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- PDB-8cip: Crystal structure of transketolase from Geobacillus stearothermophilus -

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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 / metal ion binding
Similarity search - Function
Transketolase, bacterial-like / Transketolase family / Transketolase binding site / Transketolase, thiamine diphosphate binding domain / Transketolase signature 1. / Transketolase signature 2. / Transketolase, N-terminal / Transketolase, C-terminal domain / Transketolase, C-terminal domain / Transketolase-like, pyrimidine-binding domain ...Transketolase, bacterial-like / Transketolase family / Transketolase binding site / Transketolase, thiamine diphosphate binding domain / Transketolase signature 1. / Transketolase signature 2. / Transketolase, N-terminal / Transketolase, C-terminal domain / Transketolase, C-terminal domain / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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

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Non-polymers , 6 types, 635 molecules

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


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


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


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 / Chloride


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


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

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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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.

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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

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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

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