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- PDB-5z8t: Flavin-containing monooxygenase -

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Basic information

Entry
Database: PDB / ID: 5z8t
TitleFlavin-containing monooxygenase
ComponentsAcyl-CoA dehydrogenase type 2 domain protein
KeywordsOXIDOREDUCTASE / FAD complex / flavin-containing monooxygenase / acyl-CoA dehydrogenase.
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-CH group of donors / flavin adenine dinucleotide binding
Similarity search - Function
Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Acyl-CoA dehydrogenase type 2 domain protein
Similarity search - Component
Biological speciesAlicyclobacillus acidocaldarius subsp. acidocaldarius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsChoe, J. / Moon, H. / Shin, S.
CitationJournal: To Be Published
Title: Crystal structure of putative Flavin-dependent monooxgenase
Authors: Choe, J. / Moon, H. / Shin, S.
History
DepositionFeb 1, 2018Deposition site: PDBJ / Processing site: PDBJ
SupersessionFeb 6, 2019ID: 5GJ8
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyl-CoA dehydrogenase type 2 domain protein
B: Acyl-CoA dehydrogenase type 2 domain protein
C: Acyl-CoA dehydrogenase type 2 domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,1806
Polymers131,8243
Non-polymers2,3573
Water10,989610
1
A: Acyl-CoA dehydrogenase type 2 domain protein
hetero molecules

A: Acyl-CoA dehydrogenase type 2 domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4534
Polymers87,8822
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_665-y+3/2,-x+3/2,-z+1/21
Buried area6420 Å2
ΔGint-21 kcal/mol
Surface area30360 Å2
MethodPISA
2
B: Acyl-CoA dehydrogenase type 2 domain protein
C: Acyl-CoA dehydrogenase type 2 domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4534
Polymers87,8822
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint-22 kcal/mol
Surface area30430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.256, 177.256, 285.322
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Acyl-CoA dehydrogenase type 2 domain protein


Mass: 43941.172 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alicyclobacillus acidocaldarius subsp. acidocaldarius (bacteria)
Strain: ATCC 27009 / DSM 446 / JCM 5260 / NBRC 15652 / NCIMB 11725 / NRRL B-14509 / 104-1A
Gene: Aaci_0955 / Production host: Escherichia coli (E. coli) / References: UniProt: C8WV06
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 610 / 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: 4.23 Å3/Da / Density % sol: 70.93 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 200 mM FAD, 1.5% PEG 4000, 0.1M Sodium Acetate, HCl pH4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.33→150.57 Å / Num. obs: 95626 / % possible obs: 100 % / Redundancy: 6.6 % / Net I/σ(I): 19.6
Reflection shellResolution: 2.33→2.5 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data scaling
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GJ7

5gj7


Resolution: 2.33→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / SU B: 12.885 / SU ML: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.233 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2562 4717 4.9 %RANDOM
Rwork0.2222 ---
obs0.2238 91091 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 138.87 Å2 / Biso mean: 43.843 Å2 / Biso min: 3.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å2-0 Å20 Å2
2--0.16 Å2-0 Å2
3----0.31 Å2
Refinement stepCycle: final / Resolution: 2.33→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9183 0 106 610 9899
Biso mean--26.69 42.62 -
Num. residues----1186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0199565
X-RAY DIFFRACTIONr_bond_other_d0.0030.029029
X-RAY DIFFRACTIONr_angle_refined_deg1.6051.99113024
X-RAY DIFFRACTIONr_angle_other_deg2.045320796
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.13151184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.18322.571420
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.793151544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0451599
X-RAY DIFFRACTIONr_chiral_restr0.1020.21456
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110613
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021997
LS refinement shellResolution: 2.334→2.394 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 365 -
Rwork0.302 6567 -
all-6932 -
obs--100 %
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)
12.42480.1636-0.30462.0386-0.13740.76280.0267-0.34160.01940.21690.02570.7421-0.0132-0.1052-0.05230.02450.00210.09790.07980.03360.536362.702177.35779.792
22.7698-0.1112-0.25962.13030.19190.8249-0.2220.42280.0071-0.21320.294-0.7281-0.040.0871-0.0720.0906-0.0790.08670.3086-0.12980.66925.916177.36759.905
32.1463-0.1321-0.0182.52120.24670.8749-0.2228-0.1950.81860.41860.2726-0.0266-0.1859-0.0286-0.04980.2240.0781-0.06080.2035-0.09880.72220.078203.26876.783
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 394
2X-RAY DIFFRACTION2B0 - 394
3X-RAY DIFFRACTION3C0 - 394

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