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- PDB-6yak: Split gene transketolase, active alpha2beta2 heterotetramer -

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Basic information

Entry
Database: PDB / ID: 6yak
TitleSplit gene transketolase, active alpha2beta2 heterotetramer
Components
  • C-terminal component of the split chain transketolase
  • N-terminal component of the split chain transketolase
KeywordsTRANSFERASE / Hyperthermophilic / split-gene transketolase / thermal stability / industrial applications
Function / homologyChem-8EL / (2S)-2-hydroxybutanedioic acid / D-MALATE
Function and homology information
Biological speciesCarboxydothermus hydrogenoformans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsIsupov, M.N. / Littlechild, J.A. / James, P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/L002035/1 United Kingdom
CitationJournal: Front Microbiol / Year: 2020
Title: A 'Split-Gene' Transketolase From the Hyper-Thermophilic Bacterium Carboxydothermus hydrogenoformans : Structure and Biochemical Characterization.
Authors: James, P. / Isupov, M.N. / De Rose, S.A. / Sayer, C. / Cole, I.S. / Littlechild, J.A.
History
DepositionMar 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: N-terminal component of the split chain transketolase
BBB: C-terminal component of the split chain transketolase
CCC: N-terminal component of the split chain transketolase
DDD: C-terminal component of the split chain transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,16230
Polymers139,8624
Non-polymers3,30026
Water25,6531424
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16780 Å2
ΔGint-106 kcal/mol
Surface area36840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.078, 130.047, 165.897
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11DDD-1735-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Chains AAA CCC
22Chains BBB DDD
/ NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules AAACCCBBBDDD

#1: Protein N-terminal component of the split chain transketolase


Mass: 33917.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carboxydothermus hydrogenoformans (bacteria)
Production host: Escherichia coli (E. coli)
#2: Protein C-terminal component of the split chain transketolase


Mass: 36013.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carboxydothermus hydrogenoformans (bacteria)
Production host: Escherichia coli (E. coli)

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Non-polymers , 6 types, 1450 molecules

#3: Chemical ChemComp-8EL / 2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-2H-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate


Mass: 426.322 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H20N4O7P2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C4H6O5
#6: Chemical
ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


Mass: 134.087 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H6O5
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1424 / 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: 2.37 Å3/Da / Density % sol: 48.17 %
Crystal growTemperature: 291 K / Method: microbatch / Details: 2.1 M DL-malic acid pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.34→60.878 Å / Num. obs: 288149 / % possible obs: 97.7 % / Redundancy: 6.1 % / Biso Wilson estimate: 23.4 Å2 / CC1/2: 1 / Rrim(I) all: 0.056 / Net I/σ(I): 16.4
Reflection shellResolution: 1.34→1.36 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 11686 / CC1/2: 0.266 / Rrim(I) all: 1.619 / % possible all: 81.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
Aimlessdata scaling
MOLREPphasing
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1qgd

1qgd


Resolution: 1.34→60.87 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.979 / Cross valid method: FREE R-VALUE / ESU R: 0.043 / ESU R Free: 0.045
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1588 14402 4.998 %
Rwork0.1409 --
all0.142 --
obs-288145 97.584 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.416 Å20 Å20 Å2
2--0.42 Å2-0 Å2
3----0.004 Å2
Refinement stepCycle: LAST / Resolution: 1.34→60.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8982 0 204 1424 10610
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01310377
X-RAY DIFFRACTIONr_bond_other_d0.0330.01710079
X-RAY DIFFRACTIONr_angle_refined_deg1.5341.65114219
X-RAY DIFFRACTIONr_angle_other_deg2.271.5823591
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.32251459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.43222.344529
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.682151912
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1981577
X-RAY DIFFRACTIONr_chiral_restr0.080.21371
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211921
X-RAY DIFFRACTIONr_gen_planes_other0.0130.022076
X-RAY DIFFRACTIONr_nbd_refined0.2140.21940
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2060.28736
X-RAY DIFFRACTIONr_nbtor_refined0.1610.24705
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0650.24080
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.21129
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1340.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0480.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2690.243
X-RAY DIFFRACTIONr_nbd_other0.2770.279
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2060.269
X-RAY DIFFRACTIONr_mcbond_it2.2614.7435076
X-RAY DIFFRACTIONr_mcbond_other2.264.7435075
X-RAY DIFFRACTIONr_mcangle_it3.0957.986399
X-RAY DIFFRACTIONr_mcangle_other3.0957.986400
X-RAY DIFFRACTIONr_scbond_it4.2316.1395301
X-RAY DIFFRACTIONr_scbond_other4.2276.1375300
X-RAY DIFFRACTIONr_scangle_it5.9319.8497674
X-RAY DIFFRACTIONr_scangle_other5.9319.8517675
X-RAY DIFFRACTIONr_lrange_it7.70538.51845078
X-RAY DIFFRACTIONr_lrange_other7.70538.47645035
X-RAY DIFFRACTIONr_ncsr_local_group_10.0780.059631
X-RAY DIFFRACTIONr_ncsr_local_group_20.0930.0510123
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.34-1.3750.328600.31917046X-RAY DIFFRACTION82.7334
1.375-1.4120.39860.318526X-RAY DIFFRACTION92.1029
1.412-1.4530.2759930.26818918X-RAY DIFFRACTION96.4447
1.453-1.4980.2389520.22818577X-RAY DIFFRACTION97.9732
1.498-1.5470.21410140.19618270X-RAY DIFFRACTION99.3457
1.547-1.6020.1939420.17517797X-RAY DIFFRACTION99.8242
1.602-1.6620.1869230.16217158X-RAY DIFFRACTION99.9006
1.662-1.730.1738590.15516560X-RAY DIFFRACTION99.7823
1.73-1.8070.1827880.14915889X-RAY DIFFRACTION99.588
1.807-1.8950.1598160.13715166X-RAY DIFFRACTION99.8313
1.895-1.9970.1557980.13314430X-RAY DIFFRACTION99.9016
1.997-2.1180.157150.12913718X-RAY DIFFRACTION99.9308
2.118-2.2650.146550.12212942X-RAY DIFFRACTION99.9118
2.265-2.4460.1346280.11111988X-RAY DIFFRACTION99.6761
2.446-2.6790.1325630.11211045X-RAY DIFFRACTION99.4602
2.679-2.9950.1465290.1210074X-RAY DIFFRACTION99.934
2.995-3.4580.1364780.1258877X-RAY DIFFRACTION99.8293
3.458-4.2340.1223970.1117559X-RAY DIFFRACTION99.7993
4.234-5.9830.143270.1245827X-RAY DIFFRACTION98.7484
5.983-60.870.1861790.1663376X-RAY DIFFRACTION99.5519

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