIFFRACTION99
2.9652-3.03940.26033750.21647538X-RAY DIFFRACTION97
3.0394-3.12160.28854400.21737595X-RAY DIFFRACTION99
3.1216-3.21340.26753760.21267743X-RAY DIFFRACTION100
3.2134-3.31720.2634370.20427629X-RAY DIFFRACTION100
3.3172-3.43570.25583790.19817760X-RAY DIFFRACTION100
3.4357-3.57330.25973820.20017728X-RAY DIFFRACTION99
3.5733-3.73590.24373650.2047650X-RAY DIFFRACTION99
3.7359-3.93290.23243430.18277627X-RAY DIFFRACTION98
3.9329-4.17930.21244260.17617617X-RAY DIFFRACTION98
4.1793-4.5020.19684250.16017655X-RAY DIFFRACTION100
4.502-4.95510.1844120.15617675X-RAY DIFFRACTION100
4.9551-5.67210.20384090.16427595X-RAY DIFFRACTION98
5.6721-7.14610.21784180.17417643X-RAY DIFFRACTION99
7.1461-116.89710.17784270.1647508X-RAY DIFFRACTION98

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