[English] 日本語
Yorodumi
- PDB-7zm1: Crystal structure of HsaD from Mycobacterium tuberculosis in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7zm1
TitleCrystal structure of HsaD from Mycobacterium tuberculosis in complex with Cyclophostin-like inhibitor CyC7b
Components4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase
KeywordsHYDROLASE / HsaD / M. tuberculosis / cholesterol / inhibitor
Function / homology
Function and homology information


4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase / 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 activity / 2,6-dioxo-6-phenylhexa-3-enoate hydrolase / hydrolase activity, acting on acid carbon-carbon bonds, in ketonic substances / steroid biosynthetic process / biological process involved in interaction with host / 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
Similarity search - Domain/homology
Chem-IY8 / 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsBarelier, S. / Roig-Zamboni, V. / Cavalier, J.F. / Sulzenbacher, G.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: Febs J. / Year: 2023
Title: Direct capture, inhibition and crystal structure of HsaD (Rv3569c) from M. tuberculosis.
Authors: Barelier, S. / Avellan, R. / Gnawali, G.R. / Fourquet, P. / Roig-Zamboni, V. / Poncin, I. / Point, V. / Bourne, Y. / Audebert, S. / Camoin, L. / Spilling, C.D. / Canaan, S. / Cavalier, J.F. / Sulzenbacher, G.
History
DepositionApr 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
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)67,2349
Polymers65,9732
Non-polymers1,2617
Water2,252125
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)134,46918
Polymers131,9464
Non-polymers2,52214
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area10540 Å2
ΔGint-162 kcal/mol
Surface area37900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.865, 78.386, 92.043
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

-
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: 32986.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: hsaD, bphD, Rv3569c
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
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-IY8 / methoxy-[(~{E},3~{R})-3-[(2~{R})-1-methoxy-1,3-bis(oxidanylidene)butan-2-yl]tridec-11-enyl]phosphinous acid


Mass: 390.451 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H35O6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: MES Na 0.1 M NH4SO4 1.656 M PEG400 8%

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980112 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Dec 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980112 Å / Relative weight: 1
ReflectionResolution: 2.15→47.14 Å / Num. obs: 30915 / % possible obs: 99.8 % / Redundancy: 8.1 % / Biso Wilson estimate: 17.379 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.058 / Rrim(I) all: 0.169 / Net I/σ(I): 11.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.15-2.227.80.9962026725940.7690.3731.0662.498.5
8.86-47.146.90.04136155210.9980.0160.04431.499.3

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.71 Å47.14 Å
Translation4.71 Å47.14 Å

-
Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
PHASER2.8.3phasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ZJT

7zjt


Resolution: 2.15→47.14 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / SU B: 5.253 / SU ML: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.256 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2118 1479 4.8 %RANDOM
Rwork0.1814 ---
obs0.1829 29399 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.89 Å2 / Biso mean: 26.293 Å2 / Biso min: 6.71 Å2
Baniso -1Baniso -2Baniso -3
1--3.1 Å20 Å2-0 Å2
2--1.77 Å20 Å2
3---1.33 Å2
Refinement stepCycle: final / Resolution: 2.15→47.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4388 0 75 125 4588
Biso mean--45.49 27.66 -
Num. residues----568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0134564
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154352
X-RAY DIFFRACTIONr_angle_refined_deg1.7581.6386174
X-RAY DIFFRACTIONr_angle_other_deg1.4041.5779962
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0895566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.80820.645248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78615712
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0851540
X-RAY DIFFRACTIONr_chiral_restr0.0840.2546
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025188
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021116
LS refinement shellResolution: 2.15→2.206 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 109 -
Rwork0.253 2097 -
all-2206 -
obs--98.18 %

+
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