[English] 日本語
Yorodumi
- PDB-8cip: Crystal structure of transketolase from Geobacillus stearothermophilus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8cip
TitleCrystal structure of transketolase from Geobacillus stearothermophilus
ComponentsTransketolase
KeywordsTRANSFERASE / Carboligase / ThDP-dependent / Thermostable / Transketolase
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 binding site / Transketolase signature 2. / 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 binding site / Transketolase signature 2. / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamin diphosphate-binding fold
Similarity search - Domain/homology
ACETATE ION / THIAMINE DIPHOSPHATE / Transketolase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLeogrande, C. / Rabe von Pappenheim, F. / Tittmann, K.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission956631European Union
Citation
Journal: To Be Published
Title: Crystal structure of transketolase from Geobacillus stearothermophilus
Authors: Leogrande, C. / Rabe von Pappenheim, F. / Tittman, K.
#1: Journal: Adv.Synth.Catal. / Year: 2012
Title: Thermostable Transketolase from Geobacillus stearothermophilus: Characterization and Catalytic Properties
Authors: Abdoul-Zabar, J. / Sorel, I. / Helaine, V. / Charmantray, F. / Devamani, T. / Yi, D. / de Berardinis, V. / Philippe Marliere, D.L. / Fessner, W.-D. / Hecquet, L.
History
DepositionFeb 10, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transketolase
B: Transketolase
C: Transketolase
D: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)297,36139
Polymers294,0294
Non-polymers3,33235
Water10,809600
1
A: Transketolase
B: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,73521
Polymers147,0142
Non-polymers1,72119
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12710 Å2
ΔGint-75 kcal/mol
Surface area40250 Å2
MethodPISA
2
C: Transketolase
D: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,62618
Polymers147,0142
Non-polymers1,61116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12470 Å2
ΔGint-45 kcal/mol
Surface area40480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.440, 82.710, 106.140
Angle α, β, γ (deg.)80.89, 68.34, 69.99
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Transketolase / TK


Mass: 73507.180 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Mutations respect to Uniprot accession code (L397F, D399G and H479Q) were made to introduce new restriction sites for cassette mutagenesis purposes. See the cited paper: Abdoul-Zabar, J. et ...Details: Mutations respect to Uniprot accession code (L397F, D399G and H479Q) were made to introduce new restriction sites for cassette mutagenesis purposes. See the cited paper: Abdoul-Zabar, J. et al., (2013), Thermostable Transketolase from Geobacillus stearothermophilus: Characterization and Catalytic Properties. Adv. Synth. Catal., 355: 116-128.
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: tkt / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0I9QGZ2, transketolase

-
Non-polymers , 6 types, 635 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H19N4O7P2S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 600 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1:1 mix of protein drop and reservoir drop. Protein drop: glycine 0.05 M pH 7.9, thiamine diphosphate 2 mM, magnesium chloride 10 mM, protein 8 mg/ml. Reserviur drops: PEG 3350 23.4%, Bis- ...Details: 1:1 mix of protein drop and reservoir drop. Protein drop: glycine 0.05 M pH 7.9, thiamine diphosphate 2 mM, magnesium chloride 10 mM, protein 8 mg/ml. Reserviur drops: PEG 3350 23.4%, Bis-Tris 0.1 M pH 6.5, ammonium acetate 0.2 M.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.6888 Å
DetectorType: DECTRIS EIGER2 XE CdTe 16M / Detector: PIXEL / Date: Nov 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6888 Å / Relative weight: 1
ReflectionResolution: 2.1→77.67 Å / Num. obs: 126234 / % possible obs: 91.6 % / Redundancy: 3.83 % / CC1/2: 0.996 / Rrim(I) all: 0.152 / Net I/σ(I): 7.66
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rrim(I) all% possible allRmerge(I) obs
2.1-2.153.8493250.4461.41191.4
2.15-2.2191470.5281.1621
2.21-2.2887640.6030.9790.842
2.28-2.3585240.670.8460.728
2.35-2.4282290.7560.6830.588
2.42-2.5179630.8130.5790.499
2.51-2.676180.8550.490.422
2.6-2.7173810.8980.4020.345
2.71-2.8370760.9260.340.291
2.83-2.9770030.9510.2760.238
2.97-3.1366730.970.2140.184
3.13-3.3263100.9810.1640.141
3.32-3.5558590.9910.1160.1
3.55-3.8354170.9940.0920.079
3.83-4.249800.9960.0690.059
4.2-4.744700.9970.0550.047
4.7-5.4239460.9980.0510.044
5.42-6.6435060.9980.050.043
6.64-9.3926470.9980.0390.033
9.39-77.6713960.9980.0380.032

