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- PDB-4c7v: Apo Transketolase from Lactobacillus salivarius at 2.2A resolution -

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Basic information

Entry
Database: PDB / ID: 4c7v
TitleApo Transketolase from Lactobacillus salivarius at 2.2A resolution
ComponentsTRANSKETOLASE
KeywordsTRANSFERASE
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, N-terminal / Transketolase, C-terminal domain / Transketolase, C-terminal domain / Rossmann fold - #920 / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain ...Transketolase, bacterial-like / Transketolase family / Transketolase signature 1. / Transketolase, thiamine diphosphate binding domain / 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 speciesLACTOBACILLUS SALIVARIUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLobley, C.M.C. / Lukacik, P. / Bumann, M. / Aller, P. / Douangamath, A. / O'Toole, P.W. / Walsh, M.A.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: High Resolution Crystal Structures of Lactobacillus Salivarius Transketolase in the Presence and Absence of Thiamine Pyrophosphate
Authors: Lukacik, P. / Lobley, C.M.C. / Bumann, M. / Arena De Souza, V. / Owens, R.J. / O'Toole, P.W. / Walsh, M.A.
History
DepositionSep 26, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references / Structure summary
Revision 1.2Oct 21, 2015Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRANSKETOLASE


Theoretical massNumber of molelcules
Total (without water)74,5431
Polymers74,5431
Non-polymers00
Water4,432246
1
A: TRANSKETOLASE

A: TRANSKETOLASE


Theoretical massNumber of molelcules
Total (without water)149,0862
Polymers149,0862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area8000 Å2
ΔGint-37.4 kcal/mol
Surface area42580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.150, 76.150, 194.510
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-2162-

HOH

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Components

#1: Protein TRANSKETOLASE /


Mass: 74542.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LACTOBACILLUS SALIVARIUS (bacteria) / Strain: UCC118 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS / References: UniProt: Q1WQU8, transketolase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE HIS TAG (THE FIRST 18 RESIDUES ABOVE) IS NOT VISIBLE IN THE ELECTRON DENSITY MAP

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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: 2.19 Å3/Da / Density % sol: 43.77 % / Description: NONE
Crystal growDetails: 20 % W/V PEG3350, 0.2 M SODIUM CHLORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.917
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 9, 2012 / Details: MIRRORS
RadiationMonochromator: DCM SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 2.2→39.14 Å / Num. obs: 33992 / % possible obs: 99.7 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.8
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
xia2data reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→39.14 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.947 / SU B: 11.233 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21917 1720 5.1 %RANDOM
Rwork0.16236 ---
obs0.16524 32219 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.117 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0.25 Å20 Å2
2---0.25 Å20 Å2
3---0.8 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5092 0 0 246 5338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0195234
X-RAY DIFFRACTIONr_bond_other_d0.0010.024929
X-RAY DIFFRACTIONr_angle_refined_deg1.781.9557097
X-RAY DIFFRACTIONr_angle_other_deg0.873311390
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5095671
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.72525.128234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.83115884
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.151520
X-RAY DIFFRACTIONr_chiral_restr0.1010.2772
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216007
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021157
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_it2.5393.0992657
X-RAY DIFFRACTIONr_mcbond_other2.5373.0982656
X-RAY DIFFRACTIONr_mcangle_it3.4994.6373322
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.223.4432577
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 121 -
Rwork0.238 2360 -
obs--99.92 %
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)
10.7794-0.06420.13820.27950.03940.46930.00140.0843-0.261-0.07730.00780.1702-0.0469-0.2087-0.00920.02540.0139-0.04510.1289-0.02690.17197.75154.468-10.44
20.6318-0.18160.3180.5618-0.07930.57780.02640.0482-0.2749-0.06240.0180.1810.0446-0.208-0.04450.0231-0.029-0.04410.1424-0.04570.2214.9649.212-11.783
30.4907-0.06-0.04350.33020.01160.9637-0.055-0.1516-0.11760.02690.05880.0786-0.1625-0.0666-0.00390.05130.03940.01250.08450.03630.046723.93262.28514.125
41.0997-0.008-0.04291.03140.29771.0204-0.0467-0.15460.16870.00750.0779-0.0585-0.36950.1622-0.03120.2236-0.0741-0.02230.0747-0.02490.03440.27779.85513.535
51.3010.0278-0.32625.1223-0.60040.1911-0.0879-0.2830.00210.1590.0619-0.2573-0.03340.15850.02610.1718-0.059-0.06490.2875-0.01890.080951.3367.81219.419
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 188
2X-RAY DIFFRACTION2A189 - 337
3X-RAY DIFFRACTION3A338 - 528
4X-RAY DIFFRACTION4A529 - 637
5X-RAY DIFFRACTION5A638 - 661

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