[English] 日本語
Yorodumi
- PDB-3fk0: E. coli EPSP synthase (TIPS mutation) liganded with S3P -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fk0
TitleE. coli EPSP synthase (TIPS mutation) liganded with S3P
Components3-phosphoshikimate 1-carboxyvinyltransferaseEPSP synthase
KeywordsTRANSFERASE / Inside-out alpha-beta barrel / Amino-acid biosynthesis / Aromatic amino acid biosynthesis / Cytoplasm
Function / homology
Function and homology information


3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / cytosol
3-phosphoshikimate 1-carboxyvinyltransferase / Enolpyruvate transferase domain / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / 3-phosphoshikimate 1-carboxyvinyltransferase, conserved site / Enolpyruvate transferase domain superfamily / EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) / EPSP synthase signature 1. / EPSP synthase signature 2.
3-phosphoshikimate 1-carboxyvinyltransferase
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsSchonbrunn, E.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural Basis of Glyphosate Resistance Resulting from the Double Mutation Thr97 -> Ile and Pro101 -> Ser in 5-Enolpyruvylshikimate-3-phosphate Synthase from Escherichia coli.
Authors: Funke, T. / Yang, Y. / Han, H. / Healy-Fried, M. / Olesen, S. / Becker, A. / Schonbrunn, E.
Validation Report
SummaryFull reportAbout validation report
History
DepositionDec 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name

-
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)46,81211
Polymers46,1441
Non-polymers66810
Water9,440524
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)57.491, 84.705, 87.081
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 46143.629 Da / Num. of mol.: 1 / Fragment: EPSP synthase / Mutation: Thr97Ile, Pro101Ser
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: aroA, b0908, JW0891 / Plasmid: pET-24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0A6D3, 3-phosphoshikimate 1-carboxyvinyltransferase
#2: Chemical ChemComp-S3P / SHIKIMATE-3-PHOSPHATE


Mass: 254.131 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11O8P
#3: Chemical
ChemComp-FMT / FORMIC ACID


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


Mass: 18.015 Da / Num. of mol.: 524 / Source method: isolated from a natural source / Formula: H2O / Water

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Na-formate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jan 15, 2008 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 47294 / Num. obs: 47294 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.029 / Net I/σ(I): 30.4
Reflection shellResolution: 1.7→1.8 Å / Rmerge(I) obs: 0.077 / Mean I/σ(I) obs: 12.5 / Num. unique all: 7239 / % possible all: 98.2

-
Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.006data extraction
CrystalCleardata collection
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementStarting model: 1g6t
Resolution: 1.7→20 Å / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1183 2.5 %random
Rwork0.163 ---
Obs-47294 99.6 %-
Solvent computationBsol: 38.913 Å2
Displacement parametersBiso max: 47.82 Å2 / Biso mean: 16.097 Å2 / Biso min: 4.4 Å2
Baniso -1Baniso -2Baniso -3
1--3.853 Å20 Å20 Å2
2--2.414 Å20 Å2
3---1.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3256 0 16 551 3823
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal target
c_mcbond_it1.4631.5
c_scbond_it2.7122
c_mcangle_it1.8922
c_scangle_it3.8332.5
c_angle_deg1.6
c_bond_d0.011
LS refinement shellHighest resolution: 1.7 Å
Xplor file
Refinement-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2s3p+gph+for+spp+shikimate_new.par
X-RAY DIFFRACTION3cis_peptide.param
X-RAY DIFFRACTION4CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION5CNS_TOPPAR:ion.param

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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