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- PDB-2jif: Structure of human short-branched chain acyl-CoA dehydrogenase (A... -

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Basic information

Entry
Database: PDB / ID: 2jif
TitleStructure of human short-branched chain acyl-CoA dehydrogenase (ACADSB)
ComponentsSHORT/BRANCHED CHAIN SPECIFIC ACYL-COA DEHYDROGENASE
KeywordsOXIDOREDUCTASE / MITOCHONDRION / TRANSIT PEPTIDE / FATTY ACID METABOLISM / FAD / FLAVOPROTEIN / DISEASE MUTATION / LIPID METABOLISM
Function / homology
Function and homology information


short-chain 2-methylacyl-CoA dehydrogenase / 2-methylpropanoyl-CoA dehydrogenase activity / acyl-CoA dehydrogenase activity / branched-chain amino acid catabolic process / Branched-chain amino acid catabolism / fatty acid metabolic process / flavin adenine dinucleotide binding / mitochondrial matrix / mitochondrion
Similarity search - Function
Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / 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, C-terminal domain ...Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / 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, 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 / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / 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
COENZYME A PERSULFIDE / FLAVIN-ADENINE DINUCLEOTIDE / Short/branched chain specific acyl-CoA dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPike, A.C.W. / Hozjan, V. / Smee, C. / Niesen, F.H. / Kavanagh, K.L. / Umeano, C. / Turnbull, A.P. / von Delft, F. / Weigelt, J. / Edwards, A. ...Pike, A.C.W. / Hozjan, V. / Smee, C. / Niesen, F.H. / Kavanagh, K.L. / Umeano, C. / Turnbull, A.P. / von Delft, F. / Weigelt, J. / Edwards, A. / Arrowsmith, C.H. / Sundstrom, M. / Oppermann, U.
CitationJournal: To be Published
Title: Crystal Structure of Human Short-Branched Chain Acyl-Coa Dehydrogenase
Authors: Pike, A.C.W. / Hozjan, V. / Smee, C. / Niesen, F.H. / Kavanagh, K.L. / Umeano, C. / Turnbull, A.P. / von Delft, F. / Weigelt, J. / Edwards, A. / Arrowsmith, C.H. / Sundstrom, M. / Oppermann, U.
History
DepositionFeb 28, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SHORT/BRANCHED CHAIN SPECIFIC ACYL-COA DEHYDROGENASE
B: SHORT/BRANCHED CHAIN SPECIFIC ACYL-COA DEHYDROGENASE
C: SHORT/BRANCHED CHAIN SPECIFIC ACYL-COA DEHYDROGENASE
D: SHORT/BRANCHED CHAIN SPECIFIC ACYL-COA DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,02829
Polymers177,8984
Non-polymers7,13025
Water16,448913
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)150.245, 150.245, 201.586
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.86838, -0.49574, -0.01269), (-0.49572, -0.86847, 0.00475), (-0.01338, 0.00217, -0.99991)68.34785, 257.93027, 23.23913
2given(-0.86659, 0.49901, -0.00308), (0.49895, 0.86655, 0.01192), (0.00862, 0.00879, -0.99992)156.32558, -41.68656, 20.11056
3given(-0.99984, 0.0055, 0.01725), (-0.00577, -0.99987, -0.01534), (0.01716, -0.01544, 0.99973)224.22177, 217.26875, -0.18842

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
SHORT/BRANCHED CHAIN SPECIFIC ACYL-COA DEHYDROGENASE / ACYL-COA DEHYDROGENASE / SBCAD / 2-METHYL BRANCHED CHAIN ACYL-COA DEHYDROGENASE / 2-MEBCAD / 2- ...ACYL-COA DEHYDROGENASE / SBCAD / 2-METHYL BRANCHED CHAIN ACYL-COA DEHYDROGENASE / 2-MEBCAD / 2-METHYLBUTYRYL-COENZYME A DEHYDROGENASE / 2-METHYLBUTYRYL-COA DEHYDROGENASE


