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- PDB-4rlt: Crystal Structure of (3R)-hydroxyacyl-ACP dehydratase HadAB heter... -

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Basic information

Entry
Database: PDB / ID: 4rlt
TitleCrystal Structure of (3R)-hydroxyacyl-ACP dehydratase HadAB hetero-dimer from Mycobacterium tuberculosis complexed with Fisetin
Components
  • (3R)-hydroxyacyl-ACP dehydratase subunit HadA
  • (3R)-hydroxyacyl-ACP dehydratase subunit HadB
KeywordsLYASE/LYASE INHIBITOR / double hotdog fold / (3R)-hydroxyacyl-ACP binding / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


(3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / fatty acid biosynthetic process / plasma membrane
Similarity search - Function
: / Dehydratase subunit HadA-like / : / N-terminal of MaoC-like dehydratase / FAS1-like, dehydratase domain region / MaoC-like dehydratase domain / MaoC like domain / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily ...: / Dehydratase subunit HadA-like / : / N-terminal of MaoC-like dehydratase / FAS1-like, dehydratase domain region / MaoC-like dehydratase domain / MaoC like domain / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
3,7,3',4'-TETRAHYDROXYFLAVONE / (3R)-hydroxyacyl-ACP dehydratase subunit HadB / : / UPF0336 protein Rv0635
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.049 Å
AuthorsLi, J. / Dong, Y. / Rao, Z.H.
CitationJournal: Protein Cell / Year: 2015
Title: Molecular basis for the inhibition of beta-hydroxyacyl-ACP dehydratase HadAB complex from Mycobacterium tuberculosis by flavonoid inhibitors.
Authors: Dong, Y. / Qiu, X. / Shaw, N. / Xu, Y. / Sun, Y. / Li, X. / Li, J. / Rao, Z.
History
DepositionOct 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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: (3R)-hydroxyacyl-ACP dehydratase subunit HadA
B: (3R)-hydroxyacyl-ACP dehydratase subunit HadB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2975
Polymers32,8272
Non-polymers4703
Water4,414245
1
A: (3R)-hydroxyacyl-ACP dehydratase subunit HadA
B: (3R)-hydroxyacyl-ACP dehydratase subunit HadB
hetero molecules

A: (3R)-hydroxyacyl-ACP dehydratase subunit HadA
B: (3R)-hydroxyacyl-ACP dehydratase subunit HadB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,59510
Polymers65,6544
Non-polymers9416
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area10440 Å2
ΔGint-21 kcal/mol
Surface area24570 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-10 kcal/mol
Surface area13380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.258, 82.258, 140.161
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-312-

HOH

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Components

#1: Protein (3R)-hydroxyacyl-ACP dehydratase subunit HadA / Rv0635


Mass: 17465.385 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: hadA, P425_00663, RVBD_0635 / Plasmid: pRSFDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: I6Y8B9, UniProt: P9WFK1*PLUS, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase
#2: Protein (3R)-hydroxyacyl-ACP dehydratase subunit HadB / Rv0636


Mass: 15361.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: hadB, P425_00664, Rv0636, RVBD_0636 / Plasmid: pGEX-6p-1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: I6WYY7, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase
#3: Chemical ChemComp-FSE / 3,7,3',4'-TETRAHYDROXYFLAVONE / Fisetin / 2-(3,4-DIHYDROXYPHENYL)-3,7-DIHYDROXY-4H-CHROMEN-4-ONE


Mass: 286.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10O6
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 3.61 Å3/Da / Density % sol: 65.94 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES, pH 7.5, 26% w/v PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.049→50 Å / Num. obs: 31026 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.5 % / Biso Wilson estimate: 27.92 Å2 / Rmerge(I) obs: 0.084 / Χ2: 1.061 / Net I/σ(I): 7.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.049-2.129.60.4430431.095199.9
2.12-2.219.70.33630201.093199.9
2.21-2.319.60.27930531.084199.9
2.31-2.439.60.22230761.0871100
2.43-2.589.60.18230531.0831100
2.58-2.789.60.13130681.0661100
2.78-3.069.60.09631081.0541100
3.06-3.519.50.06931050.9711100
3.51-4.429.30.05331621.092199.8
4.42-508.70.04733380.979199.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4RLJ

