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- PDB-3rim: Crystal structure of mycobacterium tuberculosis Transketolase (Rv... -

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Basic information

Entry
Database: PDB / ID: 3rim
TitleCrystal structure of mycobacterium tuberculosis Transketolase (Rv1449c)
ComponentsTransketolase
KeywordsTRANSFERASE / transketolase / mycobacterium / TPP
Function / homology
Function and homology information


transketolase / transketolase activity / pentose-phosphate shunt / peptidoglycan-based cell wall / magnesium ion binding / extracellular region / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Transketolase, bacterial-like / Transketolase family / : / Transketolase, C-terminal domain / Transketolase-like TK C-terminal domain / : / Transketolase signature 1. / Transketolase, N-terminal / Transketolase, thiamine diphosphate binding domain / Transketolase binding site ...Transketolase, bacterial-like / Transketolase family / : / Transketolase, C-terminal domain / Transketolase-like TK C-terminal domain / : / Transketolase signature 1. / Transketolase, N-terminal / Transketolase, thiamine diphosphate binding domain / Transketolase binding site / Transketolase signature 2. / 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
THIAMINE DIPHOSPHATE / Transketolase / Transketolase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsPojer, F. / Fullam, E. / Jones, T.A. / Cole, S.T.
CitationJournal: Open Biol / Year: 2012
Title: Structure and function of the transketolase from Mycobacterium tuberculosis and comparison with the human enzyme.
Authors: Fullam, E. / Pojer, F. / Bergfors, T. / Jones, T.A. / Cole, S.T.
History
DepositionApr 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)305,20920
Polymers302,6744
Non-polymers2,53516
Water7,386410
1
A: Transketolase
C: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,4218
Polymers151,3372
Non-polymers1,0836
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10810 Å2
ΔGint-80 kcal/mol
Surface area43680 Å2
MethodPISA
2
B: Transketolase
D: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,78912
Polymers151,3372
Non-polymers1,45210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11940 Å2
ΔGint-84 kcal/mol
Surface area43610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.530, 80.120, 130.100
Angle α, β, γ (deg.)82.20, 81.16, 66.37
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 1 / Auth seq-ID: 10 - 695 / Label seq-ID: 10 - 695

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Transketolase / TK


Mass: 75668.562 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: tkt, Rv1449c, MT1496, MTCY493.05 / Plasmid: PET160 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: O06811, UniProt: P9WG25*PLUS, transketolase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 2.32 Å3/Da / Density % sol: 46.88 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 17% PEG 10000, 0.1M ammonium acetate in 0.1M bis-tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 3, 2009
RadiationMonochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.494→128.12 Å / Num. obs: 91429 / % possible obs: 96.62 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.49→2.64 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.77 / Num. unique all: 13701 / Rsym value: 0.431 / % possible all: 91.16

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: model of Rv1449c with E. coli transketolase (pdb entry 2r8o) as template

2r8o


Resolution: 2.49→19.81 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.872 / SU B: 12.779 / SU ML: 0.277 / Cross valid method: THROUGHOUT / σ(F): 2.01 / ESU R Free: 0.35 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2721 4579 5 %RANDOM
Rwork0.22298 ---
obs0.22544 86846 96.69 %-
all-91429 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.069 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20.21 Å2-1.64 Å2
2--1 Å2-0.24 Å2
3----1.5 Å2
Refinement stepCycle: LAST / Resolution: 2.49→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21150 0 156 410 21716
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02121868
X-RAY DIFFRACTIONr_angle_refined_deg1.6341.95629835
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.23552786
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55523.313990
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.625153269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.45815177
X-RAY DIFFRACTIONr_chiral_restr0.0970.23283
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02117017
X-RAY DIFFRACTIONr_mcbond_it0.5661.513778
X-RAY DIFFRACTIONr_mcangle_it1.064222035
X-RAY DIFFRACTIONr_scbond_it1.57238090
X-RAY DIFFRACTIONr_scangle_it2.6034.57793
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
15202TIGHT POSITIONAL0.10.05
15202TIGHT THERMAL0.160.5
25194TIGHT POSITIONAL0.120.05
25194TIGHT THERMAL0.210.5
35202TIGHT POSITIONAL0.110.05
35202TIGHT THERMAL0.190.5
LS refinement shellResolution: 2.494→2.559 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 285 -
Rwork0.308 5639 -
obs--85.21 %

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