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

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Basic information

Entry
Database: PDB / ID: 4rlu
TitleCrystal Structure of (3R)-hydroxyacyl-ACP dehydratase HadAB hetero-dimer from Mycobacterium tuberculosis complexed with 2',4,4'-trihydroxychalcone
Components((3R)-hydroxyacyl-ACP dehydratase subunit ...) x 2
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
2',4,4'-TRIHYDROXYCHALCONE / TRIETHYLENE GLYCOL / (3R)-hydroxyacyl-ACP dehydratase subunit HadB / : / UPF0336 protein Rv0635
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.198 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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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)33,4766
Polymers32,8272
Non-polymers6494
Water2,612145
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)66,95112
Polymers65,6544
Non-polymers1,2978
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-11 kcal/mol
Surface area13300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.376, 82.376, 141.509
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-205-

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 , 4 types, 149 molecules

#3: Chemical ChemComp-HCC / 2',4,4'-TRIHYDROXYCHALCONE


Mass: 256.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H12O4
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 3.66 Å3/Da / Density % sol: 66.36 %
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
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.198→50 Å / Num. obs: 25514 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.3 % / Biso Wilson estimate: 42.23 Å2 / Rmerge(I) obs: 0.06 / Χ2: 1.067 / Net I/σ(I): 14.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.198-2.289.60.41925031.021100
2.28-2.379.60.37225011.0691100
2.37-2.489.50.27125091.071100
2.48-2.619.50.20825051.0821100
2.61-2.779.50.14925401.0451100
2.77-2.999.40.10725201.0771100
2.99-3.299.40.07625561.0341100
3.29-3.769.20.05725701.019199.8
3.76-4.7490.04725601.1198.5
4.74-508.60.03227501.155198.5

