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- PDB-7p9x: Structure of cyclohex-1-ene-1-carboxyl-CoA dehydrogenase complexe... -

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Basic information

Entry
Database: PDB / ID: 7p9x
TitleStructure of cyclohex-1-ene-1-carboxyl-CoA dehydrogenase complexed with cyclohex-1-ene-1-carboxyl-CoA
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
1-monoenoyl-CoA / FLAVIN-ADENINE DINUCLEOTIDE / Short-chain acyl-CoA dehydrogenase
Similarity search - Component
Biological speciesGeobacter metallireducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsErmler, U. / Weidenweber, S. / Boll, M.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)spp1319 (er222/5-1) 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 28, 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
C: Short-chain acyl-CoA dehydrogenase
D: Short-chain acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,63119
Polymers178,3414
Non-polymers7,29015
Water19,6001088
1
A: Short-chain acyl-CoA dehydrogenase
B: Short-chain acyl-CoA dehydrogenase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)185,53918
Polymers178,3414
Non-polymers7,19714
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445-x-1/2,-y-1/2,z1
Buried area21290 Å2
ΔGint-155 kcal/mol
Surface area49030 Å2
MethodPISA
2
C: Short-chain acyl-CoA dehydrogenase
hetero molecules

C: Short-chain acyl-CoA dehydrogenase
hetero molecules

C: Short-chain acyl-CoA dehydrogenase
hetero molecules

C: Short-chain acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,72320
Polymers178,3414
Non-polymers7,38216
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_456-x-1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area21850 Å2
ΔGint-152 kcal/mol
Surface area48940 Å2
MethodPISA
3
D: Short-chain acyl-CoA dehydrogenase
hetero molecules

D: Short-chain acyl-CoA dehydrogenase
hetero molecules

D: Short-chain acyl-CoA dehydrogenase
hetero molecules

D: Short-chain acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,72320
Polymers178,3414
Non-polymers7,38216
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area18270 Å2
ΔGint-121 kcal/mol
Surface area52880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.910, 333.850, 76.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11D-503-

GOL

21B-747-

HOH

31B-860-

HOH

41C-681-

HOH

51C-913-

HOH

61C-923-

HOH

71D-696-

HOH

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Components

#1: Protein
Short-chain acyl-CoA dehydrogenase /


Mass: 44585.328 Da / Num. of mol.: 4
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.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical
ChemComp-4KW / 1-monoenoyl-CoA / Cyclohex-1-ene-1-carbonyl-CoA


Mass: 875.672 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H44N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1088 / 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: 3.35 Å3/Da / Density % sol: 63.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 25% PEG6000, 0.3 M sodium potassium tartrate

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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 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→48.25 Å / Num. obs: 245150 / % possible obs: 93 % / Redundancy: 7.075 % / Biso Wilson estimate: 24.27 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.069 / Χ2: 0.948 / Net I/σ(I): 20.57 / Num. measured all: 1734324 / Scaling rejects: 24
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
1.65-1.755.5090.7722.3215213442343276160.6760.85265.2
1.75-1.96.9330.4774.4131208347987450170.90.51593.8
1.9-2.27.4440.20910.1445147961131606490.9820.22499.2
2.2-2.77.4140.0872237686051038508280.9960.09399.6
2.7-3.47.3230.04338.222060730198301260.9990.04699.8
3.4-4.67.3530.02660.2213394818256182160.9990.02899.8
4.6-5.97.0240.02363.38462156595658010.02499.8
5.9-87.0530.02162.08254113604360310.023100
8-125.9950.01765.07103711746173010.01999.1
12-48.256.6450.01657.02521680678510.01797.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7p98

