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- PDB-2wbi: Crystal structure of human acyl-CoA dehydrogenase 11 -

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Basic information

Entry
Database: PDB / ID: 2wbi
TitleCrystal structure of human acyl-CoA dehydrogenase 11
ComponentsACYL-COA DEHYDROGENASE FAMILY MEMBER 11
KeywordsOXIDOREDUCTASE / HUMAN / ACYL-COA / DEHYDROGENASE / PHOSPHOPROTEIN
Function / homology
Function and homology information


very-long-chain fatty acyl-CoA dehydrogenase activity / Oxidoreductases; Acting on the CH-CH group of donors; With a flavin as acceptor / long-chain fatty acyl-CoA dehydrogenase activity / medium-chain fatty acyl-CoA dehydrogenase activity / fatty acid beta-oxidation using acyl-CoA dehydrogenase / acyl-CoA dehydrogenase activity / Mitochondrial Fatty Acid Beta-Oxidation / fatty acid beta-oxidation / mitochondrial membrane / peroxisome ...very-long-chain fatty acyl-CoA dehydrogenase activity / Oxidoreductases; Acting on the CH-CH group of donors; With a flavin as acceptor / long-chain fatty acyl-CoA dehydrogenase activity / medium-chain fatty acyl-CoA dehydrogenase activity / fatty acid beta-oxidation using acyl-CoA dehydrogenase / acyl-CoA dehydrogenase activity / Mitochondrial Fatty Acid Beta-Oxidation / fatty acid beta-oxidation / mitochondrial membrane / peroxisome / flavin adenine dinucleotide binding / mitochondrial inner membrane / nucleus
Similarity search - Function
Acyl-CoA dehydrogenase family member 10/11, N-terminal / 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 / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, C-terminal domain ...Acyl-CoA dehydrogenase family member 10/11, N-terminal / 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 / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / 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 / Protein kinase-like domain superfamily / Up-down Bundle / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / PHOSPHATE ION / Acyl-CoA dehydrogenase family member 11
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMuniz, J.R.C. / Guo, K. / Savitsky, P. / Roos, A. / Yue, W. / Pilka, E. / von Delft, F. / Edwards, A.M. / Bountra, C. / Arrowsmith, C.H. ...Muniz, J.R.C. / Guo, K. / Savitsky, P. / Roos, A. / Yue, W. / Pilka, E. / von Delft, F. / Edwards, A.M. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Oppermann, U.
CitationJournal: To be Published
Title: Crystal Structure of Human Acyl-Coa Dehydrogenase 11
Authors: Muniz, J.R.C. / Guo, K. / Savitsky, P. / Roos, A. / Yue, W. / Pilka, E. / von Delft, F. / Edwards, A.M. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Oppermann, U.
History
DepositionFeb 28, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 5, 2012Group: Database references / Structure summary
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4May 8, 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 / struct_ncs_dom_lim / 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_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 / _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 FAMILY MEMBER 11
B: ACYL-COA DEHYDROGENASE FAMILY MEMBER 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,18520
Polymers95,4242
Non-polymers1,76118
Water43224
1
A: ACYL-COA DEHYDROGENASE FAMILY MEMBER 11
B: ACYL-COA DEHYDROGENASE FAMILY MEMBER 11
hetero molecules

A: ACYL-COA DEHYDROGENASE FAMILY MEMBER 11
B: ACYL-COA DEHYDROGENASE FAMILY MEMBER 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,37140
Polymers190,8494
Non-polymers3,52236
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area18370 Å2
ΔGint-111.3 kcal/mol
Surface area70100 Å2
MethodPQS
Unit cell
Length a, b, c (Å)128.089, 128.089, 129.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNGLUGLUAA23 - 5123 - 51
21GLNGLNGLUGLUBB23 - 5123 - 51
12LYSLYSARGARGAA62 - 20362 - 203
22LYSLYSARGARGBB62 - 20362 - 203
13GLNGLNARGARGAA214 - 423214 - 423
23GLNGLNARGARGBB214 - 423214 - 423

