[English] 日本語
Yorodumi
- PDB-6za4: M. tuberculosis salicylate synthase MbtI in complex with 5-(3-cya... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6za4
TitleM. tuberculosis salicylate synthase MbtI in complex with 5-(3-cyanophenyl)furan-2-carboxylate
ComponentsSalicylate synthase
KeywordsLYASE / salicylate / isochorismate / chorismate / mycobactins
Function / homology
Function and homology information


isochorismate lyase / isochorismate pyruvate lyase activity / catechol-containing siderophore biosynthetic process / isochorismate synthase / isochorismate synthase activity / oxo-acid-lyase activity / salicylic acid biosynthetic process / cellular response to iron ion starvation / chorismate mutase / chorismate mutase activity ...isochorismate lyase / isochorismate pyruvate lyase activity / catechol-containing siderophore biosynthetic process / isochorismate synthase / isochorismate synthase activity / oxo-acid-lyase activity / salicylic acid biosynthetic process / cellular response to iron ion starvation / chorismate mutase / chorismate mutase activity / response to host immune response / tryptophan biosynthetic process / magnesium ion binding / plasma membrane
Similarity search - Function
Salicylate synthase / Anthranilate synthase / Anthranilate synthase / Anthranilate synthase component I-like / ADC synthase / Chorismate-utilising enzyme, C-terminal / chorismate binding enzyme / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
5-(3-cyanophenyl)furan-2-carboxylic acid / Salicylate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.092 Å
AuthorsMori, M. / Villa, S. / Meneghetti, F. / Bellinzoni, M.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Shedding X-ray Light on the Role of Magnesium in the Activity ofMycobacterium tuberculosisSalicylate Synthase (MbtI) for Drug Design.
Authors: Mori, M. / Stelitano, G. / Gelain, A. / Pini, E. / Chiarelli, L.R. / Sammartino, J.C. / Poli, G. / Tuccinardi, T. / Beretta, G. / Porta, A. / Bellinzoni, M. / Villa, S. / Meneghetti, F.
History
DepositionJun 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 22, 2020Group: Database references / Refinement description / Category: citation / citation_author / software
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _software.name
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Salicylate synthase
B: Salicylate synthase
C: Salicylate synthase
D: Salicylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,9149
Polymers196,0264
Non-polymers8885
Water15,817878
1
A: Salicylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2202
Polymers49,0061
Non-polymers2131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Salicylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2553
Polymers49,0061
Non-polymers2492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Salicylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2202
Polymers49,0061
Non-polymers2131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Salicylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2202
Polymers49,0061
Non-polymers2131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.336, 111.687, 94.998
Angle α, β, γ (deg.)90, 92.67, 90
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Salicylate synthase / / Chorismate mutase / CM / Isochorismate synthase/isochorismate lyase / Mycobactin synthase protein


Mass: 49006.434 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: mbtI, trpE2, Rv2386c / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WFX1, chorismate mutase, isochorismate lyase, isochorismate synthase
#2: Chemical
ChemComp-M83 / 5-(3-cyanophenyl)furan-2-carboxylic acid


Mass: 213.189 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H7NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 878 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2 M Na tartrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.092→111.687 Å / Num. obs: 108510 / % possible obs: 99.9 % / Redundancy: 7 % / CC1/2: 0.99 / Rpim(I) all: 0.063 / Net I/σ(I): 8
Reflection shellResolution: 2.092→2.128 Å / Num. unique obs: 5396 / CC1/2: 0.803 / Rpim(I) all: 0.356

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RV7

3rv7


Resolution: 2.092→94.89 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.913 / SU R Cruickshank DPI: 0.219 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.22 / SU Rfree Blow DPI: 0.177 / SU Rfree Cruickshank DPI: 0.178
RfactorNum. reflection% reflectionSelection details
Rfree0.2403 5425 -RANDOM
Rwork0.2082 ---
obs0.2098 108510 99.9 %-
Displacement parametersBiso mean: 43.44 Å2
Baniso -1Baniso -2Baniso -3
1-1.7682 Å20 Å22.2624 Å2
2---8.5574 Å20 Å2
3---6.7892 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.092→94.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12651 0 65 878 13594
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00812981HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8917662HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5965SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes2244HARMONIC5
X-RAY DIFFRACTIONt_it12981HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1726SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact11489SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.5
X-RAY DIFFRACTIONt_other_torsion2.42
LS refinement shellResolution: 2.092→2.11 Å
RfactorNum. reflection% reflection
Rfree0.2603 114 -
Rwork0.2359 --
obs--99.86 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7118-0.44890.12750.88580.5292.6508-0.03650.0950.01070.0950.1102-0.0310.0107-0.031-0.0737-0.2966-0.0226-0.0036-0.2028-0.0697-0.257340.5124-6.681128.7979
21.1845-0.5409-0.14441.58740.02521.10750.0469-0.0609-0.0753-0.0609-0.0283-0.0883-0.0753-0.0883-0.0186-0.2272-0.00940.0207-0.2793-0.0154-0.21531.9256-39.420720.2739
33.00811.56320.10052.44730.43762.4604-0.0975-0.0413-0.2951-0.04130.17160.0005-0.29510.0005-0.0741-0.3461-0.02860.0244-0.22940.0289-0.2348-2.681512.889722.838
41.40820.1317-0.03551.2958-0.36581.820.023-0.00290.0689-0.0029-0.0585-0.17340.0689-0.17340.0355-0.24760.0076-0.0041-0.2219-0.0285-0.220448.7209-10.0714-15.5831
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

+
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