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

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Basic information

Entry
Database: PDB / ID: 4rlj
TitleCrystal Structure of (3R)-hydroxyacyl-ACP dehydratase HadAB hetero-dimer from Mycobacterium tuberculosis
Components((3R)-hydroxyacyl-ACP dehydratase subunit ...) x 2
KeywordsLYASE / double hotdog fold / (3R)-hydroxyacyl-ACP binding
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 / N-terminal half of MaoC dehydratase / MaoC-like dehydratase domain / MaoC like domain / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / (3R)-hydroxyacyl-ACP dehydratase subunit HadB / : / UPF0336 protein Rv0635
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 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 17, 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 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / 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)34,00210
Polymers32,8272
Non-polymers1,1758
Water3,585199
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)68,00420
Polymers65,6544
Non-polymers2,35116
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area13820 Å2
ΔGint-36 kcal/mol
Surface area24140 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-18 kcal/mol
Surface area13300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.019, 82.019, 139.774
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-324-

HOH

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Components

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(3R)-hydroxyacyl-ACP dehydratase subunit ... , 2 types, 2 molecules AB

#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

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Non-polymers , 5 types, 207 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#5: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 3.58 Å3/Da / Density % sol: 65.65 %
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-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 15, 2013 / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 17.3 % / Number: 442538 / Rmerge(I) obs: 0.1 / Χ2: 1.08 / D res high: 2.2 Å / D res low: 50 Å / Num. obs: 25553 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
4.745010.0551.06915.9
3.764.7410.0631.09617.2
3.293.7610.081.07716.6
2.993.2910.1051.02818
2.772.9910.1391.05316.7
2.612.7710.1771.0817.9
2.482.6110.2321.10918.2
2.372.4810.2691.1316.8
2.282.3710.3411.08317.8
2.22.2810.4131.03818.3
ReflectionResolution: 1.75→50 Å / Num. obs: 48837 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.5 % / Biso Wilson estimate: 23.93 Å2 / Rmerge(I) obs: 0.058 / Χ2: 1.072 / Net I/σ(I): 15.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.75-1.819.60.42448031.0921100
1.81-1.899.60.347711.0811100
1.89-1.979.60.19948271.0561100
1.97-2.079.60.14748091.0941100
2.07-2.29.70.10848280.9761100
2.2-2.389.60.08648551.0781100
2.38-2.619.60.07648661.0851100
2.61-2.999.40.06849151.1351100
2.99-3.779.20.05449700.9961100
3.77-508.90.03651931.124199.1