NCS oper: (Code: given / Matrix: (1), (1), (1))

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Components

#1: Protein ACYL-COA DEHYDROGENASE FAMILY MEMBER 11 / ACYL-COA DEHYDROGENASE 11 / ACAD-11


Mass: 47712.168 Da / Num. of mol.: 2 / Fragment: RESIDUES 355-780
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Organ: LIVER / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)-R3-PRARE2 / References: UniProt: Q709F0
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 14 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 3.53 Å3/Da / Density % sol: 64.84 % / Description: NONE
Crystal growDetails: 50% PEG 300, 0.20 M NACL, 0.1 M NA/K-PO4, PH 6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.88
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 30, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88 Å / Relative weight: 1
ReflectionResolution: 2.8→45.6 Å / Num. obs: 30800 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.8
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0085refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→45.6 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.927 / SU B: 25.811 / SU ML: 0.255 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.768 / ESU R Free: 0.326 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. UNK ATOMS RELATED TO A SECOND LIGAND WERE MODELED IN THE ACTIVE SITE.
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1550 5 %RANDOM
Rwork0.224 ---
obs0.225 29219 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.78 Å2
Baniso -1Baniso -2Baniso -3
1-1.59 Å20.79 Å20 Å2
2--1.59 Å20 Å2
3----2.38 Å2
Refinement stepCycle: LAST / Resolution: 2.8→45.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6042 0 130 24 6196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226331
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3551.9718603
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8575796
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.81424.008252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.664151061
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2721535
X-RAY DIFFRACTIONr_chiral_restr0.0930.2954
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214700
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2761.53954
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.55126340
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.07332377
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.7624.52263
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
1A1504tight positional0.050.05
2B1320medium positional0.080.5
1A1504tight thermal0.080.5
2B1320medium thermal0.092
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.404 116
Rwork0.35 2135
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)
11.4077-0.3688-0.16421.44540.27421.2080.0634-0.05330.40120.0351-0.0205-0.1753-0.31230.1308-0.0430.1126-0.08670.01810.119-0.02660.120456.049-28.246228.1288
22.2755-1.32180.89421.493-0.56381.06950.02260.03160.0935-0.00110.036-0.1334-0.07030.207-0.05870.0267-0.0450.00490.0935-0.02430.028260.3532-42.83817.9091
31.3769-0.3425-0.03881.3032-0.34661.48060.0609-0.18040.2940.0411-0.0207-0.0342-0.1880.0172-0.04010.0326-0.01380.01670.0293-0.04010.064434.0442-27.574925.2326
42.27851.0623-1.3093.2848-2.9966.5737-0.0098-0.3043-0.1650.1036-0.0316-0.05770.12990.06860.04140.01670.0043-0.00020.07040.00270.028536.5603-51.13735.0584
50.70430.0671-0.20370.83430.07290.87-0.02740.20930.1818-0.21210.08220.1078-0.1373-0.1507-0.05480.1211-0.0159-0.03570.12160.08710.071626.9385-26.2534-11.4316
67.4244-6.87320.94896.3715-0.88340.1246-0.0924-0.07850.03120.09610.09870.003-0.018-0.0293-0.00630.12050.0312-0.00360.14430.02350.165911.2678-3.6972-1.436
70.6223-0.1380.08731.3316-0.68231.2580.09390.11490.1652-0.26570.02640.1455-0.0421-0.0759-0.12030.09950.00960.00230.06180.03660.072928.7869-25.8886-1.9562
81.0948-0.0546-0.29410.87650.14330.63040.04160.20960.1529-0.0941-0.02290.2187-0.1217-0.1761-0.01880.03580.0216-0.01880.07860.03220.081320.9617-36.73767.121
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 176
2X-RAY DIFFRACTION2A177 - 275
3X-RAY DIFFRACTION3A276 - 403
4X-RAY DIFFRACTION4A404 - 425
5X-RAY DIFFRACTION5B22 - 202
6X-RAY DIFFRACTION6B203 - 215
7X-RAY DIFFRACTION7B216 - 313
8X-RAY DIFFRACTION8B314 - 424

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