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- PDB-4rv2: Crystal Structure of (3R)-hydroxyacyl-ACP dehydratase HadAB heter... -

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Basic information

Entry
Database: PDB / ID: 4rv2
TitleCrystal Structure of (3R)-hydroxyacyl-ACP dehydratase HadAB hetero-dimer from Mycobacterium smegmatis
Components
  • MaoC family protein
  • UPF0336 protein MSMEG_1340/MSMEI_1302
KeywordsLYASE / Hotdog fold
Function / homology
Function and homology information


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
UPF0336 protein MSMEG_1340 / MaoC family protein
Similarity search - Component
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.7 Å
AuthorsBiswas, R. / Hazra, D. / Dutta, D. / Das, A.K.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2015
Title: Crystal structure of dehydratase component HadAB complex of mycobacterial FAS-II pathway.
Authors: Biswas, R. / Dutta, A. / Dutta, D. / Hazra, D. / Banerjee, D.R. / Basak, A. / Das, A.K.
History
DepositionNov 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: UPF0336 protein MSMEG_1340/MSMEI_1302
B: MaoC family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4603
Polymers31,3642
Non-polymers961
Water95553
1
A: UPF0336 protein MSMEG_1340/MSMEI_1302
B: MaoC family protein
hetero molecules

A: UPF0336 protein MSMEG_1340/MSMEI_1302
B: MaoC family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9216
Polymers62,7294
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation22_565z,-y+1,x1
Buried area7870 Å2
ΔGint-81 kcal/mol
Surface area22280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.368, 132.368, 132.368
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number207
Space group name H-MP432

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Components

#1: Protein UPF0336 protein MSMEG_1340/MSMEI_1302


Mass: 16622.625 Da / Num. of mol.: 1 / Fragment: UNP residues 7-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis str. MC2 155 (bacteria)
Strain: mc2 155 / Gene: MSMEG_1340, MSMEI_1302 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: A0QS40
#2: Protein MaoC family protein / MaoC-like dehydratase


Mass: 14741.694 Da / Num. of mol.: 1 / Fragment: UNP residues 2-142
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis str. MC2 155 (bacteria)
Strain: mc2 155 / Gene: MSMEG_1341, MSMEI_1303 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: A0QS41
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 3.08 Å3/Da / Density % sol: 60.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 1.75 M (NH4)2SO4, 0.1 M HEPES, 2% PEG 400, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 12, 2014 / Details: Mirrors
RadiationMonochromator: Varimax, Osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.699→19.732 Å / Num. all: 11408 / Num. obs: 11408 / % possible obs: 99.7 % / Redundancy: 41.8 % / Rsym value: 0.158 / Net I/σ(I): 36.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.7-2.8542.20.7281.16825716170.72899.6
2.85-3.0242.60.5281.56565915400.528100
3.02-3.2342.60.3552.26199714540.355100
3.23-3.4842.40.223.55768713600.22100
3.48-3.8242.50.1445.35341112580.144100
3.82-4.27420.0997.84843211540.099100
4.27-4.9341.60.07114292410310.07100
4.93-6.04410.0859.1362688850.085100
6.04-8.5439.40.06811.2281177140.068100
8.54-19.73235.50.02925140143950.02992

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
REFMAC5.7refinement
PDB_EXTRACT3.15data extraction
StructureStudiodata collection
XDSdata reduction
SHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 2.7→19.73 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.86 / WRfactor Rfree: 0.2232 / WRfactor Rwork: 0.1739 / FOM work R set: 0.8054 / SU B: 23.032 / SU ML: 0.241 / SU R Cruickshank DPI: 0.5401 / SU Rfree: 0.3432 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.54 / ESU R Free: 0.343 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2837 548 4.8 %RANDOM
Rwork0.212 ---
obs0.2154 11408 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 57.15 Å2 / Biso mean: 34.629 Å2 / Biso min: 6.3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2045 0 5 53 2103
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192089
X-RAY DIFFRACTIONr_bond_other_d0.0010.021925
X-RAY DIFFRACTIONr_angle_refined_deg1.5641.9462850
X-RAY DIFFRACTIONr_angle_other_deg0.82634406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6965273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.4924.88990
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.6815298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.913157
X-RAY DIFFRACTIONr_chiral_restr0.0910.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022421
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02464
LS refinement shellResolution: 2.7→2.768 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 43 -
Rwork0.247 749 -
all-792 -
obs--99 %
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)
12.20750.1534-0.77011.02970.58812.2463-0.0453-0.1365-0.066-0.0201-0.0546-0.062-0.0363-0.08630.09990.0562-0.0494-0.00290.11330.04760.069313.347761.391432.0559
22.60871.9059-0.25241.90180.59761.8882-0.0216-0.3166-0.37870.1542-0.1853-0.19120.24360.17360.20680.10010.00740.01710.10790.13170.176122.438748.994836.7451
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 144
2X-RAY DIFFRACTION1A201 - 236
3X-RAY DIFFRACTION2B2 - 142
4X-RAY DIFFRACTION2B201
5X-RAY DIFFRACTION2B301 - 317

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