[English] 日本語
Yorodumi
- PDB-5hgx: Crystal Structure of Transketolase mutant - H261F from Pichia Stipitis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hgx
TitleCrystal Structure of Transketolase mutant - H261F from Pichia Stipitis
ComponentsTransketolase
KeywordsTRANSFERASE / transketolase
Function / homology
Function and homology information


transketolase / transketolase activity / pentose-phosphate shunt / metal ion binding / nucleus / cytosol
Similarity search - Function
Transketolase, bacterial-like / Transketolase family / : / Transketolase-like TK C-terminal domain / : / Transketolase signature 1. / Transketolase, N-terminal / Transketolase, thiamine diphosphate binding domain / Transketolase binding site / Transketolase signature 2. ...Transketolase, bacterial-like / Transketolase family / : / Transketolase-like TK C-terminal domain / : / Transketolase signature 1. / Transketolase, N-terminal / Transketolase, thiamine diphosphate binding domain / Transketolase binding site / Transketolase signature 2. / Transketolase, C-terminal domain / Rossmann fold - #920 / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / Thiamin diphosphate-binding fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesScheffersomyces stipitis CBS 6054 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å
AuthorsLi, T.L. / Hsu, L.J. / Hsu, N.S.
CitationJournal: Protein Eng. Des. Sel. / Year: 2016
Title: Structural and biochemical interrogation on transketolase from Pichia stipitis for new functionality
Authors: Hsu, L.J. / Hsu, N.S. / Wang, Y.L. / Wu, C.J. / Li, T.L.
History
DepositionJan 9, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3022
Polymers75,0631
Non-polymers2381
Water19,2401068
1
A: Transketolase
hetero molecules

A: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,6044
Polymers150,1272
Non-polymers4772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area9120 Å2
ΔGint-46 kcal/mol
Surface area42460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.148, 184.556, 98.848
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-827-

HOH

21A-967-

HOH

31A-1274-

HOH

41A-1539-

HOH

51A-1585-

HOH

61A-1704-

HOH

71A-1718-

HOH

81A-1829-

HOH

91A-1830-

HOH

-
Components

#1: Protein Transketolase / TK


Mass: 75063.484 Da / Num. of mol.: 1 / Mutation: H261F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scheffersomyces stipitis CBS 6054 (fungus)
Strain: CBS 6054 / Gene: TKT, TKT1, PICST_67105 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P34736, transketolase
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1068 / 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: 3.07 Å3/Da / Density % sol: 59.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG400, MES, NaCl / PH range: 6.3-6.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.974 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.974 Å / Relative weight: 1
ReflectionResolution: 1.09→30 Å / Num. obs: 380091 / % possible obs: 99.5 % / Redundancy: 4.7 % / Biso Wilson estimate: 9.95 Å2 / Rmerge(I) obs: 0.073 / Χ2: 1.163 / Net I/av σ(I): 18.948 / Net I/σ(I): 14.8 / Num. measured all: 1797707
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.09-1.133.50.513372121.16198.1
1.13-1.173.80.362378961.23199.8
1.17-1.234.20.287379631.264100
1.23-1.294.30.228380491.264100
1.29-1.374.40.187380861.242100
1.37-1.484.50.13380981.21100
1.48-1.634.70.102381811.173100
1.63-1.864.90.084382221.14599.9
1.86-2.355.50.055384191.037100
2.35-307.40.066379651.06397.1

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2152: ???)refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GPU

1gpu


Resolution: 1.09→23.871 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 9.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1217 19112 5.03 %
Rwork0.1058 --
obs0.1066 380041 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.09→23.871 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5137 0 44 1068 6249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095444
X-RAY DIFFRACTIONf_angle_d1.1727417
X-RAY DIFFRACTIONf_dihedral_angle_d16.0691975
X-RAY DIFFRACTIONf_chiral_restr0.085822
X-RAY DIFFRACTIONf_plane_restr0.008968
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0878-1.10020.23735520.223410782X-RAY DIFFRACTION90
1.1002-1.11310.21946040.199411876X-RAY DIFFRACTION98
1.1131-1.12670.1816660.176111843X-RAY DIFFRACTION99
1.1267-1.14090.17246720.159911935X-RAY DIFFRACTION99
1.1409-1.1560.17516510.147412088X-RAY DIFFRACTION100
1.156-1.17180.15456100.138712016X-RAY DIFFRACTION100
1.1718-1.18850.14736660.131412042X-RAY DIFFRACTION100
1.1885-1.20630.14756530.130312032X-RAY DIFFRACTION100
1.2063-1.22510.13476480.119512091X-RAY DIFFRACTION100
1.2251-1.24520.13136610.111612028X-RAY DIFFRACTION100
1.2452-1.26670.12246430.106812087X-RAY DIFFRACTION100
1.2667-1.28970.12076290.102312056X-RAY DIFFRACTION100
1.2897-1.31450.12046430.100312106X-RAY DIFFRACTION100
1.3145-1.34130.11396020.099412070X-RAY DIFFRACTION100
1.3413-1.37050.11766090.097212122X-RAY DIFFRACTION100
1.3705-1.40240.11086540.091812106X-RAY DIFFRACTION100
1.4024-1.43740.10586180.089712065X-RAY DIFFRACTION100
1.4374-1.47630.1035880.085112185X-RAY DIFFRACTION100
1.4763-1.51970.09966140.08312140X-RAY DIFFRACTION100
1.5197-1.56880.10256140.081512141X-RAY DIFFRACTION100
1.5688-1.62480.10026750.079112074X-RAY DIFFRACTION100
1.6248-1.68990.09546700.080912088X-RAY DIFFRACTION100
1.6899-1.76680.10766780.086812089X-RAY DIFFRACTION100
1.7668-1.85990.10446770.089712115X-RAY DIFFRACTION100
1.8599-1.97640.10116450.088712187X-RAY DIFFRACTION100
1.9764-2.12890.10346220.090712179X-RAY DIFFRACTION100
2.1289-2.34290.11286480.090912222X-RAY DIFFRACTION100
2.3429-2.68160.10776380.09712265X-RAY DIFFRACTION100
2.6816-3.3770.12576570.115112266X-RAY DIFFRACTION100
3.377-23.87660.15066050.133311633X-RAY DIFFRACTION92

+
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