[English] 日本語
Yorodumi
- PDB-3wew: Crystal structure of HtdX (Rv0241c) of Mycobacterium tuberculosis... -

+
Open data


ID or keywords:

Loading...

-
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: 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
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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

PhasingMethod: MIRAS

-
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 °

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more