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- PDB-4y9j: Crystal Structure of Caenorhabditis elegans ACDH-11 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4y9j
TitleCrystal Structure of Caenorhabditis elegans ACDH-11 in complex with C11-CoA
ComponentsProtein ACDH-11, isoform b
KeywordsOXIDOREDUCTASE / Acyl-CoA Dehydrogenase
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-CH group of donors; With unknown physiological acceptors / adaptive thermogenesis / oxidoreductase activity, acting on the CH-CH group of donors / fatty acid metabolic process / fatty acid binding / nucleotide binding
Similarity search - Function
Putative acyl-CoA dehydrogenase AidB / Adaptive response protein AidB, N-terminal / Adaptive response protein AidB N-terminal domain / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Chem-UCC / Acyl-CoA dehydrogenase family member 11 / Acyl-CoA dehydrogenase family member 11
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLi, Z.J. / Sun, F.
Funding support China, 2items
OrganizationGrant numberCountry
the 973 program of the Chinese Ministry of Science and TechnologyNos. 2006CB911001 and 2006CB806506 China
the National Natural Science Foundation of ChinaNo. 30721003 China
Citation
Journal: Cell / Year: 2015
Title: Acyl-CoA Dehydrogenase Drives Heat Adaptation by Sequestering Fatty Acids
Authors: Ma, D.K. / Li, Z. / Lu, A.Y. / Sun, F. / Chen, S. / Rothe, M. / Menzel, R. / Sun, F. / Horvitz, H.R.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Purification, crystallization and preliminary crystallographic analysis of very-long-chain acyl-CoA dehydrogenase from Caenorhabditis elegans
Authors: Li, Z. / Zhai, Y. / Fang, J. / Zhou, Q. / Geng, Y. / Sun, F.
History
DepositionFeb 17, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Data collection / Derived calculations / Source and taxonomy
Category: diffrn_source / entity_src_gen ...diffrn_source / entity_src_gen / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein ACDH-11, isoform b
B: Protein ACDH-11, isoform b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,1236
Polymers131,6802
Non-polymers3,4434
Water20,1771120
1
A: Protein ACDH-11, isoform b
B: Protein ACDH-11, isoform b
hetero molecules

A: Protein ACDH-11, isoform b
B: Protein ACDH-11, isoform b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)270,24612
Polymers263,3604
Non-polymers6,8858
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area34950 Å2
ΔGint-152 kcal/mol
Surface area75240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.561, 116.676, 115.289
Angle α, β, γ (deg.)90.000, 124.020, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1028-

HOH

21A-1238-

HOH

31A-1299-

HOH

41A-1350-

HOH

51B-1040-

HOH

61B-1303-

HOH

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Components

#1: Protein Protein ACDH-11, isoform b


Mass: 65840.109 Da / Num. of mol.: 2 / Fragment: UNP residues 10-602
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: acdh-11, CELE_Y45F3A.3, Y45F3A.3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q3T978, UniProt: Q9XWZ2*PLUS, very-long-chain acyl-CoA dehydrogenase
#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-UCC / S-{(3S,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} undecanethioate / undecanoyl coenzyme A


Mass: 935.810 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H56N7O17P3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1120 / 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: 2.76 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Tris, magnesium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 140058 / Num. obs: 139311 / % possible obs: 99.8 % / Redundancy: 7.5 % / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.061 / Χ2: 1.385 / Net I/av σ(I): 44.99 / Net I/σ(I): 11.4 / Num. measured all: 1052812
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.8-1.837.30.782.269981.144100
1.83-1.867.50.98169871.142100
1.86-1.97.50.80569931.152100
1.9-1.947.50.64369861.164100
1.94-1.987.60.48770011.106100
1.98-2.037.60.38269771.061100
2.03-2.087.60.30470131.113100
2.08-2.137.60.25870121.092100
2.13-2.27.60.19770131.079100
2.2-2.277.60.15570051.173100
2.27-2.357.60.12469791.139100
2.35-2.447.60.10470241.152100
2.44-2.557.60.08569951.178100
2.55-2.697.60.07170351.246100
2.69-2.867.60.06270011.399100
2.86-3.087.60.05370381.545100
3.08-3.397.50.05170242.094100
3.39-3.887.40.04670472.539100
3.88-4.887.20.03670622.26999.9
4.88-507.20.03168682.01595.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1000207001

Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.967 / SU B: 6.692 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.186 6857 4.9 %RANDOM
Rwork0.1455 ---
obs0.1475 132919 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 119.55 Å2 / Biso mean: 45.688 Å2 / Biso min: 17.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0 Å2-0.07 Å2
2--0.35 Å2-0 Å2
3----0.08 Å2
Refinement stepCycle: final / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9235 0 226 1120 10581
Biso mean--47.01 51.3 -
Num. residues----1185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0199734
X-RAY DIFFRACTIONr_bond_other_d0.0020.029435
X-RAY DIFFRACTIONr_angle_refined_deg1.9721.99413179
X-RAY DIFFRACTIONr_angle_other_deg0.948321698
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.40851201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.51423.59415
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.185151739
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1711580
X-RAY DIFFRACTIONr_chiral_restr0.1540.21490
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0210804
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022172
X-RAY DIFFRACTIONr_mcbond_it1.9242.2184783
X-RAY DIFFRACTIONr_mcbond_other1.9222.2174782
X-RAY DIFFRACTIONr_mcangle_it2.6213.3175976
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 523 -
Rwork0.304 9809 -
all-10332 -
obs--99.42 %
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)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
10.8290.141-0.2721.0870.03911.3147-0.00630.21150.1954-0.07550.0692-0.1193-0.16030.0549-0.0630.0323-0.04560.01570.1650.01590.0776Chain A48.8365-17.324119.5111
21.38040.4253-0.52171.1466-0.20961.3387-0.09070.42010.0134-0.09170.13790.20850.227-0.4222-0.04710.0512-0.1028-0.01120.2868-0.01210.0487Chain B20.5896-35.454322.0126
34.0218-0.2813.37820.0238-0.23392.8472-0.33190.33730.3840.00550.0059-0.0162-0.33470.27780.3260.3725-0.0484-0.01890.29920.07430.242Chain C FAD Ligand37.7957-8.972823.2703
40.09270.18680.9130.42542.03789.9160.0568-0.0503-0.0102-0.0383-0.0959-0.0185-0.0076-0.71270.03910.3229-0.09040.07020.2376-0.12150.111Chain D FAD Ligand32.1806-43.616423.7297
50.85520.2846-0.21340.7132-0.10480.7817-0.01440.06940.05980.02790.0355-0.00010.0498-0.0391-0.02110.1017-0.02320.0050.1956-0.01830.1001Chain Z water molecules37.5657-27.394326.4274
60.14880.51550.47773.0662.97952.90460.08360.1534-0.05780.24680.0546-0.1780.2269-0.0131-0.13820.23560.01660.09310.39980.01690.4101Chain E C11-CoA Ligand46.4624-7.916720.658
74.0521-1.41531.9960.711-0.86741.1219-0.06610.13070.0066-0.23260.14150.0630.2071-0.1295-0.07530.4539-0.34910.01080.3952-0.06760.1423Chain F C11-CoA Ligand23.4909-47.182421.2945
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 610
2X-RAY DIFFRACTION2B19 - 611
3X-RAY DIFFRACTION3A701
4X-RAY DIFFRACTION4B701
5X-RAY DIFFRACTION5A801 - 1391
6X-RAY DIFFRACTION5B801 - 1329
7X-RAY DIFFRACTION6A702
8X-RAY DIFFRACTION7B702

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