[English] 日本語
Yorodumi
- PDB-3eye: Crystal structure of PTS system N-acetylgalactosamine-specific II... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3eye
TitleCrystal structure of PTS system N-acetylgalactosamine-specific IIB component 1 from Escherichia coli
ComponentsPTS system N-acetylgalactosamine-specific IIB component 1
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / PHOSPHOTRANSFERASE / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / cytoplasm
Similarity search - Function
Phosphotransferase system, sorbose subfamily IIB component, subgroup / Fructose Permease / Phosphotransferase system, sorbose subfamily IIB component / Phosphotransferase system, sorbose subfamily IIB component / Phosphotransferase system, sorbose subfamily IIB component superfamily / PTS system sorbose subfamily IIB component / PTS_EIIB type-4 domain profile. / : / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-acetylgalactosamine-specific enzyme IIB component of PTS
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsBonanno, J.B. / Dickey, M. / Bain, K.T. / Do, J. / Sampathkumar, P. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of PTS system N-acetylgalactosamine-specific IIB component 1 from Escherichia coli
Authors: Bonanno, J.B. / Dickey, M. / Bain, K.T. / Do, J. / Sampathkumar, P. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionOct 20, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PTS system N-acetylgalactosamine-specific IIB component 1


Theoretical massNumber of molelcules
Total (without water)18,8441
Polymers18,8441
Non-polymers00
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.878, 31.413, 60.339
Angle α, β, γ (deg.)90.000, 103.830, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein PTS system N-acetylgalactosamine-specific IIB component 1 / EIIB-AGA / Galactosamine-specific PTS system enzyme IIB


Mass: 18844.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: agaB, ECs4018, Z4492 / Plasmid: modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8XAB8, protein-Npi-phosphohistidine-sugar phosphotransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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 Å3/Da / Density % sol: 38.47 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7
Details: 100mM Tris pH 7.0, 20% PEG 2K, Vapor diffusion, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 18, 2008
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 1.45→58.621 Å / Num. all: 26784 / Num. obs: 26422 / % possible obs: 98.65 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 10.6
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 3.3 / Num. measured all: 25454 / Num. unique all: 3833 / Rsym value: 0.422 / % possible all: 99.5

-
Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.45→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.244 / WRfactor Rwork: 0.582 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.845 / SU B: 1.397 / SU ML: 0.055 / SU R Cruickshank DPI: 0.075 / SU Rfree: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.075 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1327 5 %RANDOM
Rwork0.19 ---
obs0.192 26409 98.65 %-
all-26770 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 52.72 Å2 / Biso mean: 21.295 Å2 / Biso min: 8.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å2-1.08 Å2
2---0.82 Å20 Å2
3---0.81 Å2
Refinement stepCycle: LAST / Resolution: 1.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1216 0 0 171 1387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221236
X-RAY DIFFRACTIONr_bond_other_d0.0020.02832
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.9511676
X-RAY DIFFRACTIONr_angle_other_deg1.86332050
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2025158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.70825.26357
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81915231
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.816157
X-RAY DIFFRACTIONr_chiral_restr0.0980.2200
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021365
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02233
X-RAY DIFFRACTIONr_mcbond_it0.9321.5764
X-RAY DIFFRACTIONr_mcbond_other0.2941.5317
X-RAY DIFFRACTIONr_mcangle_it1.57221253
X-RAY DIFFRACTIONr_scbond_it2.543472
X-RAY DIFFRACTIONr_scangle_it3.9684.5420
LS refinement shellResolution: 1.45→1.487 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 98 -
Rwork0.255 1832 -
all-1930 -
obs-1832 99.38 %

+
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