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- PDB-2uxw: Crystal structure of human very long chain acyl-CoA dehydrogenase... -

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Basic information

Entry
Database: PDB / ID: 2uxw
TitleCrystal structure of human very long chain acyl-CoA dehydrogenase (ACADVL)
ComponentsVERY-LONG-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE
KeywordsOXIDOREDUCTASE / FATTY ACID METABOLISM / TRANSIT PEPTIDE / DISEASE MUTATION / LIPID METABOLISM / COENZYME A DEHYDROGENASE / VERY LONG CHAIN FATTY ACIDS / FAD / FLAVOPROTEIN / MITOCHONDRIAL FATTY ACID BETA-OXIDATION / MITOCHONDRION / CARDIOMYOPATHY
Function / homology
Function and homology information


energy derivation by oxidation of organic compounds / very-long-chain acyl-CoA dehydrogenase / very-long-chain fatty acyl-CoA dehydrogenase activity / Beta oxidation of palmitoyl-CoA to myristoyl-CoA / negative regulation of fatty acid oxidation / long-chain fatty acyl-CoA dehydrogenase activity / fatty acid beta-oxidation using acyl-CoA dehydrogenase / acyl-CoA dehydrogenase activity / fatty-acyl-CoA binding / negative regulation of fatty acid biosynthetic process ...energy derivation by oxidation of organic compounds / very-long-chain acyl-CoA dehydrogenase / very-long-chain fatty acyl-CoA dehydrogenase activity / Beta oxidation of palmitoyl-CoA to myristoyl-CoA / negative regulation of fatty acid oxidation / long-chain fatty acyl-CoA dehydrogenase activity / fatty acid beta-oxidation using acyl-CoA dehydrogenase / acyl-CoA dehydrogenase activity / fatty-acyl-CoA binding / negative regulation of fatty acid biosynthetic process / XBP1(S) activates chaperone genes / regulation of cholesterol metabolic process / temperature homeostasis / mitochondrial nucleoid / epithelial cell differentiation / response to cold / mitochondrial membrane / flavin adenine dinucleotide binding / mitochondrial inner membrane / mitochondrial matrix / nucleolus / mitochondrion / nucleoplasm / identical protein binding
Similarity search - Function
: / ACAD9/ACADV, 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 / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 ...: / ACAD9/ACADV, 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 / 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
FLAVIN-ADENINE DINUCLEOTIDE / TRANS DELTA2 PALMITENOYL-COENZYMEA / Very long-chain specific acyl-CoA dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsPike, A.C.W. / Hozjan, V. / Smee, C. / Berridge, G. / Burgess, N. / Salah, E. / Bunkoczi, G. / Uppenberg, J. / Ugochukwu, E. / von Delft, F. ...Pike, A.C.W. / Hozjan, V. / Smee, C. / Berridge, G. / Burgess, N. / Salah, E. / Bunkoczi, G. / Uppenberg, J. / Ugochukwu, E. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. / Sundstrom, M. / Oppermann, U.
CitationJournal: To be Published
Title: Crystal Structure of Human Very Long Chain Acyl- Coa Dehydrogenase (Acadvl)
Authors: Pike, A.C.W. / Hozjan, V. / Smee, C. / Berridge, G. / Burgess, N. / Salah, E. / Bunkoczi, G. / Uppenberg, J. / Ugochukwu, E. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. / ...Authors: Pike, A.C.W. / Hozjan, V. / Smee, C. / Berridge, G. / Burgess, N. / Salah, E. / Bunkoczi, G. / Uppenberg, J. / Ugochukwu, E. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. / Sundstrom, M. / Oppermann, U.
History
DepositionMar 30, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 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 / 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: VERY-LONG-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7185
Polymers65,8041
Non-polymers1,9144
Water9,080504
1
A: VERY-LONG-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE
hetero molecules

A: VERY-LONG-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,43610
Polymers131,6092
Non-polymers3,8278
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)75.001, 108.173, 149.731
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2347-

HOH

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Components

#1: Protein VERY-LONG-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE / VLCAD / ACYL-COA DEHYDROGENASE


Mass: 65804.445 Da / Num. of mol.: 1 / Fragment: RESIDUES 72-655
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) / Variant (production host): R3-PRARE2
References: UniProt: P49748, Oxidoreductases; Acting on the CH-CH group of donors; With unknown physiological acceptors
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-TH3 / TRANS DELTA2 PALMITENOYL-COENZYMEA


Mass: 1003.927 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H64N7O17P3S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 504 / 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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growpH: 7 / Details: 15% PEG3350, 0.1M SODIUM SUCCINATE PH7.0, pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9182
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 11, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9182 Å / Relative weight: 1
ReflectionResolution: 1.45→47.56 Å / Num. obs: 107669 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 16.81 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.8
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 7 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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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 2JIF

2jif


Resolution: 1.45→45 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.874 / SU ML: 0.037 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DENSITY IN THE ACTIVE SITE HAS BEEN MODELLED AS A PARTIALLY ORDERED TRANS DELTA2 PALMITENOYL COENZYME A MOLECULE. THIS ENZYME PRODUCT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DENSITY IN THE ACTIVE SITE HAS BEEN MODELLED AS A PARTIALLY ORDERED TRANS DELTA2 PALMITENOYL COENZYME A MOLECULE. THIS ENZYME PRODUCT PRESUMABLY COPURIFIED WITH THE BACTERIALLY EXPRESSED ENZYME.
RfactorNum. reflection% reflectionSelection details
Rfree0.17 5352 5 %RANDOM
Rwork0.148 ---
obs0.149 102266 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å20 Å2
2---0.31 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.45→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4275 0 85 504 4864
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224545
X-RAY DIFFRACTIONr_bond_other_d0.0020.023107
X-RAY DIFFRACTIONr_angle_refined_deg1.331.9796137
X-RAY DIFFRACTIONr_angle_other_deg0.7983.0027532
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0825565
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.91523.892185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.75715794
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8921528
X-RAY DIFFRACTIONr_chiral_restr0.0830.2698
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024976
X-RAY DIFFRACTIONr_gen_planes_other00.02903
X-RAY DIFFRACTIONr_nbd_refined0.2280.3978
X-RAY DIFFRACTIONr_nbd_other0.20.33208
X-RAY DIFFRACTIONr_nbtor_refined0.190.52296
X-RAY DIFFRACTIONr_nbtor_other0.0940.52255
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.5657
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1450.311
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3130.3100
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.572
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0632873
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.92354529
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.36371866
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.803111608
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: 1.45→1.49 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.268 362
Rwork0.233 7551
Refinement TLS params.Method: refined / Origin x: 9.6296 Å / Origin y: 23.8312 Å / Origin z: 22.2142 Å
111213212223313233
T-0.0473 Å2-0.0038 Å20.0087 Å2--0.0551 Å20.0023 Å2---0.0682 Å2
L0.5529 °20.0168 °2-0.0102 °2-0.4185 °20.0316 °2--0.4374 °2
S-0.01 Å °0.1012 Å °-0.0222 Å °-0.1226 Å °0.0001 Å °-0.0422 Å °-0.0201 Å °0.0395 Å °0.0099 Å °

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