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- PDB-7p98: Cyclohex-1-ene-1-carboxyl-CoA dehydrogenase in a substrate-free state -

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Basic information

Entry
Database: PDB / ID: 7p98
TitleCyclohex-1-ene-1-carboxyl-CoA dehydrogenase in a substrate-free state
ComponentsShort-chain acyl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / Enzyme catalysis / acyl-CoA dehydrogenase / flavin / fatty acid oxidation
Function / homology
Function and homology information


acyl-CoA dehydrogenase activity / flavin adenine dinucleotide binding
Similarity search - Function
Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / 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 ...Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / 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 / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Short-chain acyl-CoA dehydrogenase
Similarity search - Component
Biological speciesGeobacter metallireducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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

Downloads & links

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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)91,0187
Polymers89,1712
Non-polymers1,8475
Water3,243180
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)182,22016
Polymers178,3414
Non-polymers3,87912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_455-x-1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area22190 Å2
ΔGint-156 kcal/mol
Surface area48850 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)181,85212
Polymers178,3414
Non-polymers3,5118
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554x,-y+1/2,-z-1/21
crystal symmetry operation11_554-x+1/2,y,-z-1/21
crystal symmetry operation14_555-x+1/2,-y+1/2,z1
Buried area21000 Å2
ΔGint-149 kcal/mol
Surface area49730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.320, 172.200, 331.460
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
11A-662-

HOH

21B-657-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 62 or resid 64...
21(chain B and (resid 3 through 62 or resid 64...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 3 through 62 or resid 64...A3 - 62
121(chain A and (resid 3 through 62 or resid 64...A64 - 197
131(chain A and (resid 3 through 62 or resid 64...A2 - 401
141(chain A and (resid 3 through 62 or resid 64...A2 - 401
151(chain A and (resid 3 through 62 or resid 64...A323 - 368
161(chain A and (resid 3 through 62 or resid 64...A323 - 368
171(chain A and (resid 3 through 62 or resid 64...A370 - 401
211(chain B and (resid 3 through 62 or resid 64...B3 - 62
221(chain B and (resid 3 through 62 or resid 64...B64 - 197
231(chain B and (resid 3 through 62 or resid 64...B199 - 86
241(chain B and (resid 3 through 62 or resid 64...B323 - 368
251(chain B and (resid 3 through 62 or resid 64...B323 - 368
261(chain B and (resid 3 through 62 or resid 64...B370 - 401

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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 / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 3.32 Å3/Da / Density % sol: 62.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2 M sodium tatrate

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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: Aug 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→45.441 Å / Num. obs: 73530 / % possible obs: 99.9 % / Redundancy: 5.898 % / Biso Wilson estimate: 34.858 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.152 / Rrim(I) all: 0.167 / Χ2: 0.954 / Net I/σ(I): 12.17 / Num. measured all: 433654 / Scaling rejects: 81
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
2-2.15.8251.3561.9957730992799100.7141.49199.8
2.1-2.36.080.7663.639146515051150430.8920.83899.9
2.3-2.76.1390.3866.611282218386183790.9650.423100
2.7-3.25.9390.18112.177084411942119290.9890.19999.9
3.2-3.85.640.08221.740976727772650.9970.09199.8
3.8-4.65.6970.05634.2626914473447240.9980.06299.8
4.6-5.95.2110.04434.0916989327732600.9980.04999.5
5.9-85.5830.04736.69898178117730.9990.05299.6
8-124.7560.02546.3540768648570.9990.02899.2
12-45.4414.9740.02547.9919404013900.9990.02797.3

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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: 4LIF