7p98


Resolution: 1.65→48.25 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.925 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.101 / SU Rfree Blow DPI: 0.094 / SU Rfree Cruickshank DPI: 0.092
RfactorNum. reflection% reflectionSelection details
Rfree0.236 12200 4.98 %RANDOM
Rwork0.222 ---
obs0.223 245146 93 %-
Displacement parametersBiso max: 134.17 Å2 / Biso mean: 29.72 Å2 / Biso min: 7.96 Å2
Baniso -1Baniso -2Baniso -3
1-1.5556 Å20 Å20 Å2
2---1.264 Å20 Å2
3----0.2916 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: final / Resolution: 1.65→48.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11387 0 478 1089 12954
Biso mean--32.11 35.59 -
Num. residues----1511
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4364SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes284HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1775HARMONIC5
X-RAY DIFFRACTIONt_it12279HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1632SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact16245SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d12279HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg16683HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion3.09
X-RAY DIFFRACTIONt_other_torsion15.33
LS refinement shellResolution: 1.65→1.69 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 577 5.04 %
Rwork0.274 10869 -
all0.275 11446 -
obs--59.04 %
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)
11.54160.31530.11622.9114-0.49161.9927-0.07140.03870.23330.0120.0364-0.1533-0.2730.14560.0350.0174-0.00130.0031-0.0649-0.0115-0.0662-40.5789-59.79477.2856
20.30610.1524-0.12250.6895-0.04780.47520.0046-0.02550.14210.10860.00250.1581-0.2118-0.0886-0.00710.03770.06990.0295-0.0838-0.024-0.0176-55.7418-57.98263.7335
31.26710.37860.06271.40990.23972.07450.0235-0.11450.03260.181-0.09030.4067-0.0822-0.38360.0668-0.08010.06440.09-0.0051-0.04030.0327-72.2052-67.02896.3659
40.3105-0.402-0.82731.10321.22481.1025-0.00310.05420.0540.23280.07850.10780.0135-0.1474-0.07540.01730.04230.0708-0.0242-0.005-0.0241-55.5684-75.505711.5228
50.4405-0.05310.09990.72450.02070.59730.0418-0.02750.01970.0316-0.03820.0663-0.1138-0.0282-0.0036-0.02520.02560.0069-0.0762-0.003-0.0488-46.8992-68.3336-5.3402
60.8002-0.40040.49160.6092-0.21460.8367-0.0074-0.02870.04320.0344-0.01840.009-0.0533-0.06080.0258-0.01340.03190.013-0.0146-0.0074-0.0028-47.655-74.7292-8.1379
70.08190.9796-1.02572.26532.6581.0709-0.026-0.01560.16380.13680.05010.0406-0.1816-0.1416-0.02410.10180.1188-0.0407-0.1066-0.04130.0415-47.2909-52.2278-36.2951
81.5571.2853-0.22831.770.13250.9919-0.02470.05850.1078-0.2103-0.00320.1699-0.0625-0.07530.02790.01810.0292-0.0092-0.0330.0167-0.0521-43.7135-65.1771-50.1451
90.5119-0.1678-0.11450.69-0.23090.62240.01670.04740.1765-0.0374-0.006-0.1151-0.21380.0497-0.01070.0081-0.00870.0217-0.06870.010.0002-29.8909-58.2138-40.8175
101.6817-0.13770.2510.92430.08441.1333-0.02210.110.0522-0.0846-0.0613-0.2233-0.04920.18010.0834-0.0724-0.00640.05620.00020.02210.0311-13.8429-67.7659-43.6492
110.29550.4366-0.48691.8547-1.14860-0.0374-0.02710.065-0.02540.1028-0.1138-0.00850.136-0.0654-0.01450.00720.04870.0042-0.0051-0.0221-30.7127-75.907-48.6824
121.1911-0.13040.03470.4742-0.05030.35970.00250.0858-0.0324-0.0666-0.0308-0.1313-0.08250.08770.0282-0.01310.01010.0165-0.03640.0008-0.0108-30.0884-67.0038-37.2982
