[English] 日本語
Yorodumi
- PDB-6y88: IGPS (Indole-3-glycerol phosphate synthase) from Pseudomonas aeru... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6y88
TitleIGPS (Indole-3-glycerol phosphate synthase) from Pseudomonas aeruginosa in complex with substrate inhibitor rCdRP
Components(Indole-3-glycerol phosphate ...) x 2
KeywordsLYASE / Tryptophan biosynthesis / carboxylyase / ba8-barrel / indole synthesis
Function / homology
Function and homology information


indole-3-glycerol-phosphate synthase / indole-3-glycerol-phosphate synthase activity / phosphoribosylanthranilate isomerase activity / tryptophan biosynthetic process
Similarity search - Function
Indole-3-glycerol phosphate synthase signature. / Indole-3-glycerol phosphate synthase, conserved site / Indole-3-glycerol phosphate synthase domain / Indole-3-glycerol phosphate synthase / Ribulose-phosphate binding barrel / Aldolase-type TIM barrel
Similarity search - Domain/homology
Chem-137 / CITRIC ACID / PHOSPHATE ION / Indole-3-glycerol phosphate synthase / Indole-3-glycerol phosphate synthase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09983451737 Å
AuthorsSoderholm, A. / Selmer, M.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council2017-03827 Sweden
Knut and Alice Wallenberg FoundationEvolution of new genes and proteins Sweden
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structure and kinetics of indole-3-glycerol phosphate synthase from Pseudomonas aeruginosa : Decarboxylation is not essential for indole formation.
Authors: Soderholm, A. / Newton, M.S. / Patrick, W.M. / Selmer, M.
History
DepositionMar 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Indole-3-glycerol phosphate synthase
B: Indole-3-glycerol phosphate synthase
C: Indole-3-glycerol phosphate synthase
D: Indole-3-glycerol phosphate synthase
E: Indole-3-glycerol phosphate synthase
F: Indole-3-glycerol phosphate synthase
G: Indole-3-glycerol phosphate synthase,Indole-3-glycerol phosphate synthase
H: Indole-3-glycerol phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,50624
Polymers250,1168
Non-polymers3,39016
Water20,3391129
1
A: Indole-3-glycerol phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9013
Polymers31,4581
Non-polymers4432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Indole-3-glycerol phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9944
Polymers31,4581
Non-polymers5353
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Indole-3-glycerol phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9944
Polymers31,4581
Non-polymers5353
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Indole-3-glycerol phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8092
Polymers31,4581
Non-polymers3511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Indole-3-glycerol phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0944
Polymers31,4581
Non-polymers6353
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Indole-3-glycerol phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8092
Polymers31,4581
Non-polymers3511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Indole-3-glycerol phosphate synthase,Indole-3-glycerol phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0042
Polymers29,9091
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Indole-3-glycerol phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9013
Polymers31,4581
Non-polymers4432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)164.705, 150.683, 114.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

-
Components

-
Indole-3-glycerol phosphate ... , 2 types, 8 molecules ABCDEFHG

#1: Protein
Indole-3-glycerol phosphate synthase / IGPS


Mass: 31458.074 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: trpC, DT376_13060 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A367MAM9, UniProt: P20577*PLUS, indole-3-glycerol-phosphate synthase
#2: Protein Indole-3-glycerol phosphate synthase,Indole-3-glycerol phosphate synthase / IGPS / IGPS


Mass: 29909.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: trpC, DT376_13060 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A367MAM9, UniProt: P20577*PLUS, indole-3-glycerol-phosphate synthase

-
Non-polymers , 5 types, 1145 molecules

#3: Chemical
ChemComp-137 / 1-(O-CARBOXY-PHENYLAMINO)-1-DEOXY-D-RIBULOSE-5-PHOSPHATE


Mass: 351.246 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C12H18NO9P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


