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- PDB-7p9a: Structure of cyclohex-1-ene-1-carboxyl-CoA dehydrogenase complexe... -

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Basic information

Entry
Database: PDB / ID: 7p9a
TitleStructure of cyclohex-1-ene-1-carboxyl-CoA dehydrogenase complexed with cyclohex-1,5-diene-1-carboxyl-CoA
ComponentsShort-chain acyl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / enzyme catalysis / acyl-CoA dehydrogenase / flavin / fatty acid oxidation
Function / homology
Function and homology information


cyclohex-1-ene-1-carbonyl-CoA dehydrogenase / acyl-CoA dehydrogenase activity / flavin adenine dinucleotide binding
Similarity search - Function
Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily ...Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal
Similarity search - Domain/homology
1,5 Dienoyl-CoA / FLAVIN-ADENINE DINUCLEOTIDE / Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase
Similarity search - Component
Biological speciesGeobacter metallireducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsErmler, U. / Weidenweber, S. / Boll, M.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)SPP1319 (ER 222/5-1) Germany
German Research Foundation (DFG)RTG 1976 (235777276) Germany
CitationJournal: Chembiochem / Year: 2021
Title: Structural Basis of Cyclic 1,3-Diene Forming Acyl-Coenzyme A Dehydrogenases.
Authors: Kung, J.W. / Meier, A.K. / Willistein, M. / Weidenweber, S. / Demmer, U. / Ermler, U. / Boll, M.
History
DepositionJul 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Short-chain acyl-CoA dehydrogenase
B: Short-chain acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,85710
Polymers89,1712
Non-polymers3,6878
Water8,989499
1
A: Short-chain acyl-CoA dehydrogenase
hetero molecules

A: Short-chain acyl-CoA dehydrogenase
hetero molecules

A: Short-chain acyl-CoA dehydrogenase
hetero molecules

A: Short-chain acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,71520
Polymers178,3414
Non-polymers7,37416
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_545x,-y-1/2,-z+1/21
crystal symmetry operation11_555-x+1/2,y,-z+1/21
crystal symmetry operation14_545-x+1/2,-y-1/2,z1
Buried area22060 Å2
ΔGint-167 kcal/mol
Surface area48420 Å2
MethodPISA
2
B: Short-chain acyl-CoA dehydrogenase
hetero molecules

B: Short-chain acyl-CoA dehydrogenase
hetero molecules

B: Short-chain acyl-CoA dehydrogenase
hetero molecules

B: Short-chain acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,71520
Polymers178,3414
Non-polymers7,37416
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
crystal symmetry operation3_755-x+2,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area22510 Å2
ΔGint-154 kcal/mol
Surface area47960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.260, 173.590, 331.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11B-729-

HOH

21B-806-

HOH

31B-829-

HOH

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Components

#1: Protein Short-chain acyl-CoA dehydrogenase


Mass: 44585.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter metallireducens (strain ATCC 53774 / DSM 7210 / GS-15) (bacteria)
Strain: ATCC 53774 / DSM 7210 / GS-15 / Gene: Gmet_3306 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q39QF5
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-4KX / 1,5 Dienoyl-CoA / Cyclohex-1,5-diene-1-carbonyl-CoA


Mass: 873.656 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H42N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.34 Å3/Da / Density % sol: 63.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 25% 6000, 0.3 M sodium/potassium tartrate, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→46.612 Å / Num. obs: 144112 / % possible obs: 82.6 % / Redundancy: 5.769 % / Biso Wilson estimate: 25.237 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.097 / Χ2: 0.943 / Net I/σ(I): 17.36 / Num. measured all: 831405 / Scaling rejects: 23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.63.3720.5542.134022630468119310.8390.64839.2
1.6-1.84.4780.3154.3913844742527309180.9560.35572.7
1.8-2.26.2450.13511.6428343545523453850.9940.14799.7
2.2-2.86.6320.15525.3818925228552285360.9910.16899.9
2.8-3.66.6440.08535.919519114339143270.9960.09299.9
3.6-4.66.6550.04943.644460668966810.9980.05399.9
4.6-5.96.4450.04443.9621179329332860.9980.04899.8
5.9-86.5090.04344.4411684180017950.9980.04799.7
8-125.9070.03446.3150928708620.9990.03899.1
12-46.6126.2380.03248.0224394023910.9980.03697.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 7P98

