[English] 日本語
Yorodumi
- PDB-5jzb: Crystal structure of HsaD bound to 3,5-dichlorobenzene sulphonamide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jzb
TitleCrystal structure of HsaD bound to 3,5-dichlorobenzene sulphonamide
Components4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase
KeywordsHYDROLASE / HsaD / M. tuberculosis / Cholesterol / Inhibitor / MCP-hydrolase
Function / homology
Function and homology information


: / 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase / chlorophyllase activity / 4,5-9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase activity / 2,6-dioxo-6-phenylhexa-3-enoate hydrolase / 2,6-dioxo-6-phenylhexa-3-enoate hydrolase activity / chlorophyll metabolic process / biological process involved in interaction with host / steroid biosynthetic process / : ...: / 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase / chlorophyllase activity / 4,5-9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase activity / 2,6-dioxo-6-phenylhexa-3-enoate hydrolase / 2,6-dioxo-6-phenylhexa-3-enoate hydrolase activity / chlorophyll metabolic process / biological process involved in interaction with host / steroid biosynthetic process / : / lipid catabolic process / peptidoglycan-based cell wall / plasma membrane
Similarity search - Function
alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3,5-dichlorobenzene-1-sulfonamide / PHOSPHATE ION / 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.102 Å
AuthorsRyan, A. / Polycarpou, E. / Lack, N.A. / Evangelopoulos, D. / Sieg, C. / Halman, A. / Bhakta, S. / Sinclair, A. / Eleftheriadou, O. / McHugh, T.D. ...Ryan, A. / Polycarpou, E. / Lack, N.A. / Evangelopoulos, D. / Sieg, C. / Halman, A. / Bhakta, S. / Sinclair, A. / Eleftheriadou, O. / McHugh, T.D. / Keany, S. / Lowe, E. / Ballet, R. / Abihammad, A. / Ciulli, A. / Sim, E.
CitationJournal: Br. J. Pharmacol. / Year: 2017
Title: Investigation of the mycobacterial enzyme HsaD as a potential novel target for anti-tubercular agents using a fragment-based drug design approach.
Authors: Ryan, A. / Polycarpou, E. / Lack, N.A. / Evangelopoulos, D. / Sieg, C. / Halman, A. / Bhakta, S. / Eleftheriadou, O. / McHugh, T.D. / Keany, S. / Lowe, E.D. / Ballet, R. / Abuhammad, A. / ...Authors: Ryan, A. / Polycarpou, E. / Lack, N.A. / Evangelopoulos, D. / Sieg, C. / Halman, A. / Bhakta, S. / Eleftheriadou, O. / McHugh, T.D. / Keany, S. / Lowe, E.D. / Ballet, R. / Abuhammad, A. / Jacobs, W.R. / Ciulli, A. / Sim, E.
History
DepositionMay 16, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 1.2Jul 5, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0May 8, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase
B: 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5105
Polymers61,9632
Non-polymers5473
Water1,928107
1
A: 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase
B: 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase
hetero molecules

A: 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase
B: 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,02010
Polymers123,9264
Non-polymers1,0946
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545-x,-y-1/2,z1
Buried area8740 Å2
ΔGint-29 kcal/mol
Surface area40040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.030, 82.330, 194.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-455-

HOH

21A-464-

HOH

-
Components

#1: Protein 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase / 2-hydroxy-6-oxo-6-phenylhexa-2 / 4-dienoate hydrolase / HOPDA hydrolase / Meta-cleavage product ...2-hydroxy-6-oxo-6-phenylhexa-2 / 4-dienoate hydrolase / HOPDA hydrolase / Meta-cleavage product hydrolase / MCP hydrolase


Mass: 30981.389 Da / Num. of mol.: 2 / Fragment: HsaD
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: hsaD, bphD, Rv3569c / Plasmid: pVLT31 / Production host: Pseudomonas putida (bacteria) / Strain (production host): KT2442
References: UniProt: P9WNH5, 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase, 2,6-dioxo-6-phenylhexa-3-enoate hydrolase
#2: Chemical ChemComp-6OT / 3,5-dichlorobenzene-1-sulfonamide


Mass: 226.080 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5Cl2NO2S
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 9.5 / Details: 24% (w/v) PEG-3000, 0.1M CHES pH 9.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.1→50.9 Å / Num. obs: 38700 / % possible obs: 100 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 8
Reflection shellLowest resolution: 2.1 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 2.6 / % possible all: 100

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.102→50.895 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.6
RfactorNum. reflection% reflection
Rfree0.2351 1939 5.01 %
Rwork0.2055 --
obs0.207 38698 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 143.93 Å2 / Biso mean: 46.9 Å2 / Biso min: 16.44 Å2
Refinement stepCycle: final / Resolution: 2.102→50.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4364 0 39 109 4512
Biso mean--50.44 40.72 -
Num. residues----563
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054498
X-RAY DIFFRACTIONf_angle_d1.2776099
X-RAY DIFFRACTIONf_chiral_restr0.057656
X-RAY DIFFRACTIONf_plane_restr0.007799
X-RAY DIFFRACTIONf_dihedral_angle_d15.2551627
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1017-2.15430.30391390.261325752714
2.1543-2.21250.30341250.246526142739
2.2125-2.27760.25211470.225625622709
2.2776-2.35120.23681240.228926352759
2.3512-2.43520.27341540.221925502704
2.4352-2.53270.23431340.219526182752
2.5327-2.64790.27121450.227225982743
2.6479-2.78750.27121170.224926152732
2.7875-2.96220.27851230.22726392762
2.9622-3.19080.23131420.219926212763
3.1908-3.51190.24521440.211126272771
3.5119-4.01990.22291500.192126322782
4.0199-5.06390.1831520.168526782830
5.0639-50.91030.22511430.188627952938
Refinement TLS params.Method: refined / Origin x: 10.365 Å / Origin y: -11.1316 Å / Origin z: 22.7862 Å
111213212223313233
T0.2138 Å2-0.0467 Å2-0.0142 Å2-0.2811 Å2-0.0322 Å2--0.2607 Å2
L1.6785 °20.3025 °2-0.2573 °2-1.2771 °20.0908 °2--0.4511 °2
S-0.0206 Å °-0.6397 Å °0.2117 Å °-0.2955 Å °-0.0226 Å °-0.1286 Å °-0.1054 Å °0.1765 Å °0.1943 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA7 - 288
2X-RAY DIFFRACTION1allB8 - 288
3X-RAY DIFFRACTION1allH1
4X-RAY DIFFRACTION1allI1
5X-RAY DIFFRACTION1allS1 - 134
6X-RAY DIFFRACTION1allC1

+
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://pdbjlvh1.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