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- PDB-6hrd: Crystal structure of M. tuberculosis FadB2 (Rv0468) -

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Basic information

Entry
Database: PDB / ID: 6hrd
TitleCrystal structure of M. tuberculosis FadB2 (Rv0468)
Components3-hydroxybutyryl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / beta-oxidation
Function / homology
Function and homology information


3-hydroxybutyryl-CoA dehydrogenase / butyrate metabolic process / 3-hydroxybutyryl-CoA dehydrogenase activity / response to host immune response / fatty acid elongation / fatty acid beta-oxidation / NAD+ binding / peptidoglycan-based cell wall / plasma membrane / cytosol
Similarity search - Function
3-hydroxyacyl-CoA dehydrogenase / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain ...3-hydroxyacyl-CoA dehydrogenase / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
3-hydroxybutyryl-CoA dehydrogenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsCox, J.A.G. / Besra, G.S. / Futterer, K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/S000542/1 United Kingdom
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Crystal structure of Mycobacterium tuberculosis FadB2 implicated in mycobacterial beta-oxidation.
Authors: Cox, J.A.G. / Taylor, R.C. / Brown, A.K. / Attoe, S. / Besra, G.S. / Futterer, K.
History
DepositionSep 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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: 3-hydroxybutyryl-CoA dehydrogenase
B: 3-hydroxybutyryl-CoA dehydrogenase
C: 3-hydroxybutyryl-CoA dehydrogenase
D: 3-hydroxybutyryl-CoA dehydrogenase
E: 3-hydroxybutyryl-CoA dehydrogenase
F: 3-hydroxybutyryl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,5859
Polymers205,3096
Non-polymers2763
Water7,638424
1
A: 3-hydroxybutyryl-CoA dehydrogenase
B: 3-hydroxybutyryl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5283
Polymers68,4362
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 3-hydroxybutyryl-CoA dehydrogenase
D: 3-hydroxybutyryl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5283
Polymers68,4362
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: 3-hydroxybutyryl-CoA dehydrogenase
F: 3-hydroxybutyryl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5283
Polymers68,4362
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.220, 90.220, 284.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 300
2114B1 - 300
3114C1 - 300
4114D1 - 300
5114E1 - 300
6114F1 - 300

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.7969, -0.384202, 0.466195), (-0.361677, -0.314694, -0.877586), (0.48388, -0.867961, 0.111823)-65.83351, -10.99593, 19.72815
3given(-0.888783, 0.458144, -0.013011), (0.458319, 0.888591, -0.018703), (0.002993, -0.022586, -0.99974)15.35983, -25.70899, 9.65959
4given(0.541618, -0.697037, -0.469882), (0.174866, -0.453318, 0.874028), (-0.822236, -0.555555, -0.123637)-64.13779, -17.21414, 49.97066
5given(0.535701, 0.177146, -0.825617), (-0.701298, -0.451258, -0.551859), (-0.470326, 0.874635, -0.117507)-11.33668, -24.53231, -8.93626
6given(-0.407652, 0.430687, 0.805188), (0.41961, -0.694814, 0.58409), (0.811016, 0.575971, 0.102522)-52.47786, 8.30935, 34.00074

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Components

#1: Protein
3-hydroxybutyryl-CoA dehydrogenase / Beta-hydroxybutyryl-CoA dehydrogenase / BHBD


Mass: 34218.145 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: fadB2, Rv0468 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WNP7, 3-hydroxybutyryl-CoA dehydrogenase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.82 Å3/Da / Density % sol: 56.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium citrate dibasic, 20 % w/v polyethyleneglycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 2.11→90.2 Å / Num. obs: 129955 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Net I/σ(I): 13.8
Reflection shellResolution: 2.11→2.16 Å / Redundancy: 5.7 % / Rmerge(I) obs: 1.04 / CC1/2: 0.583 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KUE

4kue


Resolution: 2.11→90.2 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / SU B: 10.185 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.155 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22135 6484 5 %RANDOM
Rwork0.19018 ---
obs0.19172 123371 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.313 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20 Å2
2--0.4 Å20 Å2
3----0.8 Å2
Refinement stepCycle: 1 / Resolution: 2.11→90.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12675 0 18 424 13117
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01412876
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712185
X-RAY DIFFRACTIONr_angle_refined_deg1.6261.65117489
X-RAY DIFFRACTIONr_angle_other_deg0.9141.6328338
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.31751704
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.12420.651599
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.127152098
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.04115113
X-RAY DIFFRACTIONr_chiral_restr0.0790.21724
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214601
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022195
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_it1.2842.3726834
X-RAY DIFFRACTIONr_mcbond_other1.2832.3726833
X-RAY DIFFRACTIONr_mcangle_it2.1173.5488532
X-RAY DIFFRACTIONr_mcangle_other2.1173.5488533
X-RAY DIFFRACTIONr_scbond_it1.6582.5616042
X-RAY DIFFRACTIONr_scbond_other1.6552.5616042
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6943.7648958
X-RAY DIFFRACTIONr_long_range_B_refined4.63528.37713124
X-RAY DIFFRACTIONr_long_range_B_other4.60528.29113078
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 4094 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.30.5
Bmedium positional0.30.5
Cmedium positional0.240.5
Dmedium positional0.40.5
Emedium positional0.610.5
Fmedium positional0.370.5
Amedium thermal6.462
Bmedium thermal4.752
Cmedium thermal5.612
Dmedium thermal6.762
Emedium thermal5.672
Fmedium thermal11.592
LS refinement shellResolution: 2.11→2.165 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 570 -
Rwork0.29 9026 -
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)
10.515-0.6595-0.26691.18330.28550.5188-0.1223-0.03130.01940.07220.0415-0.06240.02420.02770.08080.0842-0.0248-0.01660.07010.01890.0284-14.672-25.73911.31
20.2170.13810.0661.27190.79941.7804-0.0174-0.10020.0250.2777-0.02010.20990.0588-0.22730.03750.15310.02350.01240.15170.02630.0668-39.527-7.73535.879
31.55180.853-0.00630.5943-0.01330.3211-0.0787-0.03270.13550.0178-0.03860.1008-0.0638-0.05230.11740.082-0.0176-0.03210.1734-0.01580.068726.708-13.758-1.376
40.10420.0697-0.14620.7994-0.76631.931-0.00160.1286-0.079-0.1889-0.0064-0.12820.1640.05110.00790.1578-0.0374-0.04040.278-0.04990.139557.081-9.148-25.892
50.58930.46750.06491.9212-0.0170.44030.01970.0843-0.0365-0.09650.1138-0.3811-0.0370.0513-0.13350.1251-0.0129-0.00530.0642-0.02840.1483-10.55917.6720.996
61.36030.65340.58741.97680.24941.2603-0.1899-0.0080.5963-0.1353-0.02140.8174-0.4122-0.38970.21130.25970.1345-0.12760.20320.00280.4686-48.00726.8648.302
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 287
2X-RAY DIFFRACTION2B3 - 287
3X-RAY DIFFRACTION3C3 - 287
4X-RAY DIFFRACTION4D3 - 287
5X-RAY DIFFRACTION5E3 - 287
6X-RAY DIFFRACTION6F3 - 287

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