[English] 日本語
Yorodumi
- PDB-2gzs: Enterobactin Hydolase IroE Complex with DFP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2gzs
TitleEnterobactin Hydolase IroE Complex with DFP
ComponentsIroE protein
KeywordsHYDROLASE / Enterobactin / Salmochelin / DFP / Catalytic Dyad
Function / homologyEsterase-like / Putative esterase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / DIISOPROPYL PHOSPHONATE / Catecholate siderophore esterase IroE
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
AuthorsLarsen, N.A. / Walsh, C.T.
CitationJournal: Biochemistry / Year: 2006
Title: Structural Characterization of Enterobactin Hydrolase IroE.
Authors: Larsen, N.A. / Lin, H. / Wei, R. / Fischbach, M.A. / Walsh, C.T.
History
DepositionMay 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: IroE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1802
Polymers31,0141
Non-polymers1661
Water3,549197
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.295, 38.361, 44.631
Angle α, β, γ (deg.)113.10, 93.99, 98.08
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein IroE protein


Mass: 31014.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: iroE / Production host: Escherichia coli (E. coli) / References: UniProt: Q6KD95
#2: Chemical ChemComp-DFP / DIISOPROPYL PHOSPHONATE


Mass: 166.155 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15O3P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 1.81 Å3/Da / Density % sol: 31.92 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 5-10% PEG 3350, 100 mM HEPES, 500 mM DFP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.97960, 0.9798, 0.9184
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 10, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.97981
30.91841
ReflectionResolution: 1.4→20 Å / Num. all: 80830 / Num. obs: 79213 / % possible obs: 93.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.4→1.45 Å / % possible all: 84.6

-
Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.4→20 Å / Num. parameters: 8651 / Num. restraintsaints: 8093 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.186 3961 RANDOM
Rwork0.174 --
all-80830 -
obs-75233 -
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2162
Refinement stepCycle: LAST / Resolution: 1.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1954 0 10 197 2161
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.035
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0292
X-RAY DIFFRACTIONs_zero_chiral_vol0.073
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.099
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.024
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.078
X-RAY DIFFRACTIONs_approx_iso_adps0

+
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