[English] 日本語
Yorodumi
- PDB-3ipr: Crystal structure of the Enterococcus faecalis gluconate specific... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ipr
TitleCrystal structure of the Enterococcus faecalis gluconate specific EIIA phosphotransferase system component
ComponentsPTS system, IIA component
KeywordsTRANSFERASE / 4 stranded parallel BETA-SHEET flanked by 3 ALPHA-HELICES on each side
Function / homology
Function and homology information


phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / metal ion binding / membrane / cytoplasm
Similarity search - Function
: / PTS system mannose/sorbose specific IIA subunit / Phosphotransferase system, mannose-type IIA component / Phosphotransferase system, mannose-type IIA component / Phosphotransferase system, mannose-type IIA component superfamily / PTS system fructose IIA component / PTS_EIIA type-4 domain profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PTS system, IIA component
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsReinelt, S. / Welti, S. / Scheffzek, K.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: Structure of the Enterococcus faecalis EIIA(gnt) PTS component.
Authors: Reinelt, S. / Koch, B. / Hothorn, M. / Hengstenberg, W. / Welti, S. / Scheffzek, K.
History
DepositionAug 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PTS system, IIA component
B: PTS system, IIA component
C: PTS system, IIA component
D: PTS system, IIA component
E: PTS system, IIA component
F: PTS system, IIA component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,19316
Polymers94,7926
Non-polymers40110
Water2,108117
1
A: PTS system, IIA component
B: PTS system, IIA component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7175
Polymers31,5972
Non-polymers1203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-31.6 kcal/mol
Surface area11210 Å2
MethodPISA
2
C: PTS system, IIA component
D: PTS system, IIA component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7586
Polymers31,5972
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-31 kcal/mol
Surface area11410 Å2
MethodPISA
3
E: PTS system, IIA component
F: PTS system, IIA component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7175
Polymers31,5972
Non-polymers1203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-31.5 kcal/mol
Surface area11400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.680, 69.400, 80.220
Angle α, β, γ (deg.)90.000, 106.530, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
PTS system, IIA component


Mass: 15798.622 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: gluconate specific EIIA phosphotransferase system component from Enterococcus faecalis
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: 26487 Wildtype / Gene: EF_3136, gntF / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q82ZC8
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.47 Å3/Da / Density % sol: 50.26 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% PEG 4000, 0.2M Ca acetate, 0.1M Ca cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1.044 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 11, 2003 / Details: mirrors
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.044 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 30490 / Num. obs: 30490 / % possible obs: 94.4 % / Observed criterion σ(I): 0 / Redundancy: 3.7 %
Reflection shellResolution: 2.5→2.6 Å / Mean I/σ(I) obs: 4.42 / % possible all: 94.3

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
EPMRphasing
CNSrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PDO

1pdo


Resolution: 2.5→20 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1519 4.7 %RANDOM
Rwork0.189 ---
all0.213 30404 --
obs0.213 30404 94.2 %-
Solvent computationBsol: 45.951 Å2
Displacement parametersBiso max: 104.14 Å2 / Biso mean: 33.949 Å2 / Biso min: 3.17 Å2
Baniso -1Baniso -2Baniso -3
1-7.827 Å20 Å2-3.508 Å2
2--6.419 Å20 Å2
3----14.246 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6079 0 10 117 6206
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.34
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param
X-RAY DIFFRACTION3CNS_TOPPAR:water.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