4lif


Resolution: 2→45.441 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2426 3634 4.95 %
Rwork0.2141 69831 -
obs0.2156 73465 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.34 Å2 / Biso mean: 38.806 Å2 / Biso min: 13.1 Å2
Refinement stepCycle: final / Resolution: 2→45.441 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5707 0 124 181 6012
Biso mean--36.99 36.29 -
Num. residues----757
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2282X-RAY DIFFRACTION6.54TORSIONAL
12B2282X-RAY DIFFRACTION6.54TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.02630.40521480.37592615100
2.0263-2.0540.36811520.36212675100
2.054-2.08340.37341490.33332619100
2.0834-2.11450.35281310.30352665100
2.1145-2.14750.32011340.27982677100
2.1475-2.18270.30381290.28012684100
2.1827-2.22040.30731270.27952656100
2.2204-2.26070.29461440.26322680100
2.2607-2.30420.3321570.25242679100
2.3042-2.35120.29591220.25092675100
2.3512-2.40240.26161410.25542671100
2.4024-2.45830.27051400.24092684100
2.4583-2.51970.24671490.22942650100
2.5197-2.58780.2671300.2212683100
2.5878-2.6640.24631270.22582684100
2.664-2.750.24651250.22162710100
2.75-2.84820.21751450.21572678100
2.8482-2.96230.23521270.22552709100
2.9623-3.0970.24821370.21022676100
3.097-3.26030.26211410.21332713100
3.2603-3.46450.25971480.20742686100
3.4645-3.73190.24521470.19912693100
3.7319-4.10720.19521500.18112704100
4.1072-4.7010.19031450.1547270699
4.701-5.92070.18451330.1915275799
5.9207-45.4410.21361560.184280298
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)
19.4372-8.40797.06372.1246-5.44955.70561.01590.8436-1.3783-0.7324-0.51650.31031.12220.6278-0.48590.5630.0879-0.10220.4802-0.0350.74991.413111.8742-87.251
21.41560.01550.17151.70990.10742.28990.1005-0.0335-0.3070.1240.00190.0530.3838-0.2256-0.11290.2682-0.06280.00670.31750.01210.3095-5.906819.7211-73.0709
31.7160.32170.20081.8738-0.65982.19340.0495-0.2541-0.09770.34120.03490.0798-0.0755-0.207-0.09670.3431-0.01430.02550.38540.04970.2716-8.131628.7685-56.5724
41.54970.6909-2.81081.6787-1.85447.6806-0.0019-0.0786-0.19080.0060.01180.07340.343-0.5115-0.05140.213-0.0306-0.01910.29720.00240.3135.410427.6277-79.7247
51.23890.2015-0.27982.5039-1.22882.03410.04650.182-0.12760.0105-0.105-0.04880.02180.12740.0860.1473-0.0093-0.00080.2605-0.02820.20412.768130.4794-86.0911
64.7123-1.64532.46491.4767-1.11922.3868-0.0622-0.2877-0.12450.01240.16560.09270.0275-0.477-0.11820.2078-0.05340.01240.31030.01520.20376.538336.0086-77.789
72.0933-4.95924.61637.4297-3.14917.4230.85450.9122-0.5339-1.2498-0.66910.71920.6744-0.1626-0.21340.51330.0724-0.04450.5515-0.05810.4067-21.0407-4.5308-31.172
81.61660.14091.16622.2017-1.94626.7919-0.03680.1399-0.1125-0.1562-0.1956-0.34330.20380.55110.22360.21060.01410.0280.2859-0.02050.3459-6.5117-0.7357-18.1546
91.4662-0.33840.00870.14740.4372.22950.07230.1791-0.0549-0.1953-0.04520.11870.05680.0505-0.0230.24280.00250.01880.18630.00440.2339-18.81465.4813-27.9497
101.311-1.70670.19272.125-4.70654.5124-0.0690.18520.10260.02460.18520.1555-0.2073-0.2493-0.10240.3486-0.0266-0.02720.20190.02730.307-16.526212.8059-22.4733
112.6766-0.6606-1.42981.87861.02864.02410.15190.17020.3075-0.2943-0.0524-0.1714-0.55050.3191-0.09160.2691-0.04520.01860.23110.0430.223-12.290720.3081-24.5787
122.74910.3756-0.05340.74010.3022.4140.04550.10210.66760.05040.1047-0.2857-0.5712-0.0333-0.13170.4778-0.04970.03380.18610.0190.441-13.101929.3283-15.9943
138.78289.3558-4.3222.0656-5.09853.77740.1009-0.22970.3750.4292-0.28950.3129-0.38420.11480.22590.3912-0.00210.03660.265-0.05920.4885-8.478712.2201-7.3005
141.66241.6514-0.43895.1032-1.02481.5702-0.04840.14930.1793-0.04160.1767-0.1322-0.29330.0147-0.13030.23070.01780.02970.1842-0.02570.2114-19.396212.9477-16.6273
151.3222-0.0319-0.03432.2182-1.95793.3710.00440.0526-0.1095-0.03560.10580.17190.0652-0.1059-0.13020.1457-0.0082-0.0050.1322-0.03090.2266-31.7356-3.5887-12.1937
164.3261-2.83171.06873.6359-1.17581.1514-0.02140.01160.38130.0738-0.0419-0.272-0.11830.01110.06920.2475-0.03630.02860.1943-0.00780.2134-25.71575.1929-7.07
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 3 through 21 )B3 - 21
2X-RAY DIFFRACTION2chain 'B' and (resid 22 through 132 )B22 - 132
3X-RAY DIFFRACTION3chain 'B' and (resid 133 through 229 )B133 - 229
4X-RAY DIFFRACTION4chain 'B' and (resid 230 through 266 )B230 - 266
5X-RAY DIFFRACTION5chain 'B' and (resid 267 through 337 )B267 - 337
6X-RAY DIFFRACTION6chain 'B' and (resid 338 through 380 )B338 - 380
7X-RAY DIFFRACTION7chain 'A' and (resid 2 through 21 )A2 - 21
8X-RAY DIFFRACTION8chain 'A' and (resid 22 through 47 )A22 - 47
9X-RAY DIFFRACTION9chain 'A' and (resid 48 through 79 )A48 - 79
10X-RAY DIFFRACTION10chain 'A' and (resid 80 through 99 )A80 - 99
11X-RAY DIFFRACTION11chain 'A' and (resid 100 through 132 )A100 - 132
12X-RAY DIFFRACTION12chain 'A' and (resid 133 through 191 )A133 - 191
13X-RAY DIFFRACTION13chain 'A' and (resid 192 through 209 )A192 - 209
14X-RAY DIFFRACTION14chain 'A' and (resid 210 through 266 )A210 - 266
15X-RAY DIFFRACTION15chain 'A' and (resid 267 through 337 )A267 - 337
16X-RAY DIFFRACTION16chain 'A' and (resid 338 through 380 )A338 - 380

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