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- PDB-1r9j: Transketolase from Leishmania mexicana -

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Basic information

Entry
Database: PDB / ID: 1r9j
TitleTransketolase from Leishmania mexicana
Componentstransketolase
KeywordsTRANSFERASE / 3 domains / each of the alpha/beta type / thiamine diphosphate binding domain
Function / homology
Function and homology information


transketolase / transketolase activity / metal ion binding
Similarity search - Function
Transketolase, bacterial-like / Transketolase family / Transketolase signature 1. / Transketolase, thiamine diphosphate binding domain / Transketolase binding site / Transketolase signature 2. / Transketolase, N-terminal / Transketolase, C-terminal domain / Transketolase, C-terminal domain / Rossmann fold - #920 ...Transketolase, bacterial-like / Transketolase family / Transketolase signature 1. / Transketolase, thiamine diphosphate binding domain / Transketolase binding site / 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
THIAMINE DIPHOSPHATE / Transketolase
Similarity search - Component
Biological speciesLeishmania mexicana mexicana (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsVeitch, N.J. / Mauger, D.A. / Cazzulo, J.J. / Lindqvist, Y. / Barrett, M.P.
CitationJournal: Biochem.J. / Year: 2004
Title: Transketolase from Leishmania mexicana has a dual subcellular localization.
Authors: Veitch, N.J. / Maugeri, D.A. / Cazzulo, J.J. / Lindqvist, Y. / Barrett, M.P.
History
DepositionOct 30, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_ref_seq_dif / 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_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.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_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_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,3396
Polymers144,4082
Non-polymers9314
Water16,412911
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10280 Å2
ΔGint-80 kcal/mol
Surface area40550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.800, 120.440, 139.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein transketolase


Mass: 72204.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania mexicana mexicana (eukaryote)
Species: Leishmania mexicana / Strain: mexicana / Production host: Escherichia coli (E. coli) / References: UniProt: Q8MPM3, transketolase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 911 / 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: 2.23 Å3/Da / Density % sol: 44.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Na-citrate, ammonium acetate, PEG 4K, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.22→25 Å / Num. all: 61529 / Num. obs: 61492 / % possible obs: 95.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.95 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 5.8
Reflection shellResolution: 2.22→2.39 Å / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 2.4 / % possible all: 85.5

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
EPMRphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1TRK

1trk


Resolution: 2.22→25 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.213 3096 RANDOM
Rwork0.17 --
all0.172 61492 -
obs0.172 61492 -
Displacement parametersBiso mean: 21.7 Å2
Baniso -1Baniso -2Baniso -3
1--6.337 Å20 Å20 Å2
2--2.26 Å20 Å2
3---4.076 Å2
Refinement stepCycle: LAST / Resolution: 2.22→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10085 0 54 911 11050
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.00541
X-RAY DIFFRACTIONc_angle_deg1.24828
X-RAY DIFFRACTIONc_mcbond_it1.1481.5
X-RAY DIFFRACTIONc_mcangle_it1.7642
X-RAY DIFFRACTIONc_scbond_it2.1692
X-RAY DIFFRACTIONc_scangle_it3.1092.5
LS refinement shellResolution: 2.22→2.24 Å / Rfactor Rfree: 0.29 / Rfactor Rwork: 0.228
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5tpp.partpp.top

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