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- PDB-4rm7: The crystal structure of acyl-COA dehydrogenase from Slackia heli... -

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Basic information

Entry
Database: PDB / ID: 4rm7
TitleThe crystal structure of acyl-COA dehydrogenase from Slackia heliotrinireducens DSM 20476
ComponentsAcyl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / ALPHA FOLD / CYTOSOLIC
Function / homology
Function and homology information


acyl-CoA dehydrogenase activity / flavin adenine dinucleotide binding
Similarity search - Function
Acyl-CoA dehydrogenases signature 1. / 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 dehydrogenases signature 1. / 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
Acyl-CoA dehydrogenase
Similarity search - Component
Biological speciesSlackia heliotrinireducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.529 Å
AuthorsWu, R. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of acyl-COA dehydrogenase from Slackia heliotrinireducens DSM 20476
Authors: Wu, R. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionOct 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyl-CoA dehydrogenase


Theoretical massNumber of molelcules
Total (without water)44,6991
Polymers44,6991
Non-polymers00
Water70339
1
A: Acyl-CoA dehydrogenase

A: Acyl-CoA dehydrogenase

A: Acyl-CoA dehydrogenase

A: Acyl-CoA dehydrogenase


Theoretical massNumber of molelcules
Total (without water)178,7974
Polymers178,7974
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area14970 Å2
ΔGint-71 kcal/mol
Surface area58700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.056, 137.056, 130.272
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Acyl-CoA dehydrogenase /


Mass: 44699.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Slackia heliotrinireducens (bacteria) / Strain: DSM 20476 / Gene: Shel_09270 / Plasmid: PMCSG73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)MAGIC
References: UniProt: C7N4Y3, short-chain acyl-CoA dehydrogenase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 3.43 Å3/Da / Density % sol: 64.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M Sodium Acetate:HCl, 4% (w/v) PEG 4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 17, 2012 / Details: MIRRORS
RadiationMonochromator: Si 111, channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.53→50 Å / Num. all: 20493 / Num. obs: 20493 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Biso Wilson estimate: 51.92 Å2 / Rsym value: 0.099 / Net I/σ(I): 7.1
Reflection shellResolution: 2.53→2.57 Å / Redundancy: 9.1 % / Mean I/σ(I) obs: 1.74 / Rsym value: 0.691 / % possible all: 98.3

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Processing

Software
NameVersionClassification
HKL-3000data collection
MLPHAREphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.529→43.341 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 20.95 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2189 1051 5.16 %
Rwork0.1735 --
obs0.1757 20381 96.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.529→43.341 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2962 0 0 39 3001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013050
X-RAY DIFFRACTIONf_angle_d1.1144123
X-RAY DIFFRACTIONf_dihedral_angle_d13.9241124
X-RAY DIFFRACTIONf_chiral_restr0.052442
X-RAY DIFFRACTIONf_plane_restr0.004540
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5292-2.64430.2751340.25752336X-RAY DIFFRACTION96
2.6443-2.78370.28571310.22062401X-RAY DIFFRACTION98
2.7837-2.95810.25661380.20062376X-RAY DIFFRACTION98
2.9581-3.18640.24641520.19742399X-RAY DIFFRACTION98
3.1864-3.5070.25521270.19252426X-RAY DIFFRACTION98
3.507-4.01410.18421470.15952410X-RAY DIFFRACTION97
4.0141-5.05610.19271150.13812460X-RAY DIFFRACTION97
5.0561-43.34730.19861070.16812522X-RAY DIFFRACTION95
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)
10.6204-0.6903-0.1682.8241.15611.9501-0.14140.0130.31470.34560.17040.7767-0.0869-0.46960.03620.62080.03990.02640.44560.0060.48016.820316.915630.2067
23.81650.09840.2514.86710.05862.5955-0.0574-0.2520.16330.3433-0.07-0.4946-0.54890.67330.1080.4907-0.0494-0.0110.4356-0.07450.323120.29817.043526.2483
32.6663-0.4625-0.67223.41540.37221.4621-0.2371-0.30990.26870.10880.0837-0.2094-0.01380.29010.09250.3413-0.012-0.0120.3172-0.01010.288418.929110.168123.0531
45.0971-2.0355-1.54043.0930.18474.2695-0.2001-0.4182-0.05340.1816-0.0536-0.64670.49420.5160.30020.4721-0.02260.00870.68640.17550.573137.60323.329620.1166
55.5443-0.28110.35784.11221.69245.0554-0.375-0.4008-0.97180.29570.15530.07090.209-0.0950.33420.4380.01520.07580.70050.19420.743237.69450.953416.5549
62.3556-2.9373-0.53422.36010.11670.0927-0.03430.28360.46860.1297-0.2512-0.0383-0.42760.09580.28870.5435-0.0681-0.04910.69640.05760.513432.609712.47018.3763
76.3661.1156-0.85463.90250.14545.0436-0.1383-0.7565-0.84820.6580.0109-0.06290.3810.28160.03230.540.0416-0.04990.70080.19360.618241.55361.090718.1007
84.9378-3.75752.75529.052-2.96913.59450.22570.02820.0142-0.4406-0.1886-0.12480.03530.2236-0.1210.3764-0.03830.02890.29410.02010.283811.91377.862616.3946
95.0504-1.56662.17893.3154-1.35534.671-0.00870.05090.3469-0.02-0.16710.24-0.1677-0.34420.05710.3667-0.02330.05510.2717-0.0430.4091-1.12199.407113.7148
102.1368-0.96840.25445.7339-2.56943.2346-0.0713-0.06530.1606-0.0428-0.0524-0.01770.097-0.00360.15240.3219-0.0105-0.0140.2678-0.02780.2997.80243.133212.099
115.37110.2820.5331.45671.77845.08680.01030.22240.6090.1585-0.0811-0.0869-0.73920.31370.04110.3397-0.08980.0110.33560.04810.428312.409214.65375.1138
123.09530.6870.4844.41612.16123.67850.1255-0.1502-0.16640.21490.0720.13870.3340.1683-0.24390.36610.1056-0.01340.4167-0.00870.519210.9081-13.536914.1547
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 23 )
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 66 )
3X-RAY DIFFRACTION3chain 'A' and (resid 67 through 100 )
4X-RAY DIFFRACTION4chain 'A' and (resid 101 through 154 )
5X-RAY DIFFRACTION5chain 'A' and (resid 155 through 188 )
6X-RAY DIFFRACTION6chain 'A' and (resid 189 through 208 )
7X-RAY DIFFRACTION7chain 'A' and (resid 209 through 230 )
8X-RAY DIFFRACTION8chain 'A' and (resid 231 through 267 )
9X-RAY DIFFRACTION9chain 'A' and (resid 268 through 308 )
10X-RAY DIFFRACTION10chain 'A' and (resid 309 through 338 )
11X-RAY DIFFRACTION11chain 'A' and (resid 339 through 365 )
12X-RAY DIFFRACTION12chain 'A' and (resid 366 through 384 )

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