[English] 日本語
Yorodumi
- PDB-1i2r: CRYSTAL STRUCTURE OF ESCHERICHIA COLI TRANSALDOLASE B MUTANT S176A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1i2r
TitleCRYSTAL STRUCTURE OF ESCHERICHIA COLI TRANSALDOLASE B MUTANT S176A
ComponentsTRANSALDOLASE B
KeywordsTRANSFERASE / alpha-beta barrel
Function / homology
Function and homology information


transketolase or transaldolase activity / transaldolase / transaldolase activity / pentose-phosphate shunt, non-oxidative branch / carbohydrate metabolic process / membrane / cytosol
Similarity search - Function
Transaldolase type 1 / Transaldolase active site. / Transaldolase, active site / Transaldolase signature 1. / Transaldolase/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsThorell, S. / Jia, J. / Schneider, G.
Citation
Journal: Eur.J.Biochem. / Year: 2001
Title: Identification of catalytically important residues in the active site of Escherichia coli transaldolase.
Authors: Schorken, U. / Thorell, S. / Schurmann, M. / Jia, J. / Sprenger, G.A. / Schneider, G.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Crystallization and Preliminary X-ray Analysis of Recombinant Transaldolase B from Escherichia coli
Authors: Jia, J. / Lindqvist, Y. / Schneider, G. / Schoerken, U. / Sahm, H. / Sprenger, G.A.
#2: Journal: Structure / Year: 1996
Title: Crystal Structure of Transaldolase B from Escherichia coli Suggests a Circular Permutation of the Alpha/beta Barrel Within the Class I Aldolase Family
Authors: Jia, J. / Huang, W. / Schoerken, U. / Sahm, H. / Sprenger, G.A. / Lindqvist, Y. / Schneider, G.
#3: Journal: Protein Sci. / Year: 1997
Title: Crystal Structure of the Reduced Schiff-base Intermediate Complex of Transaldolase B from Escherichia coli: Mechanistic Implications for Class I Aldolases
Authors: Jia, J. / Schoerken, U. / Lindqvist, Y. / Sprenger, G.A. / Schneider, G.
#4: Journal: FEBS Lett. / Year: 2000
Title: The Three-dimensional Structure of Human Transaldolase
Authors: Thorell, S. / Gergely Jr., P. / Banki, K. / Perl, A. / Schneider, G.
History
DepositionFeb 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRANSALDOLASE B
B: TRANSALDOLASE B


Theoretical massNumber of molelcules
Total (without water)70,2242
Polymers70,2242
Non-polymers00
Water5,639313
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.130, 91.875, 131.059
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe dimer is generated with a symmetry molecule from one of the monomers in the asymmetric unit

-
Components

#1: Protein TRANSALDOLASE B


Mass: 35111.965 Da / Num. of mol.: 2 / Mutation: S176A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: TALB / Plasmid: PGSJ451 / Production host: Escherichia coli (E. coli) / Strain (production host): LJ110 / References: UniProt: P0A870, transaldolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.96 Å3/Da / Density % sol: 58.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: PEG 6000, sodium citrate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Details: used microseeding, Jia, J., (1996) Acta Crystallogr., Sect.D, 52, 192.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
211-13 %(w/w)PEG60001reservoir
30.1 Msodium citrate1reservoir

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 14, 1996
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→47.5 Å / Num. all: 48519 / Num. obs: 48519 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 16
Reflection shellResolution: 2.1→2.15 Å / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2957 / % possible all: 91.6
Reflection
*PLUS
Num. measured all: 392257
Reflection shell
*PLUS
% possible obs: 91.6 %

-
Processing

Software
NameClassification
CNSrefinement
MAR345data collection
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1ONR

1onr


Resolution: 2.1→27 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2392396.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.203 2466 5.1 %RANDOM
Rwork0.183 ---
obs0.183 48494 98 %-
all-48494 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.59 Å2 / ksol: 0.323 e/Å3
Displacement parametersBiso mean: 32.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.82 Å20 Å20 Å2
2--3.82 Å20 Å2
3----5.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.1→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4938 0 0 313 5251
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d20.8
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_mcbond_it1.151.5
X-RAY DIFFRACTIONc_mcangle_it1.82
X-RAY DIFFRACTIONc_scbond_it2.22
X-RAY DIFFRACTIONc_scangle_it3.332.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.258 389 5 %
Rwork0.257 7320 -
obs-7709 95 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 27 Å / σ(F): 0 / % reflection Rfree: 5.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 32.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.71
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.258 / % reflection Rfree: 5 % / Rfactor Rwork: 0.257 / Rfactor obs: 0.272

+
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