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

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Basic information

Entry
Database: PDB / ID: 4rlw
TitleCrystal Structure of (3R)-hydroxyacyl-ACP dehydratase HadAB hetero-dimer from Mycobacterium tuberculosis complexed with Butein
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-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 / 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
Chem-BUN / (3R)-hydroxyacyl-ACP dehydratase subunit HadB / : / UPF0336 protein Rv0635
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.196 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)33,2835
Polymers32,8272
Non-polymers4563
Water3,117173
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)66,56710
Polymers65,6544
Non-polymers9136
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area9050 Å2
ΔGint-31 kcal/mol
Surface area24550 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-15 kcal/mol
Surface area13350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.373, 82.373, 140.801
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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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-BUN / (2E)-1-(2,4-dihydroxyphenyl)-3-(3,4-dihydroxyphenyl)prop-2-en-1-one / 2',3,4,4'-Tetrahydroxychalcone / Butein / Butein


Mass: 272.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H12O5
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 173 / 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: 3.64 Å3/Da / Density % sol: 66.19 %
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: 2.196→50 Å / Num. obs: 25519 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.3 % / Rmerge(I) obs: 0.084 / Χ2: 1.046 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.196-2.289.40.41525121.0921100
2.28-2.379.50.33725091.091100
2.37-2.489.50.26224811.0771100
2.48-2.619.50.20625041.0571100
2.61-2.779.40.14725311.0381100
2.77-2.999.40.1125181.0171100
2.99-3.299.40.08125481.0351100
3.29-3.769.30.06525711.061100
3.76-4.7490.0625921.001199.8
4.74-508.30.05927530.991198.9

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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: 2.196→40.779 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 19.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1953 1296 5.09 %RANDOM
Rwork0.1636 ---
obs0.1652 25440 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.3 Å2 / Biso mean: 42.3123 Å2 / Biso min: 17.23 Å2
Refinement stepCycle: LAST / Resolution: 2.196→40.779 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2281 0 32 173 2486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112385
X-RAY DIFFRACTIONf_angle_d1.3283240
X-RAY DIFFRACTIONf_chiral_restr0.057360
X-RAY DIFFRACTIONf_plane_restr0.008422
X-RAY DIFFRACTIONf_dihedral_angle_d14.492850
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 (%)
2.196-2.28360.24871420.196726382780100
2.2836-2.38750.21471240.185326462770100
2.3875-2.51330.21541330.181926432776100
2.5133-2.67080.20771430.17926472790100
2.6708-2.87690.20481460.174726442790100
2.8769-3.16640.22261640.180626512815100
3.1664-3.62430.20051460.166426962842100
3.6243-4.56520.17731530.142327102863100
4.5652-40.7860.17141450.1512869301499
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)
10.7742-0.58250.33180.71270.04650.39910.61820.6512-0.0826-0.13-0.4707-0.3557-0.23131.05770.06080.4977-0.1140.03270.66960.13170.51856.417635.013-39.1511
21.18770.19560.16011.45550.07681.47530.0203-0.1843-0.060.0218-0.05530.1885-0.0189-0.11250.1340.1731-0.0074-0.00440.2383-0.01860.2036-16.469118.8877-27.7247
34.2416-0.0310.12981.55690.54750.58020.3592-0.80440.45420.1564-0.33780.2209-0.222-0.2752-0.01520.2477-0.01480.01850.4771-0.08710.3082-21.780123.5283-20.5352
43.45360.5892-2.03811.7478-1.12183.53060.1432-0.01690.2206-0.1655-0.1144-0.1943-0.11390.48790.16730.2856-0.01350.04460.3217-0.01210.2788-3.246125.0722-36.9552
51.24050.73881.14242.0141-0.07672.12220.0267-0.01380.0711-0.0378-0.0817-0.2888-0.22150.37240.01580.2478-0.03950.00520.323-0.01940.2853-0.505627.8816-31.0398
65.8775-1.84890.43512.3317-1.07871.09890.0510.36090.0815-0.017-0.2093-0.3881-0.10910.42120.15020.273-0.0153-0.00830.40930.00830.29653.972529.9361-30.6784
74.1102-2.1579-0.24053.2864-0.45713.38840.29420.2580.0072-0.1955-0.3582-0.2391-0.30180.28350.09450.3426-0.05330.0020.3646-0.00940.2428-2.194430.5079-29.2576
85.28980.3659-1.00233.3445-0.55791.7421-0.64750.3770.0257-0.22730.2626-0.8057-0.5880.71080.59190.78340.15250.14461.81880.07540.73113.558723.5231-42.2414
97.68681.02190.22653.14810.97064.4546-0.4646-1.10990.82030.17830.55721.1808-0.3376-0.97240.41620.31940.01810.04310.6698-0.03040.6254-21.38526.589-6.5405
103.0978-0.2357-0.21063.7190.91943.30850.1754-1.01010.16930.7181-0.3811-0.12550.11670.02430.14340.2522-0.0990.01090.6204-0.02060.3022-7.474222.5684-1.1938
110.64990.90130.86121.68050.58972.19510.0850.0055-0.32690.05940.1528-0.4570.28050.4092-0.19270.24680.0569-0.03120.366-0.0410.40240.5167.0583-29.441
120.85450.40450.68061.16360.77671.09880.0587-0.3720.0620.0058-0.05660.053-0.070.09310.0070.2367-0.0242-0.03170.3558-0.00660.2759-7.663921.4805-16.4086
130.7362-0.5594-0.59222.11931.1042.6156-0.0646-0.1151-0.3997-0.36540.3217-0.31680.4340.6338-0.10130.31150.0998-0.10040.4135-0.01190.40373.57016.7088-22.4022
140.9458-0.083-0.18824.20182.012.52150.0883-0.4133-0.0350.48680.101-0.28160.08460.2956-0.03960.2483-0.0239-0.05070.59210.02890.3239-2.16618.6961-8.4114
153.4048-1.8451-0.27873.6070.62312.94560.1802-0.22410.3897-0.1183-0.1769-0.1421-0.34530.1877-0.0260.3064-0.0102-0.03740.5262-0.03670.2716-4.853127.4764-8.0222
162.02750.00780.25130.45910.20312.20450.1079-0.0079-0.05130.0766-0.0506-0.18770.1460.26550.08610.2209-0.0435-0.020.45650.02690.2988-0.176220.5457-13.3063
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 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 115 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 116 through 129 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 130 through 146 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 150 through 156 )A0
9X-RAY DIFFRACTION9chain 'B' and (resid -4 through 5 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 6 through 17 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 18 through 58 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 59 through 85 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 86 through 99 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 100 through 112 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 113 through 125 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 126 through 142 )B0

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