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- PDB-3m34: Crystal structure of transketolase in complex with thiamin diphos... -

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Basic information

Entry
Database: PDB / ID: 3m34
TitleCrystal structure of transketolase in complex with thiamin diphosphate and calcium ion
ComponentsTransketolase
KeywordsTRANSFERASE / Thiamine pyrophosphate / Calcium binding / NIAID / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases
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 ...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 speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsNocek, B. / Makowska-Grzyska, M. / Maltseva, N. / Grimshaw, S. / Joachimiak, A. / Anderson, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structure of transketolase in complex with thiamin diphosphate and calcium ion
Authors: Nocek, B. / Makowska-Grzyska, M. / Maltseva, N. / Grimshaw, S. / Joachimiak, A. / Anderson, W. / CSGID / NIAID
History
DepositionMar 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 1, 2014Group: Structure summary
Revision 1.3Sep 6, 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_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.pdbx_leaving_atom_flag / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1326
Polymers70,4211
Non-polymers7125
Water7,566420
1
A: Transketolase
hetero molecules

A: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,26512
Polymers140,8412
Non-polymers1,42310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area11540 Å2
ΔGint-64 kcal/mol
Surface area40480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.350, 70.819, 69.236
Angle α, β, γ (deg.)90.00, 109.92, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-789-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Transketolase /


Mass: 70420.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Strain: jejuni NCTC 11168 / Gene: tkt, Cj1645 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q0P7Y3, transketolase

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Non-polymers , 5 types, 425 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


Mass: 425.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 420 / 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: 2.13 Å3/Da / Density % sol: 42.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 0.1 M Ches ph 9.5 30 % PEG 400 10 mM TPP, 1mm CaCl2. Sitting drop, vapor diffusion method Temp 293 K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 11, 2009 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.65→40 Å / Num. all: 70630 / Num. obs: 70590 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 31.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.6
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3508 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L84

3l84


Resolution: 1.65→40 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.621 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.088 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18186 3566 5.1 %RANDOM
Rwork0.15141 ---
all0.17 70600 --
obs0.15294 67019 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.448 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å20.11 Å2
2--0.56 Å20 Å2
3----0.95 Å2
Refinement stepCycle: LAST / Resolution: 1.65→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4901 0 43 420 5364
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0225057
X-RAY DIFFRACTIONr_bond_other_d0.0010.023443
X-RAY DIFFRACTIONr_angle_refined_deg1.8091.9686821
X-RAY DIFFRACTIONr_angle_other_deg0.97638422
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0415635
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.02525.152231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.90515875
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6361516
X-RAY DIFFRACTIONr_chiral_restr0.1610.2737
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215656
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02997
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0371.53136
X-RAY DIFFRACTIONr_mcbond_other0.3451.51294
X-RAY DIFFRACTIONr_mcangle_it1.79324998
X-RAY DIFFRACTIONr_scbond_it3.06431921
X-RAY DIFFRACTIONr_scangle_it5.0234.51821
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.651→1.694 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 246 -
Rwork0.217 4829 -
obs--97.69 %

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