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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
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→36.68 Å / SU ML: 0.13 / σ(F): 1.34 / Phase error: 15.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1849 2469 5.06 %RANDOM
Rwork0.1572 ---
obs0.1586 48754 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.51 Å2 / Biso mean: 31.549 Å2 / Biso min: 13.95 Å2
Refinement stepCycle: LAST / Resolution: 1.75→36.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2223 0 78 199 2500
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192376
X-RAY DIFFRACTIONf_angle_d1.6823208
X-RAY DIFFRACTIONf_chiral_restr0.111354
X-RAY DIFFRACTIONf_plane_restr0.009408
X-RAY DIFFRACTIONf_dihedral_angle_d15.575862
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.7840.19431340.179525352669100
1.784-1.82050.22231350.165425232658100
1.8205-1.860.17131570.157925102667100
1.86-1.90330.15931200.150625392659100
1.9033-1.95090.18211330.150125502683100
1.9509-2.00360.18131480.146525242672100
2.0036-2.06260.17711550.143524972652100
2.0626-2.12920.18261450.137425222667100
2.1292-2.20530.16891210.142325712692100
2.2053-2.29350.16461350.151725622697100
2.2935-2.39790.18781120.147525832695100
2.3979-2.52430.15551310.153625702701100
2.5243-2.68240.18951450.152425572702100
2.6824-2.88940.18461270.157326022729100
2.8894-3.18010.19741460.163625992745100
3.1801-3.63990.18931510.153825932744100
3.6399-4.58450.18351440.146426552799100
4.5845-36.6880.19591300.1852793292399
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)
10.52621.9491-0.32147.2279-1.14562.0542-0.1538-0.52390.3110.3755-0.00160.9601-0.0379-0.90870.12030.26060.04820.08250.4747-0.09430.3515-5.671535.4793.5557
20.6171-1.0833-0.49233.41171.24131.6655-0.0686-0.07480.060.14140.0125-0.0362-0.06520.06370.03260.16380.0045-0.01430.18150.01240.149715.987320.8712-2.3987
38.81522.2229-0.54782.5241-1.07472.53280.00690.31710.0449-0.1953-0.0483-0.2644-0.0150.35140.04130.13830.0139-0.00040.22770.02370.139719.529619.8744-15.3694
47.4624-1.4853-4.22184.28292.9288.177-0.0265-0.1687-0.06820.3824-0.12210.2650.2507-0.55090.08880.1982-0.00690.01080.2180.00040.18843.097624.82261.8395
51.6852-0.73240.98642.18540.30691.9858-0.0725-0.30980.05580.1421-0.04180.3559-0.0226-0.43960.09340.15580.00130.02090.2401-0.00580.17120.518227.8281-4.069
62.2783.17640.74184.16830.99992.08130.1634-0.3492-0.04490.1917-0.25120.1997-0.0456-0.360.03560.16470.01330.00130.2150.00340.1473-0.901730.2478-5.2552
71.87651.7923-0.89562.7766-1.47070.7824-0.09051.09830.0911-0.12020.0218-0.7262-0.17981.0438-0.01860.2328-0.01950.00520.54680.040.401421.273526.2192-28.5799
83.43871.88250.38217.3307-1.4812.71920.06280.56520.1417-0.5347-0.08490.09170.27190.25420.03540.22530.0640.01250.37270.00390.16437.284822.4398-33.9908
90.7995-0.46811.4071.4566-0.19193.5190.0821-0.0851-0.1274-0.05290.02670.18870.2018-0.2095-0.08470.1815-0.0271-0.02280.20250.02540.21633.20638.0692-6.3497
102.2064-2.3668-1.38963.3418-1.01379.4203-0.3325-0.5015-0.6250.14660.43850.49680.6043-1.2830.00960.2743-0.10740.0020.53770.16150.5286-10.27393.3366-0.7858
111.03830.05320.071.3-1.42482.63920.040.0841-0.0382-0.00520.05970.06740.065-0.0379-0.10740.14980.0032-0.02210.2089-0.00660.19654.304318.129-16.1309
122.69790.5830.52418.5976-3.01433.54160.0611-0.0217-0.3102-0.25920.26220.51820.4306-0.3212-0.28970.2079-0.0763-0.07210.26090.03840.1732-3.99116.8257-12.6075
131.63040.28190.19777.0709-3.59133.72610.15150.16340.0793-0.4459-0.14580.1560.17380.03110.0190.190.0161-0.02750.2768-0.00630.19041.950318.6033-26.7198
148.14125.7215-1.89964.101-1.93123.6176-0.06260.1890.4699-0.4087-0.02980.1122-0.23860.1490.0090.2102-0.0096-0.02110.29410.03350.2184.71727.1823-27.2367
152.2391-1.23310.23953.65612.76643.36120.07410.0778-0.25830.0027-0.07580.4070.321-0.2247-0.01460.192-0.0209-0.05970.26840.02170.2381-5.980814.3152-19.9026
165.66877.0048-5.88879.9572-5.71497.97680.1613-0.06340.49120.1133-0.11310.1892-0.43510.2321-0.0630.13970.0021-0.02050.24030.02120.17237.707928.624-24.3266
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 13 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 14 through 31 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 32 through 58 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 59 through 74 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 75 through 115 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 116 through 146 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid -4 through 5 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 6 through 17 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 18 through 43 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 44 through 50 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 51 through 85 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 86 through 99 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 100 through 112 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 113 through 125 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 126 through 134 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 135 through 142 )B0

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