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- PDB-7szv: Crystal Structure of Acyl-CoA dehydrogenase from Mycobacterium ma... -

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Basic information

Entry
Database: PDB / ID: 7szv
TitleCrystal Structure of Acyl-CoA dehydrogenase from Mycobacterium marinum in complex with FDA
ComponentsAcyl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / FAD / Flavoprotein / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-CH group of donors; With unknown physiological acceptors / acyl-CoA dehydrogenase activity / flavin adenine dinucleotide binding
Similarity search - Function
Acyl-CoA dehydrogenases signature 1. / 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, 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 1. / 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, 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
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / Acyl-CoA dehydrogenase
Similarity search - Component
Biological speciesMycobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: to be published
Title: Crystal Structure of Acyl-CoA dehydrogenase from Mycobacterium marinum in complex with FDA
Authors: DeBouver, N.D. / Abendroth, J. / Sroge, C.D. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionNov 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyl-CoA dehydrogenase
B: Acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,3374
Polymers82,7612
Non-polymers1,5752
Water2,198122
1
A: Acyl-CoA dehydrogenase
B: Acyl-CoA dehydrogenase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)168,6738
Polymers165,5234
Non-polymers3,1504
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445-x-1,-y-1,z1
Buried area20710 Å2
ΔGint-133 kcal/mol
Surface area45130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.140, 120.140, 93.960
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 9 through 12 or (resid 13...
21(chain B and (resid 9 through 34 or (resid 35...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRLYSLYS(chain A and (resid 9 through 12 or (resid 13...AA9 - 129 - 12
12GLUGLUGLUGLU(chain A and (resid 9 through 12 or (resid 13...AA1313
13THRTHRLEULEU(chain A and (resid 9 through 12 or (resid 13...AA9 - 3869 - 387
14THRTHRLEULEU(chain A and (resid 9 through 12 or (resid 13...AA9 - 3869 - 387
15THRTHRLEULEU(chain A and (resid 9 through 12 or (resid 13...AA9 - 3869 - 387
16THRTHRLEULEU(chain A and (resid 9 through 12 or (resid 13...AA9 - 3869 - 387
21THRTHRALAALA(chain B and (resid 9 through 34 or (resid 35...BB9 - 349 - 34
22LYSLYSLYSLYS(chain B and (resid 9 through 34 or (resid 35...BB3535
23THRTHRLEULEU(chain B and (resid 9 through 34 or (resid 35...BB9 - 3869 - 387
24THRTHRLEULEU(chain B and (resid 9 through 34 or (resid 35...BB9 - 3869 - 387
25THRTHRLEULEU(chain B and (resid 9 through 34 or (resid 35...BB9 - 3869 - 387
26THRTHRLEULEU(chain B and (resid 9 through 34 or (resid 35...BB9 - 3869 - 387

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Components

#1: Protein Acyl-CoA dehydrogenase /


Mass: 41380.711 Da / Num. of mol.: 2 / Fragment: MymaA.01263.b.A1 / Mutation: V293I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum (bacteria) / Gene: mmgC_16, DAVIS_02721 / Plasmid: MymaA.01263.b.A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): ATCC BAA-535 / M
References: UniProt: A0A3E2MWC7, Oxidoreductases; Acting on the CH-CH group of donors; With unknown physiological acceptors
#2: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H35N9O15P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.37 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: [Barcode: 320192b12] [pin_id: ghd0-3] [collection: aps21idf 3/25/2021] [crystallization conditions: MCSG1 B12 - 0.1M Bis-Tris:HCL, pH 6.5, 28% (w/v) PEG 2000 MME] [cryo: 20% EG]