4rlj


Resolution: 2.049→40.625 Å / SU ML: 0.15 / σ(F): 1.34 / Phase error: 17.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1896 1563 5.05 %RANDOM
Rwork0.1576 ---
obs0.1592 30966 99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.05 Å2 / Biso mean: 36.2883 Å2 / Biso min: 15.61 Å2
Refinement stepCycle: LAST / Resolution: 2.049→40.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2290 0 33 245 2568
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122378
X-RAY DIFFRACTIONf_angle_d1.2343229
X-RAY DIFFRACTIONf_chiral_restr0.064359
X-RAY DIFFRACTIONf_plane_restr0.006418
X-RAY DIFFRACTIONf_dihedral_angle_d13.058840
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.049-2.11480.20461270.182126402767100
2.1148-2.19030.18171480.171326062754100
2.1903-2.2780.20411540.166326252779100
2.278-2.38170.21911270.165326292756100
2.3817-2.50720.18761300.167426502780100
2.5072-2.66430.21731260.16426752801100
2.6643-2.870.1761500.157226372787100
2.87-3.15870.17811710.163726482819100
3.1587-3.61550.19711530.156226842837100
3.6155-4.55420.17491390.13527312870100
4.5542-40.63290.1931380.16182878301699
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)
10.43370.5622-0.14342.9532-0.82072.2718-0.009-0.065-0.0304-0.2075-0.165-0.2721-0.13360.27310.10870.1782-0.0029-0.00580.21570.01850.1864-7.683226.2075-34.9848
27.6471-5.192-0.00795.31580.99053.63270.1048-0.6072-0.57290.34110.00940.44030.0172-0.3211-0.17450.1835-0.04970.01480.26440.00940.2271-17.252315.4635-19.207
37.79030.6706-1.57883.9861.57183.55290.4123-0.70170.75110.1563-0.340.4767-0.1814-0.3899-0.06020.166-0.00840.00470.312-0.05570.2123-21.714123.5521-20.4094
43.22482.2152-4.91465.0776-3.15098.82290.1360.24710.1334-0.1555-0.124-0.3556-0.31330.3624-0.01620.2083-0.0050.0020.28030.00190.2333-3.290825.061-36.9609
52.95840.43311.08761.3157-0.15052.66170.08240.03340.0078-0.1988-0.0721-0.1811-0.09060.358-0.03320.2359-0.03990.04840.2332-0.01210.2557-2.431225.4366-30.1208
62.04010.38852.2623.71350.19962.7952-0.26650.25880.4928-0.02680.0622-0.4782-0.22490.40730.15550.2647-0.0480.01250.28520.01850.25183.137832.4476-32.6203
72.7297-3.98541.6315.4846-1.84771.5835-0.19820.45290.53550.0036-0.1152-0.5662-0.02070.40270.20140.2377-0.00710.00160.32240.01940.20534.438629.5829-30.6425
82.9864-4.8493-0.68287.98030.17852.84610.1050.09940.135-0.1061-0.097-0.2527-0.29870.0875-0.02840.2467-0.043-0.00980.2564-0.00640.1505-5.033832.052-28.4183
90.95240.27121.00910.07950.18713.4569-0.47280.4106-0.2998-0.2985-0.0479-0.4511-0.48960.43530.29240.74180.09050.10941.24410.0150.592514.621722.004-40.8977
102.4837-0.9305-2.82624.48712.6823.978-0.0891-0.68310.37450.22880.09961.6641-0.4143-1.1046-0.06330.28050.02160.04250.57260.01160.6636-21.329326.594-6.4204
115.2017-0.57641.46965.3434-0.89873.73570.0173-1.03950.24920.7626-0.38780.01290.11560.04810.36760.2056-0.08630.02130.51320.00590.2102-7.524422.7306-1.1238
120.76650.42951.69691.37240.70364.2250.0936-0.1222-0.23350.10440.0017-0.13690.1776-0.0127-0.09870.1758-0.0056-0.01930.22440.00460.2431-6.11327.5583-25.1779
131.53180.3141.24525.90230.24943.9099-0.1546-0.2696-0.3756-0.01280.493-0.25030.06470.3584-0.30720.19320.01240.00430.3728-0.08090.35151.40949.2023-34.7509
146.03210.8364-2.54482.13791.39212.59280.14810.202-1.16010.1693-0.0277-0.90150.86861.5776-0.18210.33790.12530.01190.5302-0.15510.66679.72862.5567-34.0565
153.8354-2.1853-3.82013.02122.19323.86250.23730.42920.25250.56380.0675-1.10440.39050.9229-0.23710.23750.0703-0.08180.5029-0.09250.52087.14516.6636-28.2199
160.93340.16880.64391.37550.52531.94140.0786-0.31560.01320.0123-0.0871-0.0154-0.06790.03160.01240.1822-0.025-0.03090.2960.00950.2442-7.589321.4917-16.2997
171.0907-1.18310.53039.68713.33054.1159-0.07910.1182-0.3231-0.01640.4281-0.49860.4340.622-0.29440.22750.0904-0.0920.3263-0.0190.29023.51876.7888-22.2126
181.5018-0.3483-0.43247.87054.44663.61340.0784-0.3063-0.0820.4881-0.0064-0.06140.19120.3225-0.09780.2382-0.0588-0.06370.44040.03780.2421-2.16818.6995-8.2702
196.9171-7.1028-3.60589.66215.15435.35170.1242-0.30110.3056-0.0047-0.0774-0.1514-0.23030.1961-0.00140.2142-0.0394-0.04270.3991-0.03440.2112-4.140226.0193-8.4972
203.5941-1.0371.55173.0702-4.05585.49180.16680.0033-0.25780.1536-0.117-0.54890.33750.61470.04480.2360.016-0.06660.4567-0.02240.32285.91715.1113-15.0457
217.162-7.2856-5.10139.2134.64025.8510.3755-0.26070.7679-0.1916-0.1927-0.3289-0.2884-0.1657-0.19110.1543-0.0406-0.01170.3709-0.00750.23-7.791628.7361-10.7104
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 31 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 41 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 42 through 58 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 59 through 74 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 75 through 102 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 103 through 115 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 116 through 129 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 130 through 144 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 145 through 157 )A0
10X-RAY DIFFRACTION10chain 'B' and (resid -4 through 5 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 6 through 17 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 18 through 34 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 35 through 43 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 44 through 49 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 50 through 58 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 59 through 85 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 86 through 99 )B0
18X-RAY DIFFRACTION18chain 'B' and (resid 100 through 112 )B0
19X-RAY DIFFRACTION19chain 'B' and (resid 113 through 126 )B0
20X-RAY DIFFRACTION20chain 'B' and (resid 127 through 134 )B0
21X-RAY DIFFRACTION21chain 'B' and (resid 135 through 142 )B0

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