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- PDB-4x28: Crystal structure of the ChsE4-ChsE5 complex from Mycobacterium t... -

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Basic information

Entry
Database: PDB / ID: 4x28
TitleCrystal structure of the ChsE4-ChsE5 complex from Mycobacterium tuberculosis
Components(Acyl-CoA dehydrogenase) x 2
KeywordsOXIDOREDUCTASE / Dehydrogenase
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-CH group of donors; With unknown physiological acceptors / oxidoreductase activity, acting on the CH-CH group of donors / cholesterol catabolic process / : / flavin adenine dinucleotide binding
Similarity search - Function
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 ...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 / Acyl-CoA dehydrogenase FadE27 / Acyl-CoA dehydrogenase FadE26
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.99 Å
AuthorsGuja, K.E. / Yang, M. / Sampson, N. / Garcia-Diaz, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM100021 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)F30-ES022930 United States
CitationJournal: Acs Infect Dis. / Year: 2015
Title: Unraveling Cholesterol Catabolism in Mycobacterium tuberculosis: ChsE4-ChsE5 alpha 2 beta 2 Acyl-CoA Dehydrogenase Initiates beta-Oxidation of 3-Oxo-cholest-4-en-26-oyl CoA.
Authors: Yang, M. / Lu, R. / Guja, K.E. / Wipperman, M.F. / St Clair, J.R. / Bonds, A.C. / Garcia-Diaz, M. / Sampson, N.S.
History
DepositionNov 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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


Theoretical massNumber of molelcules
Total (without water)168,5536
Polymers166,9784
Non-polymers1,5752
Water16,195899
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19780 Å2
ΔGint-132 kcal/mol
Surface area53040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.745, 108.095, 82.019
Angle α, β, γ (deg.)90.00, 93.04, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-432-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12D
22C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 398
2010B1 - 398
1020D1 - 373
2020C1 - 373

NCS ensembles :
ID
1
2

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Components

#1: Protein Acyl-CoA dehydrogenase / / Acyl-CoA dehydrogenase FadE26 / Probable acyl-CoA dehydrogenase FadE26


Mass: 44301.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: fadE26, Rv3504, RVBD_3504, LH57_19105, P425_03646 / Production host: Escherichia coli (E. coli) / References: UniProt: I6YCA3
#2: Protein Acyl-CoA dehydrogenase / / Acyl-CoA dehydrogenase FadE27 / Probable acyl-CoA dehydrogenase FadE27


Mass: 39187.402 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: fadE27, Rv3505, RVBD_3505, LH57_19110, P425_03647 / Production host: Escherichia coli (E. coli) / References: UniProt: I6Y3Q0
#3: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 899 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 25% PEG MME 550, 50 mM MgCl2, 50 mM HEPES sodium pH 7.0
PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.99→46.4 Å / Num. all: 739658 / Num. obs: 109767 / % possible obs: 99 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 19.9 / Phase calculation details: SAD
Reflection shellResolution: 1.99→2 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.624 / Mean I/σ(I) obs: 2.9 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.99→46.4 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.844 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18615 5476 5 %RANDOM
Rwork0.15079 ---
obs0.15261 -99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.384 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å2-1.71 Å2
2--3.89 Å20 Å2
3----3.13 Å2
Refinement stepCycle: 1 / Resolution: 1.99→46.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11213 0 106 899 12218
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01911573
X-RAY DIFFRACTIONr_bond_other_d0.0060.0210969
X-RAY DIFFRACTIONr_angle_refined_deg1.7011.9715770
X-RAY DIFFRACTIONr_angle_other_deg1.154325055
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7551492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.11323.055491
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.849151678
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.04715101
X-RAY DIFFRACTIONr_chiral_restr0.1010.21794
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02113303
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022692
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_it3.0923.4525977
X-RAY DIFFRACTIONr_mcbond_other3.0873.4525976
X-RAY DIFFRACTIONr_mcangle_it4.0745.1537454
X-RAY DIFFRACTIONr_mcangle_other4.0765.1537455
X-RAY DIFFRACTIONr_scbond_it4.1333.7895596
X-RAY DIFFRACTIONr_scbond_other4.1333.7895597
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9215.5418313
X-RAY DIFFRACTIONr_long_range_B_refined7.33828.96614299
X-RAY DIFFRACTIONr_long_range_B_other7.33928.95314292
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 / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A215460.1
12B215460.1
21D204760.08
22C204760.08
LS refinement shellResolution: 1.996→2.047 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 414 -
Rwork0.249 7657 -
obs--99.99 %

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