7p98


Resolution: 1.5→46.612 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2053 1999 1.39 %
Rwork0.1855 141963 -
obs0.1858 143962 82.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90 Å2 / Biso mean: 28.916 Å2 / Biso min: 11.14 Å2
Refinement stepCycle: final / Resolution: 1.5→46.612 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5724 0 242 500 6466
Biso mean--29.99 34.07 -
Num. residues----759
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5-1.53750.474540.41380331
1.5375-1.57910.3672720.314514742
1.5791-1.62550.3148900.2813638853
1.6255-1.6780.26931090.2571773063
1.678-1.7380.27081290.2494920075
1.738-1.80760.22681580.23661115891
1.8076-1.88990.28521710.23421217799
1.8899-1.98950.23091720.233512166100
1.9895-2.11410.25111730.230612240100
2.1141-2.27740.20211710.205312234100
2.2774-2.50650.20151730.157812303100
2.5065-2.86920.19591740.159412352100
2.8692-3.61470.181750.16612403100
3.6147-46.6120.17351780.159612662100
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)
12.0037-7.21638.81892.0105-5.62096.39960.58640.9905-0.8363-0.7756-0.30310.88150.2625-0.046-0.25320.44220.0713-0.1320.6552-0.07570.43435.5675-47.429851.6822
21.3702-0.11420.13772.4756-1.62263.5196-0.00670.30440.0882-0.2055-0.0156-0.1355-0.08530.2430.02270.1107-0.02590.02590.20540.00770.139343.7642-35.370158.2239
31.36620.0771-0.18741.01940.29821.61250.08560.08180.4558-0.14420.0521-0.1774-0.38550.175-0.11670.2203-0.0660.03150.16680.0430.27344.1099-16.780566.4481
47.53086.6031-5.3098.6399-6.24644.62880.2411-0.51020.43390.6245-0.3774-0.0111-0.60060.36970.14920.1759-0.0607-0.03110.2475-0.0280.270348.9199-31.694675.4477
51.12250.4763-0.15491.8025-0.41571.153-0.01180.11640.0473-0.09670.06160.0125-0.03790.0032-0.04970.06640.00890.01240.1156-0.01250.099930.9886-40.033769.0885
69.4024-6.94981.48147.1958-1.64621.1460.11780.28890.5353-0.0857-0.2102-0.3728-0.03860.10160.09540.0909-0.02810.01150.0963-0.00220.094631.0606-36.477474.957
72.0019-7.89757.656.1556-6.52729.74121.03460.655-1.2847-0.7692-0.35720.26841.36880.5762-0.65860.44260.0237-0.11710.3265-0.06640.671559.2931-31.2269-3.9878
82.9134-3.54870.30686.5858-2.71892.46420.01820.172-0.2094-0.3360.19660.75560.2766-0.3802-0.20930.1286-0.0711-0.04750.3075-0.00340.229144.6297-18.1773-0.644
91.06810.1499-0.03311.3860.63312.05260.0491-0.0966-0.30030.19920.00890.08850.4036-0.26-0.04840.1814-0.0522-0.01810.22450.05650.236353.7472-25.19313.1964
103.28040.7329-1.39233.5111-0.95514.24610.1412-0.361-0.08650.4759-0.04190.06490.0391-0.1389-0.0960.2254-0.02780.0240.25420.07320.163950.6049-15.528729.4894
111.99995.6781.99752.9608-5.70981.99960.1746-0.1420.18480.27740.11010.1355-0.3109-0.0878-0.28280.17940.01510.05810.39910.04980.259846.5639-7.218811.5382
121.61780.5344-2.91760.9058-1.25177.5668-0.0037-0.087-0.15640.1069-0.01720.01160.3279-0.1270.02990.1417-0.0491-0.0390.16460.02220.187757.2531-16.335913.0022
130.8571-0.27680.26917.2364-7.49068.77810.02650.1352-0.0732-0.2463-0.1306-0.13750.21720.12680.10440.10410.0189-0.00590.2126-0.05020.142970.1885-12.5488-8.7331
142.5112-0.71242.20275.1354-5.47059.10450.0608-0.0653-0.06620.0262-0.3768-0.43070.2580.34610.31610.0979-0.010.00420.18960.00360.143869.7612-12.43874.1266
158.1352-1.8966.39161.5421-2.45798.23190.1548-0.4665-0.30370.02480.10680.11360.1349-0.5113-0.27070.1033-0.01620.02280.1128-0.01360.126363.5792-7.02635.124
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 21 )A1 - 21
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 112 )A22 - 112
3X-RAY DIFFRACTION3chain 'A' and (resid 113 through 191 )A113 - 191
4X-RAY DIFFRACTION4chain 'A' and (resid 192 through 209 )A192 - 209
5X-RAY DIFFRACTION5chain 'A' and (resid 210 through 343 )A210 - 343
6X-RAY DIFFRACTION6chain 'A' and (resid 344 through 380 )A344 - 380
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 21 )B2 - 21
8X-RAY DIFFRACTION8chain 'B' and (resid 22 through 47 )B22 - 47
9X-RAY DIFFRACTION9chain 'B' and (resid 48 through 132 )B48 - 132
10X-RAY DIFFRACTION10chain 'B' and (resid 133 through 191 )B133 - 191
11X-RAY DIFFRACTION11chain 'B' and (resid 192 through 209 )B192 - 209
12X-RAY DIFFRACTION12chain 'B' and (resid 210 through 266 )B210 - 266
13X-RAY DIFFRACTION13chain 'B' and (resid 267 through 306 )B267 - 306
14X-RAY DIFFRACTION14chain 'B' and (resid 307 through 337 )B307 - 337
15X-RAY DIFFRACTION15chain 'B' and (resid 338 through 380 )B338 - 380

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