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- PDB-2vig: Crystal structure of human short-chain acyl CoA dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 2vig
TitleCrystal structure of human short-chain acyl CoA dehydrogenase
ComponentsSHORT-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE,
KeywordsOXIDOREDUCTASE / FATTY ACID METABOLISM / FAD / POLYMORPHISM / FLAVOPROTEIN / MITOCHONDRION / DISEASE MUTATION / LIPID METABOLISM / BETA OXIDATION / TRANSIT PEPTIDE
Function / homology
Function and homology information


butyrate catabolic process / Beta oxidation of butanoyl-CoA to acetyl-CoA / Beta oxidation of hexanoyl-CoA to butanoyl-CoA / short-chain acyl-CoA dehydrogenase / butyryl-CoA dehydrogenase activity / fatty acid beta-oxidation using acyl-CoA dehydrogenase / acyl-CoA dehydrogenase activity / fatty acid beta-oxidation / flavin adenine dinucleotide binding / mitochondrial matrix ...butyrate catabolic process / Beta oxidation of butanoyl-CoA to acetyl-CoA / Beta oxidation of hexanoyl-CoA to butanoyl-CoA / short-chain acyl-CoA dehydrogenase / butyryl-CoA dehydrogenase activity / fatty acid beta-oxidation using acyl-CoA dehydrogenase / acyl-CoA dehydrogenase activity / fatty acid beta-oxidation / flavin adenine dinucleotide binding / mitochondrial matrix / centrosome / mitochondrion / nucleoplasm / nucleus
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 / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / 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 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 / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / 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-chain specific acyl-CoA dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPike, A.C.W. / Pantic, N. / Parizotto, E. / Gileadi, O. / Ugochukwu, E. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A. / Oppermann, U.
CitationJournal: To be Published
Title: Crystal Structure of Human Short-Chain Acyl Coa Dehydrogenase
Authors: Pike, A.C.W. / Pantic, N. / Parizotto, E. / Gileadi, O. / Ugochukwu, E. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A. / Oppermann, U.
History
DepositionNov 30, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Dec 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 / struct_ncs_dom_lim
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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SHORT-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE,
B: SHORT-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE,
C: SHORT-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE,
D: SHORT-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE,
E: SHORT-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE,
F: SHORT-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE,
G: SHORT-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE,
H: SHORT-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE,
hetero molecules


Theoretical massNumber of molelcules
Total (without water)348,33533
Polymers337,3088
Non-polymers11,02725
Water20,3211128
1
A: SHORT-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE,
B: SHORT-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE,
C: SHORT-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE,
D: SHORT-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE,
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,44315
Polymers168,6544
Non-polymers5,78911
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18840 Å2
ΔGint-97 kcal/mol
Surface area59910 Å2
MethodPQS
2
E: SHORT-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE,
F: SHORT-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE,
G: SHORT-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE,
H: SHORT-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE,
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,89218
Polymers168,6544
Non-polymers5,23814
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19070 Å2
ΔGint-79.4 kcal/mol
Surface area59140 Å2
MethodPQS
Unit cell
Length a, b, c (Å)85.714, 157.620, 260.843
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUALAALA4AA34 - 1726 - 144
21LEULEUALAALA4BB34 - 1726 - 144
31LEULEUALAALA4CC34 - 1726 - 144
41LEULEUALAALA4DD34 - 1726 - 144
51LEULEUALAALA4EE34 - 1726 - 144
61LEULEUALAALA4FF34 - 1726 - 144
71LEULEUALAALA4GG34 - 1726 - 144
81LEULEUALAALA4HH34 - 1726 - 144
12GLUGLUTRPTRP6AA173 - 177145 - 149
22GLUGLUTRPTRP6BB173 - 177145 - 149
32GLUGLUTRPTRP6CC173 - 177145 - 149
42GLUGLUTRPTRP6DD173 - 177145 - 149
52GLUGLUTRPTRP6EE173 - 177145 - 149
62GLUGLUTRPTRP6FF173 - 177145 - 149
72GLUGLUTRPTRP6GG173 - 177145 - 149
82GLUGLUTRPTRP6HH173 - 177145 - 149
13VALVALTHRTHR4AA178 - 201150 - 173
23VALVALTHRTHR4BB178 - 201150 - 173
33VALVALTHRTHR4CC178 - 201150 - 173
43VALVALTHRTHR4DD178 - 201150 - 173
53VALVALTHRTHR4EE178 - 201150 - 173
63VALVALTHRTHR4FF178 - 201150 - 173
73VALVALTHRTHR4GG178 - 201150 - 173
83VALVALTHRTHR4HH178 - 201150 - 173
14SERSERARGARG4AA211 - 411183 - 383
24SERSERARGARG4BB211 - 411183 - 383
34SERSERARGARG4CC211 - 411183 - 383
44SERSERARGARG4DD211 - 411183 - 383
54SERSERARGARG4EE211 - 411183 - 383
64SERSERARGARG4FF211 - 411183 - 383
74SERSERARGARG4GG211 - 411183 - 383
84SERSERARGARG4HH211 - 411183 - 383

