[English] 日本語
Yorodumi
- PDB-5jy8: An iron-bound structure of the isochorismate synthase EntC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jy8
TitleAn iron-bound structure of the isochorismate synthase EntC
ComponentsIsochorismate synthase EntC
KeywordsISOMERASE
Function / homology
Function and homology information


isochorismate synthase / isochorismate synthase activity / enterobactin biosynthetic process / magnesium ion binding
Similarity search - Function
Isochorismate synthase / Anthranilate synthase / Anthranilate synthase / ADC synthase / Chorismate-utilising enzyme, C-terminal / chorismate binding enzyme / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Chem-ISJ / Isochorismate synthase EntC
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.942 Å
AuthorsMeneely, K.M. / Sundlov, J.A. / Gulick, A.M. / Lamb, A.L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI77725 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)K02 AI093675 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM116957 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: An Open and Shut Case: The Interaction of Magnesium with MST Enzymes.
Authors: Meneely, K.M. / Sundlov, J.A. / Gulick, A.M. / Moran, G.R. / Lamb, A.L.
History
DepositionMay 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Isochorismate synthase EntC
B: Isochorismate synthase EntC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,6298
Polymers85,9532
Non-polymers6766
Water00
1
A: Isochorismate synthase EntC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3144
Polymers42,9761
Non-polymers3383
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Isochorismate synthase EntC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3144
Polymers42,9761
Non-polymers3383
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.377, 81.377, 262.283
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Isochorismate synthase EntC / Isochorismate mutase


Mass: 42976.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: entC, Z0735, ECs0632 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P0AEJ3, isochorismate synthase
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-ISJ / (3R,4R)-3-[(1-carboxyethenyl)oxy]-4-hydroxycyclohexa-1,5-diene-1-carboxylic acid / Chorismic Acid


Mass: 226.183 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H10O6

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.31 %
Crystal growTemperature: 298.15 K / Method: microbatch / pH: 6
Details: 0.1 M MES pH 6.0, 60% PEG 200, 0.05 M ammonium chloride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.739 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 31, 2015 / Details: Mirror: Rh coated flat mirror
RadiationMonochromator: Si(111) side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.739 Å / Relative weight: 1
ReflectionResolution: 2.94→38.86 Å / Num. obs: 19603 / % possible obs: 99.4 % / Redundancy: 27.6 % / CC1/2: 0.998 / Rsym value: 0.167 / Net I/σ(I): 21.6
Reflection shellResolution: 2.94→3.12 Å / Redundancy: 27.3 % / Rmerge(I) obs: 0.754 / Mean I/σ(I) obs: 5.6 / % possible all: 96.7

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HWO

3hwo


Resolution: 2.942→38.861 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2566 1952 10 %Random selection
Rwork0.2116 ---
obs0.2163 19521 99.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.942→38.861 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5663 0 36 0 5699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045822
X-RAY DIFFRACTIONf_angle_d0.7667918
X-RAY DIFFRACTIONf_dihedral_angle_d13.5583532
X-RAY DIFFRACTIONf_chiral_restr0.045889
X-RAY DIFFRACTIONf_plane_restr0.0061054
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.942-3.01560.36551270.26521152X-RAY DIFFRACTION93
3.0156-3.09710.33651360.22271217X-RAY DIFFRACTION100
3.0971-3.18820.29381380.22361232X-RAY DIFFRACTION100
3.1882-3.2910.251360.2121235X-RAY DIFFRACTION100
3.291-3.40860.25421370.22281235X-RAY DIFFRACTION100
3.4086-3.5450.27631390.22151242X-RAY DIFFRACTION100
3.545-3.70620.261380.20511245X-RAY DIFFRACTION100
3.7062-3.90140.27371380.20281241X-RAY DIFFRACTION100
3.9014-4.14560.22751390.20081245X-RAY DIFFRACTION100
4.1456-4.46520.21021380.17921254X-RAY DIFFRACTION100
4.4652-4.91380.20051410.17481276X-RAY DIFFRACTION100
4.9138-5.6230.26581420.20861276X-RAY DIFFRACTION100
5.623-7.07740.26661450.24031307X-RAY DIFFRACTION100
7.0774-38.86440.26681580.2351412X-RAY DIFFRACTION100

+
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