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- PDB-6yaj: Split gene transketolase, inactive beta4 tetramer -

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Basic information

Entry
Database: PDB / ID: 6yaj
TitleSplit gene transketolase, inactive beta4 tetramer
ComponentsC-terminal chain of split transketolase from Carboxydothermus hydrogenoformans
KeywordsTRANSFERASE / Hyperthermophilic / split-gene transketolase / thermal stability / industrial applications
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesCarboxydothermus hydrogenoformans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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

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Assembly

Deposited unit
AAA: C-terminal chain of split transketolase from Carboxydothermus hydrogenoformans
BBB: C-terminal chain of split transketolase from Carboxydothermus hydrogenoformans
CCC: C-terminal chain of split transketolase from Carboxydothermus hydrogenoformans
DDD: C-terminal chain of split transketolase from Carboxydothermus hydrogenoformans
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,64326
Polymers144,0534
Non-polymers1,59022
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13820 Å2
ΔGint-5 kcal/mol
Surface area43430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.878, 101.878, 164.546
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Chains AAA BBB
22Chains AAA CCC
33Chains AAA DDD
44Chains BBB CCC
55Chains BBB DDD
66Chains CCC DDD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
C-terminal chain of split transketolase from Carboxydothermus hydrogenoformans


Mass: 36013.340 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carboxydothermus hydrogenoformans (bacteria)
Production host: Escherichia coli (E. coli) / References: transketolase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.96 Å3/Da / Density % sol: 58.5 %
Crystal growTemperature: 291 K / Method: microbatch / Details: ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.9→86.62 Å / Num. obs: 131289 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / CC1/2: 0.999 / Rrim(I) all: 0.053 / Net I/σ(I): 13.1
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 6524 / CC1/2: 0.339 / Rrim(I) all: 4.245

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Processing

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

1qgd


Resolution: 1.9→64.008 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.969 / SU B: 4.921 / SU ML: 0.123 / Cross valid method: FREE R-VALUE / ESU R: 0.117 / ESU R Free: 0.113
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2077 6613 5.041 %
Rwork0.1776 --
all0.179 --
obs-131176 99.757 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 59.984 Å2
Baniso -1Baniso -2Baniso -3
1-2.167 Å2-0 Å20 Å2
2--2.167 Å2-0 Å2
3----4.333 Å2
Refinement stepCycle: LAST / Resolution: 1.9→64.008 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9005 0 103 334 9442
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0129745
X-RAY DIFFRACTIONr_angle_refined_deg1.6051.63513258
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.12551360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.74621.554444
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.756151749
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2471573
X-RAY DIFFRACTIONr_chiral_restr0.1050.21339
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027279
X-RAY DIFFRACTIONr_nbd_refined0.2060.24321
X-RAY DIFFRACTIONr_nbtor_refined0.3110.26694
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.2478
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2590.285
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1430.212
X-RAY DIFFRACTIONr_mcbond_it4.7015.6235012
X-RAY DIFFRACTIONr_mcangle_it6.5248.386291
X-RAY DIFFRACTIONr_scbond_it7.16.284733
X-RAY DIFFRACTIONr_scangle_it9.8539.0636887
X-RAY DIFFRACTIONr_lrange_it12.015106.50640906
X-RAY DIFFRACTIONr_ncsr_local_group_10.0850.059532
X-RAY DIFFRACTIONr_ncsr_local_group_20.0880.059555
X-RAY DIFFRACTIONr_ncsr_local_group_30.1050.059509
X-RAY DIFFRACTIONr_ncsr_local_group_40.090.059285
X-RAY DIFFRACTIONr_ncsr_local_group_50.0920.059290
X-RAY DIFFRACTIONr_ncsr_local_group_60.0970.059374
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.9-1.9490.4264600.40992130.4196970.3550.36399.75250.404
1.949-2.0030.3775170.37789070.37794780.5040.49699.43030.368
2.003-2.0610.3314780.33486840.33491660.6260.63499.95640.31
2.061-2.1240.3344210.29685080.29889560.740.75599.69850.269
2.124-2.1940.2694590.27281670.27286370.840.82999.87260.242
2.194-2.2710.2924080.24579640.24783910.8630.88199.77360.212
2.271-2.3560.2733840.23976650.2480740.8960.90499.69040.201
2.356-2.4520.2843720.22373930.22577760.910.92899.85850.184
2.452-2.5610.2274050.20270500.20474700.9350.94199.79920.166
2.561-2.6860.263410.20367990.20671430.9250.94599.9580.17
2.686-2.8310.2453690.19264230.19568010.9390.95399.86770.164
2.831-3.0020.2223530.19360630.19464180.950.95799.96880.171
3.002-3.2090.2412950.1857510.18360480.9420.9699.96690.165
3.209-3.4660.2162430.17153630.17356110.9570.96799.91090.166
3.466-3.7950.1772350.15449710.15552090.970.97699.94240.155
3.795-4.2410.1732540.13344240.13546890.9740.98199.76540.141
4.241-4.8940.1482220.11938960.1241390.9810.98499.49260.133
4.894-5.9850.1581740.14133190.14235170.9740.97799.31760.158
5.985-8.4270.1591460.14925680.1527350.9730.97799.23220.17
8.427-64.0080.195770.17314350.17415360.9670.97298.43750.206

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