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- PDB-3hyl: Crystal Structure of Transketolase from Bacillus anthracis -

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Basic information

Entry
Database: PDB / ID: 3hyl
TitleCrystal Structure of Transketolase from Bacillus anthracis
ComponentsTransketolase
KeywordsTRANSFERASE / alpha-beta structure / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
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, 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 / 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
FORMIC ACID / DI(HYDROXYETHYL)ETHER / Transketolase / :
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.16 Å
AuthorsMaltseva, N. / Kim, Y. / Kwon, K. / Joachimiak, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Transketolase from Bacillus anthracis
Authors: Maltseva, N. / Kim, Y. / Kwon, K. / Joachimiak, A. / Anderson, W.F.
History
DepositionJun 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transketolase
B: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,90623
Polymers152,6112
Non-polymers1,29521
Water10,881604
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12050 Å2
ΔGint-80 kcal/mol
Surface area41860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.801, 70.975, 145.795
Angle α, β, γ (deg.)90.00, 117.35, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Transketolase /


Mass: 76305.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames Ancestor / Gene: BAA_3769, tkt-2, tkt2 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-magic
References: UniProt: C3P4P9, UniProt: A0A6L7H165*PLUS, transketolase

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Non-polymers , 7 types, 625 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 604 / Source method: isolated from a natural source / Formula: H2O

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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: 2.09 Å3/Da / Density % sol: 41.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 0.2 M Magnesium formate pH 5.9, 20 % PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 4, 2009 / Details: Mirrors
RadiationMonochromator: Double crystal monochromator / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.16→36.35 Å / Num. all: 67767 / Num. obs: 67767 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 31.89 Å2 / Rsym value: 0.09 / Net I/σ(I): 13.6
Reflection shellResolution: 2.16→2.2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 4.76 / Num. unique all: 3287 / % possible all: 99.4

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXmodel building
MLPHAREphasing
DMmodel building
SOLVEphasing
RESOLVEmodel building
PHENIX(phenix.refine)refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.16→36.35 Å / SU ML: 0.3 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.23 3423 5.06 %RANDOM
Rwork0.176 ---
all0.178 67620 --
obs0.178 67620 99.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.876 Å2 / ksol: 0.347 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.9597 Å20 Å2-1.0171 Å2
2--1.7217 Å20 Å2
3----5.8481 Å2
Refinement stepCycle: LAST / Resolution: 2.16→36.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10142 0 81 604 10827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01410465
X-RAY DIFFRACTIONf_angle_d1.53214177
X-RAY DIFFRACTIONf_chiral_restr0.11551
X-RAY DIFFRACTIONf_plane_restr0.0071858
X-RAY DIFFRACTIONf_dihedral_angle_d19.4663720
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.16-2.1880.2741230.24442447257092
2.188-2.22070.32631400.244626992839100
2.2207-2.25540.31611520.242926202772100
2.2554-2.29230.3131450.24112688283399
2.2923-2.33190.30471370.22532611274899
2.3319-2.37420.24091520.222726912843100
2.3742-2.41990.30451440.23212650279499
2.4199-2.46930.28661360.225426682804100
2.4693-2.5230.30831540.22526952849100
2.523-2.58160.27881300.219526742804100
2.5816-2.64620.31391580.210226562814100
2.6462-2.71770.24451450.208626522797100
2.7177-2.79760.27121520.209626782830100
2.7976-2.88790.27951470.198127182865100
2.8879-2.99110.23461540.207526402794100
2.9911-3.11080.26371280.194127142842100
3.1108-3.25230.25811510.190626752826100
3.2523-3.42360.2421520.177626752827100
3.4236-3.63790.20291310.160726992830100
3.6379-3.91850.18161410.142327182859100
3.9185-4.31230.16621360.122127072843100
4.3123-4.9350.15991300.116727252855100
4.935-6.21250.17361370.128727352872100
6.2125-36.35440.17121480.14262762291098

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