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- PDB-3wew: Crystal structure of HtdX (Rv0241c) of Mycobacterium tuberculosis... -

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Basic information

Entry
Database: PDB / ID: 3wew
TitleCrystal structure of HtdX (Rv0241c) of Mycobacterium tuberculosis at 2.4 A resolution
ComponentsHtdX dehydratase
KeywordsLYASE / hotdog fold / dehydratase
Function / homology
Function and homology information


3-hydroxybutyryl-CoA dehydratase / enoyl-CoA hydratase 2 / 3-hydroxyacyl-CoA dehydratase activity / fatty acid synthase complex / Lyases; Carbon-oxygen lyases; Hydro-lyases / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / fatty acid synthase activity / fatty acid metabolic process / fatty acid biosynthetic process / plasma membrane
Similarity search - Function
Fatty acid synthase / 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-hydroxyacyl-thioester dehydratase X
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 2.4 Å
AuthorsBiswas, R. / Dutta, D. / Das, A.K.
CitationJournal: To be Published
Title: Crystal structure of a putative dehydratase HtdX of Mycobacterium tuberculosis
Authors: Biswas, R. / Dutta, D. / Das, A.K.
History
DepositionJul 16, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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: HtdX dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1852
Polymers28,1601
Non-polymers241
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.504, 61.504, 143.803
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-436-

HOH

21A-469-

HOH

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Components

#1: Protein HtdX dehydratase


Mass: 28160.348 Da / Num. of mol.: 1 / Fragment: UNP residues 29-280
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv0242c, RVBD_0241c / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: O53664
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.41 Å3/Da / Density % sol: 49.06 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 3M NaCl, 0.1M HEPES pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 3, 2013 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→56.552 Å / Num. all: 11816 / Num. obs: 11816 / % possible obs: 99.8 % / Redundancy: 15.2 % / Rsym value: 0.096 / Net I/σ(I): 30.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.3-2.4314.90.6971.10.697199.6
2.43-2.57150.4521.70.452199.8
2.57-2.7515.10.3072.50.3071100
2.75-2.9715.20.2053.70.2051100
2.97-3.2515.30.1246.20.1241100
3.25-3.6415.30.0710.80.071100
3.64-4.215.40.04915.20.0491100
4.2-5.1515.40.03222.40.0321100
5.15-7.2815.40.03719.60.0371100
7.28-19.486150.022290.022195.1

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Phasing

PhasingMethod: MIRAS

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
SHARPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
XSCALEdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.4→19.49 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.914 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 14.925 / SU ML: 0.177 / SU R Cruickshank DPI: 0.2673 / Cross valid method: THROUGHOUT / ESU R: 0.339 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23037 500 4.8 %RANDOM
Rwork0.16476 ---
obs0.16795 9922 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.347 Å2
Baniso -1Baniso -2Baniso -3
1-1.23 Å20 Å20 Å2
2--1.23 Å2-0 Å2
3----2.45 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1757 0 1 78 1836
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191805
X-RAY DIFFRACTIONr_bond_other_d0.0010.021731
X-RAY DIFFRACTIONr_angle_refined_deg1.6551.9442477
X-RAY DIFFRACTIONr_angle_other_deg0.83533944
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4865231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.99122.22272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.48215245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6761513
X-RAY DIFFRACTIONr_chiral_restr0.0880.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212058
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02429
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.399→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 28 -
Rwork0.242 754 -
obs--99.24 %
Refinement TLS params.Method: refined / Origin x: 11.9987 Å / Origin y: 19.5036 Å / Origin z: -0.3801 Å
111213212223313233
T0.027 Å2-0.01 Å20.006 Å2-0.0335 Å2-0.011 Å2--0.0411 Å2
L0.2002 °2-0.1972 °20.0443 °2-0.4163 °2-0.0622 °2--0.869 °2
S0.0161 Å °0.0177 Å °0.0503 Å °0.0196 Å °-0.012 Å °-0.0013 Å °0.0081 Å °0.0452 Å °-0.0041 Å °

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