130.70940.5975-0.08151.30060.0330.61120.0335-0.06890.04620.0253-0.04590.1084-0.1102-0.07930.0123-0.02750.038-0.0019-0.0453-0.004-0.0256-51.1532-70.4064-24.5
141.13940.39560.44650.56050.0840.9708-0.0055-0.13520.0837-0.0525-0.07460.0612-0.1071-0.02340.0801-0.00470.02820.0114-0.0018-0.00820.0134-41.9046-74.1061-27.3961
150.27140.1020.32260.38760.14650.91230.01830.03010.002-0.05810.0054-0.0303-0.04590.0891-0.0237-0.02190.01360.0191-0.00740.0048-0.0025-35.7006-75.5323-30.2908
162.5022-1.58522.224800.77090.1640.0173-0.07910.00880.0805-0.0218-0.1322-0.08090.15750.0045-0.0614-0.0787-0.04880.09750.064-0.0138-55.12474.124620.7637
170.67420.2363-0.10630.5980.16460.49230.00190.0645-0.1057-0.0222-0.0118-0.18530.03530.25910.0099-0.01090.04380.01550.0082-0.006-0.0782-63.0886-9.345713.4294
180.91630.0195-0.00011.37730.13290.9588-0.03460.0506-0.2794-0.0141-0.0492-0.00590.20710.13580.08380.08510.08960.0271-0.0897-0.0357-0.0083-70.7211-29.243912.7975
190.3929-0.0623-0.030.03760.0340.55690.02050.0569-0.129-0.0517-0.0282-0.04440.13180.15090.00760.04410.04690.0072-0.0424-0.0126-0.061-72.4094-12.764216.3349
200.9601-0.82720.15711.7503-0.2880.9101-0.0147-0.06370.11680.02430.0297-0.0541-0.17780.1524-0.0150.0237-0.0249-0.0084-0.04720.0054-0.0764-74.61819.556831.9901
211.2428-1.04440.46912.265-0.89241.7086-0.0430.0003-0.03110.1167-0.0552-0.10990.05940.24270.09810.02520.0093-0.005-0.03870.0076-0.0823-73.6714-4.451631.5754
220.3521-0.01880.087600.05361.13480.02890.0458-0.0184-0.0707-0.0393-0.0190.10620.10580.01040.06040.01550.0101-0.0317-0.005-0.0416-79.38-5.255925.5351
230.2228-0.00050.67560-0.03580-0.004-0.006-0.00520.00590.01860.02090.004-0.0429-0.0146-0.0060.1514-0.0508-0.0569-0.0607-0.0027-31.05943.378120.0121
240.716-0.0122-0.10561.8987-0.43111.06160.0141-0.0908-0.3220.0718-0.08040.24660.1318-0.18320.0663-0.0096-0.05420.0362-0.09840.0022-0.0755-18.7646-18.182127.8692
250.5149-0.5172-0.246300.01410.82640.016-0.04660.0118-0.0155-0.10920.14290.0067-0.14860.09320.0638-0.0066-0.0153-0.0595-0.0063-0.1186-11.2837-1.064212.2781
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|3 - A|47 }A3 - 47
2X-RAY DIFFRACTION2{ A|48 - A|132 }A48 - 132
3X-RAY DIFFRACTION3{ A|133 - A|191 }A133 - 191
4X-RAY DIFFRACTION4{ A|192 - A|209 }A192 - 209
5X-RAY DIFFRACTION5{ A|210 - A|309 }A210 - 309
6X-RAY DIFFRACTION6{ A|310 - A|380 }A310 - 380
7X-RAY DIFFRACTION7{ B|3 - B|21 }B3 - 21
8X-RAY DIFFRACTION8{ B|22 - B|47 }B22 - 47
9X-RAY DIFFRACTION9{ B|48 - B|132 }B48 - 132
10X-RAY DIFFRACTION10{ B|133 - B|191 }B133 - 191
11X-RAY DIFFRACTION11{ B|192 - B|209 }B192 - 209
12X-RAY DIFFRACTION12{ B|210 - B|266 }B210 - 266
13X-RAY DIFFRACTION13{ B|267 - B|309 }B267 - 309
14X-RAY DIFFRACTION14{ B|310 - B|343 }B310 - 343
15X-RAY DIFFRACTION15{ B|344 - B|380 }B344 - 380
16X-RAY DIFFRACTION16{ C|3 - C|21 }C3 - 21
17X-RAY DIFFRACTION17{ C|22 - C|132 }C22 - 132
18X-RAY DIFFRACTION18{ C|133 - C|191 }C133 - 191
19X-RAY DIFFRACTION19{ C|192 - C|266 }C192 - 266
20X-RAY DIFFRACTION20{ C|267 - C|306 }C267 - 306
21X-RAY DIFFRACTION21{ C|307 - C|337 }C307 - 337
22X-RAY DIFFRACTION22{ C|338 - C|380 }C338 - 380
23X-RAY DIFFRACTION23{ D|3 - D|21 }D3 - 21
24X-RAY DIFFRACTION24{ D|22 - D|229 }D22 - 229
25X-RAY DIFFRACTION25{ D|230 - D|380 }D230 - 380

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