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- PDB-3kom: Crystal structure of apo transketolase from Francisella tularensis -

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Basic information

Entry
Database: PDB / ID: 3kom
TitleCrystal structure of apo transketolase from Francisella tularensis
ComponentsTransketolase
KeywordsTRANSFERASE / Rossmann fold / transketolase / 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 / 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
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsAnderson, S.M. / Wawrzak, Z. / Skarina, T. / Gordon, E. / Kwon, K. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of apo transketolase from Francisella tularensis
Authors: Anderson, S.M. / Wawrzak, Z. / Skarina, T. / Gordon, E. / Kwon, K. / Savchenko, A. / Anderson, W.F.
History
DepositionNov 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Dec 14, 2011Group: Structure summary
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transketolase
B: Transketolase


Theoretical massNumber of molelcules
Total (without water)148,8142
Polymers148,8142
Non-polymers00
Water23,3291295
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7650 Å2
ΔGint-32.3 kcal/mol
Surface area43510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.49, 109.29, 128.56
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Transketolase /


Mass: 74406.969 Da / Num. of mol.: 2 / Mutation: W313R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Strain: SCHU S4 / Gene: tktA, FTT1369c, FTT_1369c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5NF74, transketolase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1295 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT MUTATION W313R IS A CLONING ERROR.

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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: 2.04 Å3/Da / Density % sol: 39.76 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 30% PEG MME 2000, 200mM Ammonium acetate, 100mM Sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 23, 2009 / Details: Beryllium lens
RadiationMonochromator: C(111) diamond laue / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 309132 / Num. obs: 306041 / % possible obs: 99 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.081 / Χ2: 1.028 / Net I/σ(I): 11
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.626 / Mean I/σ(I) obs: 2.6 / Num. unique all: 30186 / Χ2: 0.98 / % possible all: 97.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
BLU-MAXdata collection
HKL-2000data reduction
HKL-2000data scaling
CRANKphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→29.04 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.205 / WRfactor Rwork: 0.17 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.888 / SU B: 3.474 / SU ML: 0.055 / SU R Cruickshank DPI: 0.09 / SU Rfree: 0.091 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2.6 / ESU R: 0.09 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. The Friedel pairs were used in phasing. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 3. U VALUES: RESIDUAL ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.199 7930 5 %RANDOM
Rwork0.163 ---
all0.165 160642 --
obs0.165 157911 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 46.94 Å2 / Biso mean: 8.44 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2--0.17 Å2-0 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10163 0 0 1295 11458
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02210622
X-RAY DIFFRACTIONr_angle_refined_deg1.3561.94714456
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6651358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.54124.773484
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.843151797
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1321545
X-RAY DIFFRACTIONr_chiral_restr0.0990.21567
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218151
X-RAY DIFFRACTIONr_mcbond_it1.4091.56576
X-RAY DIFFRACTIONr_mcangle_it2.328210624
X-RAY DIFFRACTIONr_scbond_it3.97934046
X-RAY DIFFRACTIONr_scangle_it5.9184.53801
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 555 -
Rwork0.269 9884 -
all-10439 -
obs-11104 89.08 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.73070.0967-0.00420.99140.26720.2438-0.02930.0985-0.01070.00020.0242-0.0120.0226-0.00210.00510.1699-0.0025-0.00350.06170.01690.09414.26726.7362.665
21.96570.19590.58721.06330.56660.6542-0.05350.4628-0.095-0.06050.0767-0.07430.0150.2043-0.02310.1805-0.01790.01880.14830.00710.090520.41719.077-5.713
30.2984-0.551-0.2321.70110.32990.251-0.075-0.0951-0.05160.25930.03240.10870.1154-0.01330.04260.3171-0.01980.02570.11780.01650.08940.48137.95227.458
40.4456-0.1323-0.1340.74530.09560.44580.0282-0.02260.04510.0706-0.03340.0779-0.0389-0.07370.00520.1863-0.00050.01080.0654-0.01730.0798-4.35658.11515.129
50.60490.23910.10831.05920.28940.41430.0524-0.06120.04010.04630.0044-0.1678-0.05630.0374-0.05680.1881-0.01920.01080.0628-0.00270.159830.76766.9679.039
61.01590.16650.62562.2642-0.08530.9680.0077-0.14180.0460.34260.0695-0.35880.05520.0027-0.07720.21890.0145-0.06210.0829-0.01720.261137.54954.90814.758
71.0620.09790.21960.47710.34310.4983-0.00630.13210.06-0.11320.0454-0.1228-0.13690.1075-0.03910.2653-0.03850.05210.05550.02310.134626.67568.885-6.458
80.51330.07740.23830.5407-0.08230.4491-0.01480.06820.0158-0.14110.02250.0268-0.0196-0.0506-0.00760.21140.0086-0.00810.0765-0.00150.07320.72456.907-13.255
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 212
2X-RAY DIFFRACTION2A213 - 301
3X-RAY DIFFRACTION3A302 - 390
4X-RAY DIFFRACTION4A391 - 663
5X-RAY DIFFRACTION5B1 - 196
6X-RAY DIFFRACTION6B197 - 265
7X-RAY DIFFRACTION7B266 - 389
8X-RAY DIFFRACTION8B390 - 663

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