NCS oper:
IDCodeMatrixVector
1given(-0.97195, 0.23499, 0.00919), (0.23494, 0.96849, 0.08261), (0.01051, 0.08245, -0.99654)-15.05459, -0.89465, 64.60194
2given(0.95494, -0.24623, 0.16574), (-0.24527, -0.96909, -0.02659), (0.16716, -0.01526, -0.98581)-7.55474, -15.63447, 64.82802
3given(-0.98415, -0.00122, -0.17732), (0.01155, -0.9983, -0.05719), (-0.17695, -0.05833, 0.98249)-10.98226, -12.68379, -1.45823
4given(-0.91067, -0.02367, -0.41246), (-0.05662, -0.98179, 0.18135), (-0.40924, 0.18851, 0.89274)-27.63089, -23.21614, 66.88654
5given(0.87868, -0.27521, 0.39009), (-0.17927, -0.94753, -0.26467), (0.44246, 0.16262, -0.88192)-40.12488, -9.65566, 130.82877
6given(-0.93753, 0.24527, 0.24675), (0.2066, 0.96312, -0.17238), (-0.27993, -0.11064, -0.95362)-46.97618, 4.59595, 125.26363
7given(0.97045, 0.04617, -0.23683), (0.01541, 0.96766, 0.25178), (0.2408, -0.248, 0.93836)-17.01266, -10.53792, 67.91837

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Components

#1: Protein
SHORT-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE, / SCAD / BUTYRYL-COA DEHYDROGENASE / ACYL COA DEHYDROGENASE


Mass: 42163.449 Da / Num. of mol.: 8 / Fragment: RESIDUES 30-412
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-CTHF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: P16219, EC: 1.3.99.2
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-COS / COENZYME A PERSULFIDE


Mass: 799.599 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H36N7O16P3S2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1128 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGLY209 -> SER CHANGE IS A NATURAL VARIANT

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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: 2.58 Å3/Da / Density % sol: 52.43 % / Description: NONE
Crystal growpH: 8
Details: 0.2M AMMONIUM CHLORIDE, 20% PEG6000, 10% ETHYLENE GLYCOL, 0.1M TRIS-HCL PH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98074
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 20, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98074 Å / Relative weight: 1
ReflectionResolution: 1.9→17.9 Å / Num. obs: 275882 / % possible obs: 99.4 % / Redundancy: 4.98 % / Biso Wilson estimate: 22.56 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.23
Reflection shellResolution: 1.9→1.99 Å / Redundancy: 4.99 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.3.0040refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JQI

1jqi


Resolution: 1.9→17.89 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.187 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DENSITY ADJACENT TO FAD IN THE ACTIVE SITE HAS BEEN MODELLED AS COENZYME-A PERSULPHIDE. BOUND COS IS MOST APPARENT IN CHAIN G BUT NOT FULLY ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DENSITY ADJACENT TO FAD IN THE ACTIVE SITE HAS BEEN MODELLED AS COENZYME-A PERSULPHIDE. BOUND COS IS MOST APPARENT IN CHAIN G BUT NOT FULLY OCCUPIED IN OTHER CHAINS. NO ATTEMPT WAS MADE TO MODEL OCCUPANCY SO TEMPERATURE FACTORS ARE HIGH.
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1730 0.6 %RANDOM
Rwork0.198 ---
obs0.199 274018 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.87 Å2
Baniso -1Baniso -2Baniso -3
1-3.44 Å20 Å20 Å2
2---2.53 Å20 Å2
3----0.91 Å2
Refinement stepCycle: LAST / Resolution: 1.9→17.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22282 0 600 1128 24010
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02223326
X-RAY DIFFRACTIONr_bond_other_d0.0030.0215457
X-RAY DIFFRACTIONr_angle_refined_deg1.361.99931633
X-RAY DIFFRACTIONr_angle_other_deg1.0283.00237556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.50352993
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.42224.194837
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.423153816
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.89315118
X-RAY DIFFRACTIONr_chiral_restr0.0830.23620
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0225737
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024433
X-RAY DIFFRACTIONr_nbd_refined0.1990.24952
X-RAY DIFFRACTIONr_nbd_other0.1850.215924
X-RAY DIFFRACTIONr_nbtor_refined0.1720.211292
X-RAY DIFFRACTIONr_nbtor_other0.090.211520
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.21206
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0780.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.230.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.94315362
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.597523579
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.15189311
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.062118054
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
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A4377medium positional0.220.5
2B4377medium positional0.190
3C4377medium positional0.190
4D4377medium positional0.190
5E4377medium positional0.180
6F4377medium positional0.230
7G4377medium positional0.20
8H4377medium positional0.190
1A55loose positional0.655
2B55loose positional0.270.09
3C55loose positional0.290
4D55loose positional0.570
5E55loose positional0.490
6F55loose positional0.320
7G55loose positional0.260
8H55loose positional0.60
1A4377medium thermal1.392
2B4377medium thermal1.190
3C4377medium thermal1.040
4D4377medium thermal1.020
5E4377medium thermal1.160
6F4377medium thermal1.310
7G4377medium thermal1.130
8H4377medium thermal1.180
1A55loose thermal2.0810
2B55loose thermal0.990.18
3C55loose thermal0.940
4D55loose thermal0.830
5E55loose thermal0.930
6F55loose thermal1.470
7G55loose thermal0.940
8H55loose thermal1.10
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.353 101
Rwork0.344 19885

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