-
Processing

Software
NameVersionClassification
PHENIXv1.20.1-4487refinement
XDSv10 Jan 2022 BUILT= 0220220data reduction
XSCALEv10 Jan 2022 BUILT= 0220220data scaling
PHENIXv1.20.1-4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→49.29 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2281 6311 5 %Random selection
Rwork0.1679 ---
obs0.1709 126209 91.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→49.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20292 0 97 600 20989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011
X-RAY DIFFRACTIONf_angle_d1.123
X-RAY DIFFRACTIONf_dihedral_angle_d14.8157495
X-RAY DIFFRACTIONf_chiral_restr0.0553064
X-RAY DIFFRACTIONf_plane_restr0.0123687
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.120.33852110.25914011X-RAY DIFFRACTION91
2.12-2.150.30392080.25173960X-RAY DIFFRACTION92
2.15-2.170.32472120.24234027X-RAY DIFFRACTION91
2.17-2.20.29162080.24583934X-RAY DIFFRACTION91
2.2-2.230.29092080.23823953X-RAY DIFFRACTION91
2.23-2.260.31052110.23494020X-RAY DIFFRACTION91
2.26-2.290.30012090.22743961X-RAY DIFFRACTION91
2.29-2.330.28982100.22723998X-RAY DIFFRACTION91
2.33-2.370.29452060.21473904X-RAY DIFFRACTION91
2.37-2.40.27222080.20143955X-RAY DIFFRACTION91
2.4-2.450.27212080.19173947X-RAY DIFFRACTION90
2.45-2.490.24012080.18873956X-RAY DIFFRACTION91
2.49-2.540.28952070.19253947X-RAY DIFFRACTION91
2.54-2.590.27472070.193933X-RAY DIFFRACTION90
2.59-2.650.26552040.18113872X-RAY DIFFRACTION89
2.65-2.710.27092100.18093975X-RAY DIFFRACTION91
2.71-2.770.2742080.17733957X-RAY DIFFRACTION91
2.77-2.850.26692080.17523961X-RAY DIFFRACTION91
2.85-2.930.2462150.17284085X-RAY DIFFRACTION94
2.93-3.030.22462170.17254117X-RAY DIFFRACTION94
3.03-3.140.22242140.16734060X-RAY DIFFRACTION93
3.14-3.260.23042120.15964030X-RAY DIFFRACTION93
3.26-3.410.24322150.16774083X-RAY DIFFRACTION93
3.41-3.590.22352140.1564071X-RAY DIFFRACTION93
3.59-3.820.20912120.14844023X-RAY DIFFRACTION92
3.82-4.110.19122110.13824009X-RAY DIFFRACTION92
4.11-4.520.17092080.12593957X-RAY DIFFRACTION91
4.52-5.180.17372100.12933982X-RAY DIFFRACTION91
5.18-6.520.19562180.15694143X-RAY DIFFRACTION95
6.52-49.290.18442140.14744067X-RAY DIFFRACTION93
Refinement TLS params.Method: refined / Origin x: -3.2743 Å / Origin y: -57.3088 Å / Origin z: -6.4167 Å
111213212223313233
T0.2459 Å2-0.0251 Å20.045 Å2-0.2086 Å2-0.0146 Å2--0.2592 Å2
L0.1348 °2-0.1243 °20.1626 °2-0.3136 °2-0.2482 °2--0.4195 °2
S-0.002 Å °-0.0175 Å °-0.0062 Å °0.0128 Å °0.0167 Å °0.0341 Å °-0.0657 Å °-0.0086 Å °-0.0184 Å °
Refinement TLS groupSelection details: all

+
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