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- PDB-3mpi: Structure of the glutaryl-coenzyme A dehydrogenase glutaryl-CoA c... -

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Basic information

Entry
Database: PDB / ID: 3mpi
TitleStructure of the glutaryl-coenzyme A dehydrogenase glutaryl-CoA complex
ComponentsGlutaryl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / alpha-beta fold / DEHYDROGENASE
Function / homology
Function and homology information


glutaryl-CoA dehydrogenase (acceptor) / 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 / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / 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 dehydrogenases signature 1. / Acyl-CoA dehydrogenase, conserved site / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / 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
FLAVIN-ADENINE DINUCLEOTIDE / glutaryl-coenzyme A / Glutaryl-CoA dehydrogenase
Similarity search - Component
Biological speciesDesulfococcus multivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsWischgoll, S. / Warkentin, E. / Boll, M. / Ermler, U.
CitationJournal: Biochemistry / Year: 2010
Title: Structural basis for promoting and preventing decarboxylation in glutaryl-coenzyme a dehydrogenases.
Authors: Wischgoll, S. / Demmer, U. / Warkentin, E. / Gunther, R. / Boll, M. / Ermler, U.
History
DepositionApr 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 31, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 20, 2023Group: 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: Glutaryl-CoA dehydrogenase
B: Glutaryl-CoA dehydrogenase
C: Glutaryl-CoA dehydrogenase
D: Glutaryl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,43812
Polymers173,7694
Non-polymers6,6698
Water8,575476
1
A: Glutaryl-CoA dehydrogenase
B: Glutaryl-CoA dehydrogenase
hetero molecules

A: Glutaryl-CoA dehydrogenase
B: Glutaryl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,43812
Polymers173,7694
Non-polymers6,6698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area22450 Å2
ΔGint-143 kcal/mol
Surface area48130 Å2
MethodPISA
2
C: Glutaryl-CoA dehydrogenase
D: Glutaryl-CoA dehydrogenase
hetero molecules

C: Glutaryl-CoA dehydrogenase
D: Glutaryl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,43812
Polymers173,7694
Non-polymers6,6698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area22590 Å2
ΔGint-144 kcal/mol
Surface area49230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.990, 114.790, 122.240
Angle α, β, γ (deg.)90.00, 133.95, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12C
22A
32B
42D
/ NCS ensembles :
ID
1
2

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Components

#1: Protein
Glutaryl-CoA dehydrogenase /


Mass: 43442.336 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfococcus multivorans (bacteria) / Gene: acd, gi228015642 / Production host: Escherichia coli (E. coli) / References: UniProt: C3UVB0, glutaryl-CoA dehydrogenase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-GRA / glutaryl-coenzyme A / Glutaryl-CoA


Mass: 881.633 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H42N7O19P3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 476 / 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: 2.54 Å3/Da / Density % sol: 51.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.01M MES, 0.5M KCL, 10% (w/v) glycerol, 1 mM dithiothreitol, 1 mM FAD, 2 mM glutaryl-CoA, 15% (v,v) MPD, 0.1 M imidazole, pH 6.5, 0.2 M KCl and 2% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å
DetectorType: MAR225 / Detector: CCD / Date: Nov 14, 2008
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 100328 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 12.3
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 3.2 / % possible all: 96.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0046refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SIQ

1siq


Resolution: 2.05→30 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 10.356 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21931 5245 5 %RANDOM
Rwork0.17559 ---
obs0.17771 100328 97.01 %-
all-100328 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.937 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å2-0.09 Å2
2---0.06 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 2.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11984 0 436 476 12896
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02212728
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4812.00217250
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.26851569
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.41824.455550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.118152083
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3251568
X-RAY DIFFRACTIONr_chiral_restr0.1020.21822
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219620
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1543TIGHT POSITIONAL0.140.05
12B1543TIGHT POSITIONAL0.150.05
13C1543TIGHT POSITIONAL0.130.05
14D1543TIGHT POSITIONAL0.130.05
11A1454MEDIUM POSITIONAL0.290.5
12B1454MEDIUM POSITIONAL0.330.5
13C1454MEDIUM POSITIONAL0.320.5
14D1454MEDIUM POSITIONAL0.260.5
11A1543TIGHT THERMAL1.810.5
12B1543TIGHT THERMAL2.110.5
13C1543TIGHT THERMAL1.880.5
14D1543TIGHT THERMAL1.860.5
11A1454MEDIUM THERMAL2.922
12B1454MEDIUM THERMAL3.22
13C1454MEDIUM THERMAL3.162
14D1454MEDIUM THERMAL2.812
21C56TIGHT POSITIONAL0.050.05
22A56TIGHT POSITIONAL0.040.05
23B56TIGHT POSITIONAL0.040.05
24D56TIGHT POSITIONAL0.040.05
21C56TIGHT THERMAL7.620.5
22A56TIGHT THERMAL3.830.5
23B56TIGHT THERMAL8.450.5
24D56TIGHT THERMAL3.590.5
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 379 -
Rwork0.299 7225 -
obs--95.19 %
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)
11.75080.1570.44260.80440.12791.19290.026-0.0186-0.0681-0.0465-0.00370.17870.0564-0.1642-0.02240.0599-0.01680.00760.10880.01270.0747-19.47957.283-2.666
21.14540.1586-0.24670.92140.25961.39450.0462-0.22930.51990.1601-0.05930.2203-0.2484-0.12940.0130.20390.04480.02830.1665-0.13950.4366-13.68694.46514.342
31.29430.1081-0.41340.7927-0.24051.7313-0.0635-0.1759-0.09520.1754-0.0162-0.00140.18270.02890.07970.08090.0162-0.00910.09950.01550.099141.31328.283-24.326
41.6150.37660.05640.929-0.11141.0723-0.0456-0.16340.22240.1651-0.0138-0.1353-0.41530.22990.05940.236-0.0982-0.0850.1635-0.04720.19557.7765.456-31.576
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 402
2X-RAY DIFFRACTION2B1 - 402
3X-RAY DIFFRACTION3C1 - 402
4X-RAY DIFFRACTION4D1 - 402

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