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


Mass: 18.015 Da / Num. of mol.: 1129 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 56.38 %
Crystal growTemperature: 281.15 K / Method: vapor diffusion, sitting drop / pH: 3.4
Details: 0.07 M Citric acid, 0.03 M Bis-Tris propane pH 3.4 (Condition G12 from PEG/Ion screen from Hampton Research)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.099→50 Å / Num. obs: 321139 / % possible obs: 100 % / Redundancy: 7.03 % / Biso Wilson estimate: 30.2458918458 Å2 / CC1/2: 0.994 / Net I/σ(I): 7.61
Reflection shellResolution: 2.099→2.23 Å / Mean I/σ(I) obs: 1.73 / Num. unique obs: 51980 / CC1/2: 0.73

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TSM
Resolution: 2.09983451737→48.0433596166 Å / SU ML: 0.23247016633 / Cross valid method: FREE R-VALUE / σ(F): 1.1861589204 / Phase error: 21.7744224305
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.218055634217 16096 5.01281544206 %
Rwork0.172852520379 305001 -
obs0.175092930297 321097 99.985676163 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.8851359205 Å2
Refinement stepCycle: LAST / Resolution: 2.09983451737→48.0433596166 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16162 0 221 1129 17512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011787944277916651
X-RAY DIFFRACTIONf_angle_d1.0998938078822571
X-RAY DIFFRACTIONf_chiral_restr0.1140743491182702
X-RAY DIFFRACTIONf_plane_restr0.007011092616462994
X-RAY DIFFRACTIONf_dihedral_angle_d17.30334447846334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0999-2.12370.3001827427565380.25772416932910287X-RAY DIFFRACTION99.9630621479
2.1237-2.14870.2970258488225410.24899972329810139X-RAY DIFFRACTION100
2.1487-2.17490.2819726097945310.24032837442110152X-RAY DIFFRACTION99.9812821713
2.1749-2.20240.2837688995785330.23427683632210173X-RAY DIFFRACTION100
2.2024-2.23140.2521437871835360.22213567552610143X-RAY DIFFRACTION99.9719153717
2.2314-2.2620.2860882799795360.23260790035910168X-RAY DIFFRACTION100
2.262-2.29430.275187816155290.22955832692510107X-RAY DIFFRACTION99.9811994736
2.2943-2.32850.2476273584675370.21785741314110207X-RAY DIFFRACTION99.9906933457
2.3285-2.36490.2559212948165410.2149815080910208X-RAY DIFFRACTION100
2.3649-2.40370.2564136701415400.20639384508110120X-RAY DIFFRACTION100
2.4037-2.44510.2389534061635440.19663723826910161X-RAY DIFFRACTION100
2.4451-2.48960.2680109675865350.19749388255910164X-RAY DIFFRACTION100
2.4896-2.53750.2557800796435460.20194493861410230X-RAY DIFFRACTION100
2.5375-2.58930.2560549095655320.1964407877310105X-RAY DIFFRACTION100
2.5893-2.64560.2023590197375350.17129203761110175X-RAY DIFFRACTION100
2.6456-2.70710.2202595775035430.17319370728210172X-RAY DIFFRACTION100
2.7071-2.77480.2437443175875370.17606708864510126X-RAY DIFFRACTION100
2.7748-2.84980.21250041235380.17296692400310181X-RAY DIFFRACTION100
2.8498-2.93360.2364095915595430.17895057651910192X-RAY DIFFRACTION100
2.9336-3.02830.2406262708035300.17636745024310092X-RAY DIFFRACTION100
3.0283-3.13650.2371674844975350.17067778100410218X-RAY DIFFRACTION100
3.1365-3.26210.2304446087175380.17490414833410199X-RAY DIFFRACTION100
3.2621-3.41050.2070301035055330.16237790551310109X-RAY DIFFRACTION100
3.4105-3.59030.1944914443535360.15104516109710222X-RAY DIFFRACTION100
3.5903-3.81510.2095629165155290.14737072352710141X-RAY DIFFRACTION100
3.8151-4.10950.1889999028875390.13973063133110162X-RAY DIFFRACTION100
4.1095-4.52280.1730984119825340.13325881544910153X-RAY DIFFRACTION100
4.5228-5.17660.1482095455665420.1304038786310184X-RAY DIFFRACTION100
5.1766-6.51940.2092191809045370.17160547886710148X-RAY DIFFRACTION100
6.5194-48.04330.201683720625280.18000306212110163X-RAY DIFFRACTION99.682983683

+
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