[English] 日本語
Yorodumi
- PDB-1q36: EPSP synthase (Asp313Ala) liganded with tetrahedral reaction inte... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1q36
TitleEPSP synthase (Asp313Ala) liganded with tetrahedral reaction intermediate
Components3-phosphoshikimate 1-carboxyvinyltransferase
KeywordsTRANSFERASE / inside-out alpha-beta barrel
Function / homology
Function and homology information


3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / cytosol
Similarity search - Function
EPSP synthase signature 1. / 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase, conserved site / EPSP synthase signature 2. / Enolpyruvate transferase domain / Alpha-beta prism / UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain / Enolpyruvate transferase domain / Enolpyruvate transferase domain superfamily / EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) ...EPSP synthase signature 1. / 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase, conserved site / EPSP synthase signature 2. / Enolpyruvate transferase domain / Alpha-beta prism / UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain / Enolpyruvate transferase domain / Enolpyruvate transferase domain superfamily / EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Chem-SKP / 3-phosphoshikimate 1-carboxyvinyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsEschenburg, S. / Kabsch, W. / Healy, M.L. / Schonbrunn, E.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: A New View of the Mechanisms of UDP-N-Acetylglucosamine Enolpyruvyl Transferase (MurA) and 5-Enolpyruvylshikimate-3-phosphate Synthase (AroA) Derived from X-ray Structures of Their Tetrahedral ...Title: A New View of the Mechanisms of UDP-N-Acetylglucosamine Enolpyruvyl Transferase (MurA) and 5-Enolpyruvylshikimate-3-phosphate Synthase (AroA) Derived from X-ray Structures of Their Tetrahedral Reaction Intermediate States.
Authors: Eschenburg, S. / Kabsch, W. / Healy, M.L. / Schonbrunn, E.
History
DepositionJul 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations / Category: 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 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-phosphoshikimate 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,93411
Polymers46,0981
Non-polymers83610
Water9,710539
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.810, 85.049, 87.545
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein 3-phosphoshikimate 1-carboxyvinyltransferase / 5-enolpyruvylshikimate-3-phosphate synthase / EPSP synthase / EPSPS


Mass: 46097.605 Da / Num. of mol.: 1 / Mutation: D313A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: aroa / Plasmid: pET24D / Production host: Escherichia coli (E. coli) / Strain (production host): STBL2-DE3
References: UniProt: P0A6D3, 3-phosphoshikimate 1-carboxyvinyltransferase
#2: Chemical ChemComp-SKP / 5-(1-CARBOXY-1-PHOSPHONOOXY-ETHOXYL)-4-HYDROXY-3-PHOSPHONOOXY-CYCLOHEX-1-ENECARBOXYLIC ACID / 5-(1-CARBOXY-1-PHOSPHONOOXY-ETHOXYL)-SHIKIMATE-3-PHOSPHATE


Mass: 422.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16O14P2
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 539 / 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: 2.33 Å3/Da / Density % sol: 47.29 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: sodium formate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.6→15 Å / Num. all: 55905 / Num. obs: 55905 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 17.4
Reflection shellResolution: 1.6→1.65 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 5.3 / Num. unique all: 4795 / % possible all: 95.1

-
Processing

Software
NameClassification
MAR345data collection
XDSdata reduction
CNSrefinement
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1G6T

1g6t


Resolution: 1.6→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.187 1678 random
Rwork0.155 --
obs0.155 55905 -
all-55905 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.262 Å20 Å20 Å2
2--1.08 Å20 Å2
3---0.181 Å2
Refinement stepCycle: LAST / Resolution: 1.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3268 0 26 566 3860
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0163
X-RAY DIFFRACTIONc_angle_deg1.794
X-RAY DIFFRACTIONc_mcbond_it1.3671.5
X-RAY DIFFRACTIONc_mcangle_it1.8032
LS refinement shellResolution: 1.6→1.62 Å
RfactorNum. reflection
Rfree0.186 49
Rwork0.173 -
obs-1564
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2spp+for.par
X-RAY DIFFRACTION3cis_peptide.param
X-RAY DIFFRACTION4water_rep.param
X-RAY DIFFRACTION5ion.param

+
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