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- PDB-4oob: Crystal structure of HtdX(Rv0241c) from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 4oob
TitleCrystal structure of HtdX(Rv0241c) from Mycobacterium tuberculosis
ComponentsUncharacterized protein HtdX
KeywordsOXIDOREDUCTASE / Hotdog fold
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsBiswas, R. / Dutta, D. / Das, A.K.
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2025
Title: Crystal structure and molecular dynamics simulation of Mycobacterium tuberculosis MaoC-like dehydratase HtdX provide insights into substrate binding and membrane interactions.
Authors: Biswas, R. / Bhattacharje, G. / Singh, B.K. / Dutta, D. / Basak, A. / Das, A.K.
History
DepositionJan 31, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 4, 2015Provider: 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
Revision 1.2Jun 25, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein HtdX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3402
Polymers28,3041
Non-polymers351
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Uncharacterized protein HtdX
hetero molecules

A: Uncharacterized protein HtdX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6804
Polymers56,6092
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3020 Å2
ΔGint-46 kcal/mol
Surface area20290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.001, 64.001, 139.941
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-417-

HOH

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Components

#1: Protein Uncharacterized protein HtdX


Mass: 28304.477 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: Rv0241c / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: O53664
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.53 Å3/Da / Density % sol: 51.41 % / Mosaicity: 0 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.5M NaCl, 0.1M Tris-HCl, 20%(W/V) PEG 3350, pH 7.5, 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: Oct 13, 2013 / 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: 2.298→58.203 Å / Num. all: 13436 / Num. obs: 13436 / % possible obs: 99 % / Redundancy: 28.2 % / Rsym value: 0.111 / Net I/σ(I): 36.6
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.3-2.4228.80.4951.55345618590.0920.4959.798
2.42-2.5728.80.3825265218290.0710.3812.598.5
2.57-2.7528.80.2642.94877816940.0490.26417.198.7
2.75-2.9728.60.1884.14585816010.0350.18823.499.2
2.97-3.2528.50.1335.74230214830.0250.13331.399.4
3.25-3.6328.40.0789.73872413620.0150.07849.999.7
3.63-4.228.10.05413.53418812180.010.0546599.8
4.2-5.1427.60.03917.82921410580.0070.0398399.9
5.14-7.2726.70.04914.4225118430.010.04967.6100
7.27-19.44223.90.0319.6116954890.0060.039494.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
MOLREPphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.14data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.45 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.901 / WRfactor Rfree: 0.2158 / WRfactor Rwork: 0.1752 / FOM work R set: 0.8326 / SU B: 12.605 / SU ML: 0.161 / SU R Cruickshank DPI: 0.2975 / SU Rfree: 0.2352 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.297 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2573 664 5 %RANDOM
Rwork0.2043 ---
obs0.2069 13411 98.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.81 Å2 / Biso mean: 23.781 Å2 / Biso min: 5.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2--0.26 Å2-0 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1854 0 1 75 1930
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191904
X-RAY DIFFRACTIONr_bond_other_d0.0010.021829
X-RAY DIFFRACTIONr_angle_refined_deg1.8981.952610
X-RAY DIFFRACTIONr_angle_other_deg0.89334174
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7615242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.73522.20877
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.58815263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7251515
X-RAY DIFFRACTIONr_chiral_restr0.0980.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212164
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02449
LS refinement shellResolution: 2.298→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 61 -
Rwork0.204 874 -
all-935 -
obs--96.99 %
Refinement TLS params.Method: refined / Origin x: -24.6596 Å / Origin y: -0.0388 Å / Origin z: 1.8879 Å
111213212223313233
T0.0402 Å2-0.0057 Å20.0047 Å2-0.0272 Å20.0039 Å2--0.0065 Å2
L0.5072 °2-0.2568 °20.0437 °2-0.471 °2-0.0664 °2--0.3599 °2
S0.0184 Å °0.0897 Å °0.0064 Å °0.0952 Å °-0.046 Å °0.0263 Å °-0.0283 Å °-0.0032 Å °0.0276 Å °

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