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 25, 2021 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.4→42.82 Å / Num. obs: 30213 / % possible obs: 100 % / Redundancy: 8.915 % / Biso Wilson estimate: 53.29 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.066 / Χ2: 0.93 / Net I/σ(I): 21.39 / Num. measured all: 269364
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.4-2.468.9360.5394.2122240.9140.571100
2.46-2.538.930.4185.4521650.9460.444100
2.53-2.68.9550.3436.5621100.9650.364100
2.6-2.688.9410.2638.2620350.9790.279100
2.68-2.778.9650.20810.5219880.9850.221100
2.77-2.878.9420.16812.6819260.990.179100
2.87-2.988.9540.13415.2818460.9930.143100
2.98-3.18.9560.10818.0818070.9960.115100
3.1-3.248.9660.09121.7917130.9960.096100
3.24-3.398.9560.07325.9116310.9980.077100
3.39-3.588.9340.06229.8115500.9980.066100
3.58-3.798.9390.05533.6514840.9980.058100
3.79-4.068.9080.05136.5613820.9980.055100
4.06-4.388.9130.04939.5713140.9980.052100
4.38-4.88.9160.04641.2411950.9980.049100
4.8-5.378.8960.04741.0410760.9980.05100
5.37-6.28.8610.04740.119620.9980.05100
6.2-7.598.7760.04642.348170.9990.048100
7.59-10.738.6840.04544.876330.9990.04899.8
10.73-42.827.8680.04741.873550.9970.0598.3

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Processing

Software
NameVersionClassification
PHENIX1.20-4438refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OL2

5ol2


Resolution: 2.4→42.82 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2174 1973 6.53 %
Rwork0.18 28232 -
obs0.1824 30205 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 167.24 Å2 / Biso mean: 74.5519 Å2 / Biso min: 35.13 Å2
Refinement stepCycle: final / Resolution: 2.4→42.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5400 0 106 123 5629
Biso mean--68.67 61.36 -
Num. residues----742
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3286X-RAY DIFFRACTION5.035TORSIONAL
12B3286X-RAY DIFFRACTION5.035TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4-2.460.2941550.232620032158
2.46-2.530.26451370.214119802117
2.53-2.60.24421490.222719952144
2.6-2.680.29041610.217420002161
2.68-2.780.28631330.238520192152
2.78-2.890.24841500.211419992149
2.89-3.020.23421060.22420322138
3.02-3.180.24011360.207320372173
3.18-3.380.26941430.22120082151
3.38-3.640.22311330.184620282161
3.64-4.010.19371490.170420142163
4.01-4.590.17721270.143220192146
4.59-5.780.21341510.159720302181
5.78-42.820.18211430.155420682211
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)
11.2112-0.6198-0.73383.0655-0.76553.8351-0.11220.4276-0.2186-0.4971-0.2896-0.6194-0.01380.86650.39420.46520.06290.09610.77630.17450.6373-7.2629-40.4508-10.9175
21.51460.02970.61773.7059-1.47064.01540.04730.72520.4887-0.255-0.3861-0.304-0.8409-0.18770.2160.63640.1350.04550.79720.25070.4271-18.5903-28.3348-13.338
32.5874-0.59360.3413.1549-1.49742.1594-0.00170.45641.15090.0871-0.1457-0.4003-1.42470.020.34161.05750.1363-0.03540.58920.30030.8184-19.5658-16.7109-4.58
42.38541.3348-0.07442.16750.81593.2187-0.25520.1585-0.2042-0.1199-0.0217-0.2832-0.06990.25750.19040.3220.09460.0530.4610.08420.3596-21.0671-47.79880.1125
51.36851.03340.55250.9683-0.07241.6170.4697-0.9659-0.73270.7149-0.8217-0.9715-0.01560.64550.27160.5823-0.1248-0.40871.18630.4870.9626-1.7325-46.008131.4119
62.95122.0823-0.08161.64060.50211.97510.1593-0.50140.11790.3316-0.4213-0.1406-0.13970.10280.14770.40020.056-0.05370.59550.03050.3571-22.2221-45.51122.2941
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 53 )A9 - 53
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 144 )A54 - 144
3X-RAY DIFFRACTION3chain 'A' and (resid 145 through 246 )A145 - 246
4X-RAY DIFFRACTION4chain 'A' and (resid 247 through 386 )A247 - 386
5X-RAY DIFFRACTION5chain 'B' and (resid 9 through 237 )B9 - 237
6X-RAY DIFFRACTION6chain 'B' and (resid 238 through 386 )B238 - 386

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