[English] 日本語
Yorodumi
- PDB-4c7v: Apo Transketolase from Lactobacillus salivarius at 2.2A resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4c7v
TitleApo Transketolase from Lactobacillus salivarius at 2.2A resolution
ComponentsTRANSKETOLASE
KeywordsTRANSFERASE
Function / homology
Function and homology information


transketolase / transketolase activity / pentose-phosphate shunt / metal ion binding / 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, C-terminal domain / Rossmann fold - #920 / Transketolase-like, pyrimidine-binding domain ...Transketolase, bacterial-like / Transketolase family / Transketolase-like TK C-terminal domain / : / Transketolase signature 1. / Transketolase, N-terminal / Transketolase, thiamine diphosphate binding domain / 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 speciesLACTOBACILLUS SALIVARIUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLobley, C.M.C. / Lukacik, P. / Bumann, M. / Aller, P. / Douangamath, A. / O'Toole, P.W. / Walsh, M.A.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: High Resolution Crystal Structures of Lactobacillus Salivarius Transketolase in the Presence and Absence of Thiamine Pyrophosphate
Authors: Lukacik, P. / Lobley, C.M.C. / Bumann, M. / Arena De Souza, V. / Owens, R.J. / O'Toole, P.W. / Walsh, M.A.
History
DepositionSep 26, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references / Structure summary
Revision 1.2Oct 21, 2015Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRANSKETOLASE


Theoretical massNumber of molelcules
Total (without water)74,5431
Polymers74,5431
Non-polymers00
Water4,432246
1
A: TRANSKETOLASE

A: TRANSKETOLASE


Theoretical massNumber of molelcules
Total (without water)149,0862
Polymers149,0862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area8000 Å2
ΔGint-37.4 kcal/mol
Surface area42580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.150, 76.150, 194.510
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-2162-

HOH

-
Components

#1: Protein TRANSKETOLASE


Mass: 74542.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LACTOBACILLUS SALIVARIUS (bacteria) / Strain: UCC118 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS / References: UniProt: Q1WQU8, transketolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE HIS TAG (THE FIRST 18 RESIDUES ABOVE) IS NOT VISIBLE IN THE ELECTRON DENSITY MAP

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.77 % / Description: NONE
Crystal growDetails: 20 % W/V PEG3350, 0.2 M SODIUM CHLORIDE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.917
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 9, 2012 / Details: MIRRORS
RadiationMonochromator: DCM SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 2.2→39.14 Å / Num. obs: 33992 / % possible obs: 99.7 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.8
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
xia2data reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→39.14 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.947 / SU B: 11.233 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21917 1720 5.1 %RANDOM
Rwork0.16236 ---
obs0.16524 32219 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.117 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0.25 Å20 Å2
2---0.25 Å20 Å2
3---0.8 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5092 0 0 246 5338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0195234
X-RAY DIFFRACTIONr_bond_other_d0.0010.024929
X-RAY DIFFRACTIONr_angle_refined_deg1.781.9557097
X-RAY DIFFRACTIONr_angle_other_deg0.873311390
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5095671
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.72525.128234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.83115884
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.151520
X-RAY DIFFRACTIONr_chiral_restr0.1010.2772
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216007
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021157
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5393.0992657
X-RAY DIFFRACTIONr_mcbond_other2.5373.0982656
X-RAY DIFFRACTIONr_mcangle_it3.4994.6373322
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.223.4432577
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 121 -
Rwork0.238 2360 -
obs--99.92 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7794-0.06420.13820.27950.03940.46930.00140.0843-0.261-0.07730.00780.1702-0.0469-0.2087-0.00920.02540.0139-0.04510.1289-0.02690.17197.75154.468-10.44
20.6318-0.18160.3180.5618-0.07930.57780.02640.0482-0.2749-0.06240.0180.1810.0446-0.208-0.04450.0231-0.029-0.04410.1424-0.04570.2214.9649.212-11.783
30.4907-0.06-0.04350.33020.01160.9637-0.055-0.1516-0.11760.02690.05880.0786-0.1625-0.0666-0.00390.05130.03940.01250.08450.03630.046723.93262.28514.125
41.0997-0.008-0.04291.03140.29771.0204-0.0467-0.15460.16870.00750.0779-0.0585-0.36950.1622-0.03120.2236-0.0741-0.02230.0747-0.02490.03440.27779.85513.535
51.3010.0278-0.32625.1223-0.60040.1911-0.0879-0.2830.00210.1590.0619-0.2573-0.03340.15850.02610.1718-0.059-0.06490.2875-0.01890.080951.3367.81219.419
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 188
2X-RAY DIFFRACTION2A189 - 337
3X-RAY DIFFRACTION3A338 - 528
4X-RAY DIFFRACTION4A529 - 637
5X-RAY DIFFRACTION5A638 - 661

+
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