Mass: 44474.492 Da / Num. of mol.: 4 / Fragment: RESIDUES 52-432
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P45954, Oxidoreductases; Acting on the CH-CH group of donors; With unknown physiological acceptors

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Non-polymers , 5 types, 938 molecules

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


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-COS / COENZYME A PERSULFIDE


Mass: 799.599 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 913 / 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: 3.7 Å3/Da / Density % sol: 66.7 %
Crystal growpH: 6.3
Details: 30% PEG6000, 0.15M AMMONIUM CHLORIDE PH6.3, 10% ETHYLENE GLYCOL, pH 6.30

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 21, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2→70.36 Å / Num. obs: 175824 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 25.84 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.7
Reflection shellResolution: 2→2.11 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.6 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JQI

1jqi


Resolution: 2→70 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.099 / SU ML: 0.078 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ACETOACETYL COA WAS ADDED TO THE PROTEIN PRIOR TO CRYSTALLIZATION. HOWEVER THE DENSITY IN THE ACTIVE SITE IS MORE CONSISTENT WITH AND HAS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ACETOACETYL COA WAS ADDED TO THE PROTEIN PRIOR TO CRYSTALLIZATION. HOWEVER THE DENSITY IN THE ACTIVE SITE IS MORE CONSISTENT WITH AND HAS BEEN MODELLED AS COA PERSULPHIDE. COA PERSULPHIDE PRESUMABLY COPURIFIES WITH THE BACTERIALLY EXPRESSED ENZYME.
RfactorNum. reflection% reflectionSelection details
Rfree0.209 8809 5 %RANDOM
Rwork0.184 ---
obs0.185 166944 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.08 Å20 Å2
2--0.16 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 2→70 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11620 0 446 913 12979
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02212467
X-RAY DIFFRACTIONr_bond_other_d0.0010.028258
X-RAY DIFFRACTIONr_angle_refined_deg1.2872.00516907
X-RAY DIFFRACTIONr_angle_other_deg1.043.00320072
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.11451520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.15524.826516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.629152134
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1551548
X-RAY DIFFRACTIONr_chiral_restr0.0790.21895
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213570
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022374
X-RAY DIFFRACTIONr_nbd_refined0.2010.22539
X-RAY DIFFRACTIONr_nbd_other0.1790.28297
X-RAY DIFFRACTIONr_nbtor_refined0.1750.25999
X-RAY DIFFRACTIONr_nbtor_other0.0850.25933
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2758
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2520.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1950.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6421.57857
X-RAY DIFFRACTIONr_mcbond_other0.1451.53126
X-RAY DIFFRACTIONr_mcangle_it0.943212091
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.62735486
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4394.54812
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 620 -
Rwork0.233 11549 -
obs--94.03 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.995-0.07450.46640.9431-0.19911.38650.04780.0349-0.1087-0.10520.06740.28430.1502-0.2898-0.1151-0.1304-0.0618-0.0703-0.06240.0171-0.02991.16894.57222.6429
20.9131-0.0686-0.29690.85150.47471.51210.0138-0.13590.2580.11070.01370.2036-0.2335-0.2472-0.0275-0.06510.05490.024-0.074-0.03260.0011100.8251130.78819.782
30.49890.0361-0.02880.9283-0.65331.15120.0043-0.0769-0.093-0.0071-0.0156-0.0990.07310.15140.0113-0.1315-0.0061-0.0144-0.1397-0.0135-0.1206124.378185.51319.4021
40.94770.2771-0.57490.7151-0.38941.16070.01390.00180.0590.0222-0.0124-0.0483-0.05730.1089-0.0016-0.1547-0.0304-0.0073-0.1511-0.0127-0.1483133.7147122.23852.3341
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 404
2X-RAY DIFFRACTION2B28 - 404
3X-RAY DIFFRACTION3C28 - 404
4X-RAY DIFFRACTION4D24 - 404

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