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- PDB-6cxt: Crystal structure of FAD-dependent dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 6cxt
TitleCrystal structure of FAD-dependent dehydrogenase
Components
  • Alpha/beta hydrolase fold protein
  • Butyryl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / acyl carrier protein / FAD-dependent enzyme / natural product biosynthesis
Function / homology
Function and homology information


short-chain acyl-CoA dehydrogenase / : / flavin adenine dinucleotide binding / hydrolase activity
Similarity search - Function
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 ...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 / Alpha/beta hydrolase family / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Alpha/beta hydrolase fold-1 / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold / Up-down Bundle / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Chem-FK4 / Alpha/beta hydrolase fold protein / Butyryl-CoA dehydrogenase
Similarity search - Component
Biological speciesMarinomonas mediterranea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAgarwal, V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)R00ES026620 United States
CitationJournal: Biochemistry / Year: 2019
Title: Insights into Thiotemplated Pyrrole Biosynthesis Gained from the Crystal Structure of Flavin-Dependent Oxidase in Complex with Carrier Protein.
Authors: Thapa, H.R. / Robbins, J.M. / Moore, B.S. / Agarwal, V.
History
DepositionApr 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha/beta hydrolase fold protein
B: Butyryl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6426
Polymers50,2972
Non-polymers1,3454
Water6,215345
1
A: Alpha/beta hydrolase fold protein
B: Butyryl-CoA dehydrogenase
hetero molecules

A: Alpha/beta hydrolase fold protein
B: Butyryl-CoA dehydrogenase
hetero molecules

A: Alpha/beta hydrolase fold protein
B: Butyryl-CoA dehydrogenase
hetero molecules

A: Alpha/beta hydrolase fold protein
B: Butyryl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,56724
Polymers201,1878
Non-polymers5,38016
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_556y,x,-z+4/31
crystal symmetry operation10_666-y+1,-x+1,-z+4/31
Buried area34200 Å2
ΔGint-149 kcal/mol
Surface area59830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.416, 104.416, 234.139
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-230-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Alpha/beta hydrolase fold protein / Bmp1(CP)


Mass: 8592.757 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinomonas mediterranea (strain ATCC 700492 / JCM 21426 / NBRC 103028 / MMB-1) (bacteria)
Strain: ATCC 700492 / JCM 21426 / NBRC 103028 / MMB-1 / Gene: Marme_4088 / Production host: Escherichia coli (E. coli) / References: UniProt: F2K074
#2: Protein Butyryl-CoA dehydrogenase / Bmp3


Mass: 41703.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinomonas mediterranea (strain ATCC 700492 / JCM 21426 / NBRC 103028 / MMB-1) (bacteria)
Strain: ATCC 700492 / JCM 21426 / NBRC 103028 / MMB-1 / Gene: Marme_4091 / Production host: Escherichia coli (E. coli)
References: UniProt: F2K077, short-chain acyl-CoA dehydrogenase

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Non-polymers , 4 types, 349 molecules

#3: Chemical ChemComp-FK4 / S-[2-({N-[(2R)-2-hydroxy-4-{[(R)-hydroxy(oxo)-lambda~5~-phosphanyl]oxy}-3,3-dimethylbutanoyl]-beta-alanyl}amino)ethyl] 1H-pyrrole-2-carbothioate


Mass: 435.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H26N3O7PS / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 3.66 Å3/Da / Density % sol: 66.42 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 15 mM magnesium acetate, 50 mM sodium cacodylate, pH 6.0, 1.8 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 7, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→45 Å / Num. obs: 60078 / % possible obs: 100 % / Redundancy: 23.1 % / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.021 / Rrim(I) all: 0.102 / Χ2: 1.357 / Net I/σ(I): 7.7 / Num. measured all: 1386667
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.9322.20.64529320.9710.1390.660.467100
1.93-1.9722.90.54629500.9770.1160.5580.473100
1.97-2.0123.20.4529480.9910.0950.460.502100
2.01-2.0523.40.38129280.9870.080.390.542100
2.05-2.0923.40.32129450.990.0670.3280.596100
2.09-2.1423.50.26629500.9930.0560.2720.646100
2.14-2.1923.50.23229600.9940.0490.2370.71100
2.19-2.2523.50.2229570.9940.0460.2250.77100
2.25-2.3223.50.1929730.9960.040.1940.815100
2.32-2.3923.60.16929690.9970.0350.1720.882100
2.39-2.4823.70.14829650.9970.0310.1511.01100
2.48-2.5823.70.13729750.9970.0290.141.116100
2.58-2.723.70.12430000.9980.0260.1271.29100
2.7-2.8423.60.11329890.9980.0240.1161.528100
2.84-3.0223.50.10930230.9970.0230.1111.891100
3.02-3.2523.10.09630230.9980.020.0982.481100
3.25-3.5822.50.09130380.9970.020.0933.221100
3.58-4.0921.70.07630720.9990.0170.0783.425100
4.09-5.1522.30.06231280.9990.0130.0642.90899.9
5.15-4521.60.04333530.9990.010.0441.83499.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 4IRN & 4ETW

4irn

4etw


Resolution: 1.9→45 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.497 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21072 1933 3.3 %RANDOM
Rwork0.18184 ---
obs0.1828 56340 96.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.042 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.9→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3415 0 89 345 3849
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193611
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8811.9774897
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2835449
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.7324.643168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.19615585
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.581518
X-RAY DIFFRACTIONr_chiral_restr0.1430.2539
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022740
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_it2.7942.7091781
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.9384.0392223
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4963.0341826
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.64238.2855955
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 128 -
Rwork0.223 3708 -
obs--88.55 %

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