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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: 2.198→36.657 Å / SU ML: 0.18 / σ(F): 1.33 / Phase error: 20.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2131 1294 5.08 %RANDOM
Rwork0.1855 ---
obs0.1868 25449 99.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.28 Å2 / Biso mean: 52.2593 Å2 / Biso min: 28.85 Å2
Refinement stepCycle: LAST / Resolution: 2.198→36.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2277 0 45 145 2467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032384
X-RAY DIFFRACTIONf_angle_d0.7113230
X-RAY DIFFRACTIONf_chiral_restr0.028359
X-RAY DIFFRACTIONf_plane_restr0.003419
X-RAY DIFFRACTIONf_dihedral_angle_d14.479848
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.198-2.28610.25891370.227826522789100
2.2861-2.39010.27671430.224226232766100
2.3901-2.51610.21351510.225326322783100
2.5161-2.67370.25721550.220426292784100
2.6737-2.880.24691530.213226412794100
2.88-3.16970.23811400.212626822822100
3.1697-3.6280.22591450.185526872832100
3.628-4.56960.1741410.16272723286499
4.5696-36.66250.19361290.16322886301599
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)
15.19181.54963.09422.87980.37563.89050.25380.45590.38840.0024-0.1783-0.5238-0.581.1284-0.1060.6357-0.21990.03360.70370.1030.66126.359634.9-39.3636
20.97570.29170.01052.1622-0.24941.3722-0.07650.05980.0076-0.1299-0.06530.1518-0.1426-0.1240.05440.3492-0.0178-0.03970.3519-0.02530.3049-16.15521.2074-32.9241
34.6767-1.66710.04652.4060.1731.69240.4156-0.5042-0.50340.5839-0.20590.38670.0911-0.18590.04230.3892-0.06880.05890.4250.01130.404-17.344315.1586-19.3916
49.82070.07-0.83293.03651.55332.8328-0.0946-0.43090.81480.1866-0.15950.2367-0.3029-0.53890.12810.33450.0193-0.01150.5174-0.07850.3951-21.918323.544-20.6815
56.37910.5967-4.12813.5084-2.04136.81820.06580.42890.3618-0.11570.099-0.3771-0.49550.0326-0.16140.4427-0.04230.01470.4213-0.03640.3946-3.362725.1305-37.1353
63.4127-0.064-0.71992.0513-0.61275.5768-0.00720.0556-0.0923-0.19210.0586-0.42290.43190.9027-0.05450.3942-0.03410.01840.5377-0.0360.49774.039423.1249-32.086
76.05351.4250.55281.35960.44943.6180.0151-0.26720.0323-0.0565-0.43980.5402-0.5865-0.42920.43840.37110.04030.0350.4127-0.06310.4413-17.190530.4553-26.7588
84.61791.06230.30832.40990.31962.9764-0.0007-0.26290.04310.1097-0.1471-0.3425-0.35460.65950.13350.505-0.12810.02480.5447-0.00160.53583.07532.6069-32.7393
93.1523-3.74651.50014.4458-1.50242.3439-0.3510.7266-0.26450.1754-0.0908-0.3037-0.04920.81920.3410.4124-0.0446-0.00660.58960.06080.4254.354529.6715-30.8189
108.3819-5.3310.28455.4885-0.94413.5848-0.00790.06160.32950.1184-0.1401-0.3752-0.14990.13590.09730.4552-0.0927-0.01930.4045-0.050.3773-3.14531.026-29.101
111.54750.56290.83863.1422-0.05520.49930.04090.25550.05250.1508-0.0151-1.38450.28190.7741-0.46741.11490.07720.26191.487-0.02781.073313.153522.3106-42.33
122.7988-1.4307-1.28386.50811.23234.4337-0.8354-1.64451.15310.42810.60621.1554-0.5468-0.9501-0.03840.4370.05850.02950.7536-0.11810.7517-21.566526.5607-6.6888
134.112-0.95320.27234.3043-0.36582.4774-0.0795-1.15240.31441.0487-0.32720.02150.11310.02760.31630.3776-0.09160.00070.7845-0.06820.4694-7.586222.6338-1.4093
141.4740.56850.55631.59741.01932.98240.0357-0.035-0.23050.01160.0952-0.22340.13820.2868-0.12380.30480.0066-0.03350.3947-0.01670.3955-2.711112.5899-24.7264
153.15960.92660.63649.70583.08814.15090.0933-0.1244-0.53780.04470.2999-0.51340.3110.5031-0.33220.41410.102-0.10270.5818-0.05510.46873.48766.972-22.5965
162.5475-0.7802-0.41219.43774.9094.54720.07-0.6542-0.13070.77730.1984-0.6790.26170.4064-0.32790.3403-0.0002-0.05570.68750.02850.4258-2.270418.7195-8.5945
173.56120.01330.43750.7405-0.9173.40230.1978-0.51230.50840.0106-0.1648-0.1671-0.56470.3401-0.10860.4567-0.0396-0.02260.672-0.0840.3541-5.009227.4974-8.1666
181.4640.3125-0.88431.9852-0.37182.5857-0.0466-0.15770.05740.40350.0033-0.41660.24410.5722-0.06380.41290.0197-0.06660.683-0.01710.48245.567214.4392-15.3069
197.394-3.6713-2.64654.09022.26535.23850.1369-0.38510.5978-0.2978-0.1029-0.1151-0.5097-0.4402-0.07880.3887-0.0337-0.04020.6294-0.03330.4805-8.213228.7496-10.7724
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 13 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 14 through 31 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 32 through 41 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 42 through 58 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 59 through 74 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 75 through 93 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 94 through 102 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 103 through 115 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 116 through 129 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 130 through 145 )A0
11X-RAY DIFFRACTION11chain 'A' and (resid 146 through 156 )A0
12X-RAY DIFFRACTION12chain 'B' and (resid -4 through 5 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 6 through 17 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 18 through 85 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 86 through 99 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 100 through 112 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 113 through 125 )B0
18X-RAY DIFFRACTION18chain 'B' and (resid 126 through 134 )B0
19X-RAY DIFFRACTION19chain 'B' and (resid 135 through 142 )B0

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