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- PDB-4n5f: Crystal Structure of a Putative acyl-CoA dehydrogenase with bound... -

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Basic information

Entry
Database: PDB / ID: 4n5f
TitleCrystal Structure of a Putative acyl-CoA dehydrogenase with bound FADH2 from Burkholderia cenocepacia J2315
ComponentsPutative acyl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / acyl-CoA dehydrogenase
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 2. / Acyl-CoA dehydrogenase, conserved site / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / 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 dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / 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
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / Putative acyl-CoA dehydrogenase
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of a Putative acyl-CoA dehydrogenase with bound FADH2 from Burkholderia cenocepacia J2315
Authors: Dranow, D.M. / Fairman, J.W. / Edwards, T.E. / Lorimer, D.
History
DepositionOct 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative acyl-CoA dehydrogenase
B: Putative acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,95625
Polymers83,3812
Non-polymers1,57523
Water2,630146
1
A: Putative acyl-CoA dehydrogenase
hetero molecules

A: Putative acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,95626
Polymers83,3812
Non-polymers1,57524
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6860 Å2
ΔGint-39 kcal/mol
Surface area26300 Å2
MethodPISA
2
B: Putative acyl-CoA dehydrogenase
hetero molecules

B: Putative acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,95624
Polymers83,3812
Non-polymers1,57522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5900 Å2
ΔGint-36 kcal/mol
Surface area26920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.470, 97.470, 168.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-538-

HOH

DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN

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Components

#1: Protein Putative acyl-CoA dehydrogenase /


Mass: 41690.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Strain: J2315 / Gene: BCAM2196, BceJ2315_56330 / Production host: Escherichia coli (E. coli)
References: UniProt: B4EGC8, 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
#3: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 21 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.41 Å3/Da / Density % sol: 48.88 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: JCSG+(d10): 40% PEG-300, 100mM Sodium Cacodylate/HCl, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 1, 2013 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 42127 / Num. obs: 41958 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.05 % / Biso Wilson estimate: 47.203 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 19.57
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.2-2.260.5623.6825067305899.6
2.26-2.320.4324.8624798298599.7
2.32-2.390.3695.6623573287399.8
2.39-2.460.3126.5523223280599.9
2.46-2.540.2448.2922535273599.8
2.54-2.630.1981021916266999.9
2.63-2.730.16111.9620913255899.9
2.73-2.840.13114.5320222246299.9
2.84-2.970.11716.2619640239599.9
2.97-3.110.0822.0218307224799.8
3.11-3.280.0725.2817717218199.8
3.28-3.480.05829.9316673206499.8
3.48-3.720.04934.0715510193099.6
3.72-4.020.04238.6814262180199.8
4.02-4.40.0440.6913144167399.5
4.4-4.920.03742.9911990154899.7
4.92-5.680.03741.5410477135299.6
5.68-6.960.03341.748997118399.7
6.96-9.840.02945.25684292698.6
9.840.02843.3336951391.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.78 Å48.76 Å
Translation4.78 Å48.76 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1JQI

1jqi


Resolution: 2.2→19.77 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.2278 / WRfactor Rwork: 0.1841 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8669 / SU B: 9.592 / SU ML: 0.124 / SU R Cruickshank DPI: 0.2369 / SU Rfree: 0.1905 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.237 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2237 2111 5 %RANDOM
Rwork0.1809 ---
all0.183 44010 --
obs0.183 41899 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.22 Å2 / Biso mean: 49.714 Å2 / Biso min: 13.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2--0.32 Å2-0 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5457 0 127 146 5730
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195681
X-RAY DIFFRACTIONr_bond_other_d0.0010.025273
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.9757735
X-RAY DIFFRACTIONr_angle_other_deg0.83312034
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6795745
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.48424.008237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.08215837
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7511538
X-RAY DIFFRACTIONr_chiral_restr0.0810.2865
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216631
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021299
X-RAY DIFFRACTIONr_mcbond_it1.6262.7092988
X-RAY DIFFRACTIONr_mcbond_other1.622.7082987
X-RAY DIFFRACTIONr_mcangle_it2.4294.053731
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 147 -
Rwork0.202 2846 -
all-2993 -
obs--99.67 %
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)
10.9739-0.09760.38720.9252-0.38971.5232-0.09930.12580.0837-0.1129-0.00170.08690.1074-0.42720.10090.0488-0.0873-0.02220.3412-0.07570.1177-9.879620.0515-14.2714
20.4696-0.0467-0.03160.9547-0.31060.9404-0.11620.01820.07360.1128-0.0751-0.0159-0.0184-0.19380.19130.141-0.0656-0.02980.1929-0.04330.18277.20922.49692.2371
32.0292-0.0808-1.35871.1858-0.03542.77960.1709-0.22310.34830.1864-0.1077-0.2024-0.82490.223-0.06320.4585-0.1177-0.14020.0667-0.02570.341524.672154.284614.4766
40.76-0.0681-0.22580.793-0.18170.9723-0.06660.08440.1960.0314-0.0967-0.1495-0.1719-0.05050.16330.1637-0.0618-0.07860.10450.02390.252421.620437.1845-1.7092
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 246
2X-RAY DIFFRACTION2A247 - 377
3X-RAY DIFFRACTION3B9 - 246
4X-RAY DIFFRACTION4B247 - 377

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